def rMap_full(f_in, f_out):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(bioSeq) # default linear = TRUE
analysis = Analysis(AllEnzymes, fSeq) # linear = true
result = analysis.full()
header = "==============================================\nRestriction analysis for " + reagentID + "\n==============================================\n"
analysis.print_that(title=header + '\n\n')
def rMap_full(f_in, f_out):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(bioSeq) # default linear = TRUE
analysis = Analysis(AllEnzymes, fSeq) # linear = true
result = analysis.full()
header = "==============================================\nRestriction analysis for " + reagentID + "\n==============================================\n"
analysis.print_that(title=header+'\n\n')
def __init__(self):
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
self.__db = db
self.__cursor = cursor
self.__hostname = hostname
def __init__(self): dbConn = DatabaseConn() db = dbConn.databaseConnect() cursor = db.cursor() hostname = dbConn.getHostname() self.__db = db self.__cursor = cursor self.__hostname = hostname
def add_members():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
pHandler = PacketHandler(db, cursor)
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Get form values
projectID = form.getvalue("packets")
projectMembers = form.getlist("projectMembers")
pHandler.insertProjectMembers(projectID, projectMembers)
redirect(hostname)
def add_members():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
pHandler = PacketHandler(db, cursor)
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Get form values
projectID = form.getvalue("packets")
projectMembers = form.getlist("projectMembers")
pHandler.insertProjectMembers(projectID, projectMembers)
redirect(hostname)
def preview():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
rHandler = ReagentHandler(db, cursor)
propMapper = ReagentPropertyMapper(db, cursor)
prop_Alias_ID_Map = propMapper.mapPropAliasID()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html" # REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
propVal = ""
if form.has_key("PV"):
pvVal = form.getvalue("PV")
pvID = rHandler.convertReagentToDatabaseID(pvVal)
if form.has_key("propAlias"):
propAlias = form.getvalue("propAlias")
if prop_Alias_ID_Map.has_key(propAlias):
propID = prop_Alias_ID_Map[propAlias]
propVal = rHandler.findSimplePropertyValue(pvID, propID)
print "Content-type:text/html" # REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
print # DITTO
print propVal
def __init__(self):
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
clone_request = dbConn.getMailCloneRequest()
mail_programmer = dbConn.getProgrammerEmail()
mail_biologist = dbConn.getBiologistEmail()
mail_admin = dbConn.getAdminEmail() # August 19, 2011
mail_server = dbConn.getMailServer() # August 19, 2011
self.__db = db
self.__cursor = cursor
self.__hostname = hostname
self.__clone_request = clone_request
self.__mail_programmer = mail_programmer # July 30, 2010
self.__mail_biologist = mail_biologist # July 30, 2010
self.__mail_admin = mail_admin # August 19, 2011
self.__mail_server = mail_server # August 19, 2011
def __init__(self):
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
clone_request = dbConn.getMailCloneRequest()
mail_programmer = dbConn.getProgrammerEmail()
mail_biologist = dbConn.getBiologistEmail()
mail_admin = dbConn.getAdminEmail() # August 19, 2011
mail_server = dbConn.getMailServer() # August 19, 2011
self.__db = db
self.__cursor = cursor
self.__hostname = hostname
self.__clone_request = clone_request
self.__mail_programmer = mail_programmer # July 30, 2010
self.__mail_biologist = mail_biologist # July 30, 2010
self.__mail_admin = mail_admin # August 19, 2011
self.__mail_server = mail_server # August 19, 2011
def printProjectInfo(self, cmd, project):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
gOut = GeneralOutputClass()
currUser = Session.getUser()
if cmd == 'view':
projectID = project.getNumber()
projectOwner = project.getOwner()
ownerName = projectOwner.getFullName()
ownerID = projectOwner.getUserID()
projectName = project.getName()
projectDescr = project.getDescription()
# private or public
isPrivate = project.isPrivate()
if isPrivate:
accessType = 'Private'
else:
accessType = 'Public'
# Only allow modification by owner or admin AND disallow project deletion if there are reagents in it!!!
modify_disabled = True
delete_disabled = True
if (currUser.getUserID() == ownerID) or (currUser.getCategory() == 'Admin'):
modify_disabled = False
if project.isEmpty():
delete_disabled = False
# Aug. 18/08: Changed b/c of new format
#content = gOut.printHeader() + gOut.printMainMenu()
content = gOut.printHeader()
content += '''
<FORM name="project_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="username_hidden" NAME="username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE height="100%%">
<TABLE width="770px" cellpadding="5px" cellspacing="5px" class="detailedView_tbl">
<TR>
<TD class="detailedView_heading" style="white-space:nowrap;">
PROJECT DETAILS PAGE
</TD>
<TD class="detailedView_heading" style="text-align:right">
'''
content += "<INPUT TYPE=\"submit\" name=\"modify_project\" value=\"Modify Project\""
if modify_disabled:
content += " disabled>"
else:
content += ">"
content += "<INPUT TYPE=\"submit\" style=\"margin-left:2px;\" name=\"delete_project\" value=\"Delete Project\" onClick=\"return confirmDeleteProject();\""
if modify_disabled or delete_disabled:
content += " disabled>"
else:
content += ">"
content += '''
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project #
</TD>
<TD class="detailedView_value" width="87%%">
%d
<INPUT TYPE="hidden" name="packetID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Owner:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="packetOwner" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Name:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="packetName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Description:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="packetDescription" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Access type:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="private_or_public" value="%s">
</TD>
</TR>
<TR>
<TD colspan="2">
<HR/>
</TD>
</TR>
'''
# Now here, show or hide members section depending on the user's access level
# Condition is the same as for determining whether modification is allowed - so use 'modify_disabled' variable
if not modify_disabled:
content += '''
<TR>
<TD class="projectDetailedViewName">
Project Members:
</TD>
<TD> </TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="2">
<TABLE width="100%%">
<TR>
<TD style="font-weight:bold; padding-left:10px" width="30%%">
Readers:
</TD>
<TD style="font-weight:bold; padding-left:10px">
Writers:
</TD>
</TR>
<TR>
<TD class="detailedView_value" style="vertical-align:top">
<UL>
'''
if not isPrivate:
content += "All OpenFreezer Users"
else:
# maintain the indent
readers = project.getReaders()
# sort by labs
labs = []
rdrLabs = {}
# First, iterate over readers list to extract all the labs
for rdr in readers:
lab = rdr.getLab().getID()
if lab not in labs:
labs.append(lab)
# Now iterate over the list of labs and link its readers to it
for lab in labs:
tmpRdrs = [] # list of members in one lab
for rdr in readers:
tmpLab = rdr.getLab().getID()
if tmpLab == lab:
# append reader to list of members of this lab
if rdrLabs.has_key(lab):
tmpRdrs = rdrLabs[lab]
tmpRdrs.append(rdr)
rdrLabs[lab] = tmpRdrs
#for rdr in readers:
for lab_id in rdrLabs.keys():
rdrs = rdrLabs[lab_id] # list of objects!!
tmp_lab_name = lHandler.findLabName(lab_id)
# print out the lab name
if currUser.getCategory() == 'Admin':
content += "<span class=\"linkShow\" style=\"color:#2E8B57\" onClick=\"goToLabViewFromProject(" + `lab_id` + ");\">" + tmp_lab_name + "</span><BR/>"
else:
content += "<span style=\"color:#2E8B57\">" + tmp_lab_name + "</span><BR/>"
# print reader names
for rdr in rdrs:
content += "<INPUT TYPE=\"hidden\" name=\"projectReaders\" value=\"" + `rdr.getUserID()` + "\"></INPUT>"
# Only show hyperlinks if the viewer is an Admin; otherwise just output plain names
if currUser.getCategory() == 'Admin':
content += "<LI style=\"list-style:none; padding-left:6px;\">-- <span class=\"linkShow\" onClick=\"redirectToUserFromProject(" + `rdr.getUserID()` + ");\">" + rdr.getFullName() + "</span></LI>"
else:
content += "<LI style=\"list-style:none; padding-left:6px;\">-- " + rdr.getFullName() + "</LI>"
content += '''
</UL>
</TD>
<TD class="detailedView_value" style="width:250px; vertical-align:top">
<UL>
'''
writers = project.getWriters()
# sort them by lab too, same as for readers
labs = []
wrtrLabs = {}
# First, iterate over readers list to extract all the labs
for wrtr in writers:
lab = wrtr.getLab().getID()
if lab not in labs:
labs.append(lab)
# Now iterate over the list of labs and link its readers to it
for lab in labs:
tmpWrtrs = [] # list of members in one lab
for wrtr in writers:
tmpLab = wrtr.getLab().getID()
if tmpLab == lab:
# append reader to list of members of this lab
if wrtrLabs.has_key(lab):
tmpWrtrs = wrtrLabs[lab]
tmpWrtrs.append(wrtr)
wrtrLabs[lab] = tmpWrtrs
for lab_id in wrtrLabs.keys():
wrtrs = wrtrLabs[lab_id] # list of objects!!
tmp_lab_name = lHandler.findLabName(lab_id)
# print out the lab name
if currUser.getCategory() == 'Admin':
content += "<span class=\"linkShow\" style=\"color:#2E8B57\" onClick=\"goToLabViewFromProject(" + `lab_id` + ");\">" + tmp_lab_name + "</span><BR/>"
else:
content += "<span style=\"color:#2E8B57\" " + `lab_id` + ");\">" + tmp_lab_name + "</span><BR/>"
for wrtr in wrtrs:
content += "<INPUT TYPE=\"hidden\" name=\"projectWriters\" value=\"" + `wrtr.getUserID()` + "\">"
if currUser.getCategory() == 'Admin':
content += "<LI style=\"list-style:none; padding-left:6px;\">-- <span class=\"linkShow\" onClick=\"redirectToUserFromProject(" + `wrtr.getUserID()` + ");\">" + wrtr.getFullName() + "</span></LI>"
else:
content += "<LI style=\"list-style:none; padding-left:6px;\">-- " + wrtr.getFullName() + "</LI>"
content += '''
</UL>
</TD>
</TR>
</TABLE>
</TD>
</TR>
</TABLE>
</FORM>
<FORM id="viewUserForm" method="POST" action="%s">
<INPUT type="hidden" id="view_user_hidden" name="view_user">
<INPUT type="hidden" ID="curr_userid_hidden" NAME="curr_user_id" value="%d">
</FORM>
<FORM id="viewLabForm" method="POST" action="%s">
<INPUT type="hidden" ID="curr_userid_hidden" NAME="curr_user_id" value="%d">
<INPUT type="hidden" id="view_lab_hidden" name="view_lab">
</FORM>
</TABLE>
'''
content += gOut.printFooter()
else:
content += '''
</TABLE>
</FORM>
</TABLE>
'''
content += gOut.printFooter()
# and here, depending on what sections of the project view were printed, the number of arguments would vary
if not modify_disabled:
page_content = content % (hostname + "cgi/project_request_handler.py", projectID, projectID, ownerName, ownerID, projectName, projectName, projectDescr, projectDescr, accessType, accessType, hostname + "cgi/user_request_handler.py", currUser.getUserID(), hostname + "cgi/user_request_handler.py", currUser.getUserID())
else:
page_content = content % (hostname + "cgi/project_request_handler.py", projectID, projectID, ownerName, ownerID, projectName, projectName, projectDescr, projectDescr, accessType, accessType)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
elif cmd == 'edit':
projectID = project.getNumber()
projectOwner = project.getOwner()
ownerName = projectOwner.getFullName()
ownerID = projectOwner.getUserID()
projectName = project.getName()
projectDescr = project.getDescription()
isPrivate = project.isPrivate()
content = gOut.printHeader()
#content += gOut.printMainMenu()
content += '''
<FORM name="project_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="username_hidden" NAME="username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="770px" cellpadding="5px" cellspacing="5px" style="border:1px solid black" frame="box" rules="rows">
<TR>
<TD colspan="3" style="padding-left:200px; text-align:center">
<span style="color:#0000FF; font-weight:bold">MODIFY PROJECT </span>
<span style="color:#FF0000; font-weight:bold">%d</span>
<INPUT TYPE="hidden" name="packetID" value="%d">
<INPUT TYPE="submit" style="margin-left:200px;" name="save_project" value="Save" onClick=\"alert('Please note: If your project writers list contains names of users who have read-only access to OpenFreezer, their names will be removed from the list during saving.'); addProjectOwnerToWritersList(); selectAllElements('readers_target_list'); selectAllElements('writers_target_list'); return verifyProjectOwner('projectOwnersList') && verifyProjectName('packet_name') && verifyProjectDescr('packet_descr') && verifyMembers('readers_target_list') && verifyMembers('writers_target_list');\">
<INPUT TYPE="submit" style="margin-left:20px;" name="cancel_project" value="Cancel">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Owner:
</TD>
<TD class="detailedView_value" colspan="2">
<SELECT ID="projectOwnersList" name="packetOwner">
'''
# Get list of all potential project owners - users with 'CREATOR' or higher privileges
# Returns list of User **objects**
creators = uHandler.findAllMembersInCategory('Creator', False, '<=')
creatorsDict = {} # name, uid
for creator in creators:
uid = creator.getUserID()
name = creator.getFullName()
creatorsDict[name] = uid
names = creatorsDict.keys()
names.sort()
#print "Content-type:text/html"
#print
for name in names:
#print name
uid = creatorsDict[name]
#print uid
#print ownerID
if uid == ownerID:
content += "<OPTION SELECTED value=" + `uid` + ">" + name + "</OPTION>"
else:
content += "<OPTION value=" + `uid` + ">" + name + "</OPTION>"
content += '''
</SELECT>
<DIV ID="projectOwnerWarning" STYLE="display:none; color:#FF0000; font-weight:normal;">
<BR>Please select a name from the list above.
</DIV>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Name:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" id="packet_name" name="packetName" value="%s">
<DIV ID="projectNameWarning" STYLE="display:none; color:#FF0000; font-weight:normal;">
<BR>Please provide a project name.
</DIV>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Description:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" id="packet_descr" name="packetDescription" value="%s">
<DIV ID="projectDescrWarning" STYLE="display:none; color:#FF0000; font-weight:normal;">
<BR>Please provide a project description.
</DIV>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Access type:
</TD>
<TD class="detailedView_value" style="width:400px">
'''
if not isPrivate:
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"public\" checked>Public "
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"private\">Private"
else:
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"public\">Public "
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"private\" checked>Private"
content += '''
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Members:
</TD>
<TD class="detailedView_value" colspan="2">
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Edit existing project members lists:
</TD>
</TR>
<TR>
<TD style="width:100px">
<SELECT multiple size="10" id="readers_target_list" name="readersList">
'''
# Readers and writers associated with this project
currReaders = project.getReaders()
currWriters = project.getWriters()
# Since object comparison is done by reference, cannot check if a User object returned by findAllMembers is a member of this project by using 'in array'. Need to compare user IDs explicitly
currReaderIDs = []
currWriterIDs = []
currReaderNames = []
currWriterNames = []
currReadersDict = {} # name, id
currWritersDict = {}
# need lab IDs too - to match members to their labs when moved between lists, but having a 'memberID, labID' dictionary is too clumsy. Easiest approach: have 'memberID, Member Object' dictionary
currReaderObjDict = {} # id, User object
currWriterObjDict = {}
for r in currReaders:
rID = r.getUserID()
rName = r.getFullName()
# associate rID with its containing object
currReaderObjDict[rID] = r
currReaderIDs.append(rID)
currReaderNames.append(rName)
currReadersDict[rName] = rID
for w in currWriters:
wID = w.getUserID()
wName = w.getFullName()
currWriterObjDict[wID] = w
currWriterIDs.append(wID)
currWriterNames.append(wName)
currWritersDict[wName] = wID
currReaderNames.sort()
currWriterNames.sort()
for rName in currReaderNames:
rID = currReadersDict[rName]
rdr = currReaderObjDict[rID]
rdrLabID = rdr.getLab().getID()
#content += "<OPTION id=" + `rID` + " value=" + `rID` + ">" + rName + "</OPTION>"
# June 28/07: Include labID in the option id
content += "<OPTION id=\"user_" + `rID` + "_lab_" + `rdrLabID` + "\" value=" + `rID` + ">" + rName + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT TYPE="checkbox" style="margin-top:10px" onClick="selectAll(this.id, 'readers_target_list')" id="select_all_reader_chkbx"> Select All</INPUT>
</TD>
<TD width="30px">
<input onclick="addMembers('readers_target_list', 'write')" value=" Make Writer >>" type="button"></INPUT><BR/>
<input style="margin-top:10px;" onclick="addMembers('writers_target_list', 'read')" value="<< Make Reader" type="button"></INPUT><BR/>
<input style="margin-top:10px;" onclick="removeProjectMembers()" value="Remove Selected" type="button"></INPUT>
</TD>
<TD>
<SELECT multiple size="10" id="writers_target_list" name="writersList">
'''
for wName in currWriterNames:
wID = currWritersDict[wName]
wrtr = currWriterObjDict[wID]
wrtrLabID = wrtr.getLab().getID()
#content += "<OPTION id=" + `wID` + " value=" + `wID` + ">" + wName + "</OPTION>"
# June 28/07: Include labID in the option id
content += "<OPTION id=\"user_" + `wID` + "_lab_" + `wrtrLabID` + "\" value=" + `wID` + ">" + wName + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'writers_target_list')" id="select_all_writer_chkbx"> Select All</INPUT>
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Add new members to this project:
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Laboratory:
<SELECT id="labList" name="labs" onChange="showLabMembersList()">
'''
# fetch lab list - Updated August 90/7: Fetch ALL labs, with any access - then if a read-only lab has members with higher access, would show these members in list
#labs = lHandler.findAllLabs('Writer', '<=')
labs = lHandler.findAllLabs()
# sort lab names alphabetically
labNames = []
labsDict = {} # name, id
for labID in labs.keys():
labName = labs[labID]
labNames.append(labName)
labsDict[labName] = labID
labNames.sort()
currLab = projectOwner.getLab()
currLabID = currLab.getID()
#for labID in labs.keys():
for labName in labNames:
#labName = labs[labID]
labID = labsDict[labName]
if labID == currLabID:
content += "<OPTION SELECTED id='" + `labID` + "' NAME='lab_optn' value=" + `labName` + ">" + labName + "</OPTION>"
else:
content += "<OPTION id='" + `labID` + "' NAME='lab_optn' value=" + `labName` + ">" + labName + "</OPTION>"
content += '''
</SELECT>
</TD>
</TR>
<TR>
<TD width="100px">
'''
# For each lab, print a list of its members
for labID in labs.keys():
# First, fetch a list of users
# These are **User instances** - need to get their names and IDs for comparison
# August 9/07: Don't fetch only writers, fetch readers too - it's up to the project owner to grant them access to the project
#writers = uHandler.findAllMembersInCategory('Writer', True, '<=', labID)
writers = uHandler.findAllMembersInCategory('Reader', True, '<=', labID)
writersDict = {} # name, uid
writersObjDict = {} # id, User object
# Fetch user IDs and sort their names alphabetically
for writer in writers:
name = writer.getFullName()
uid = writer.getUserID()
labID = (writer.getLab()).getID()
writersDict[name] = uid
writersObjDict[uid] = writer
names = writersDict.keys()
names.sort()
# Show members for one lab at a time
if labID == currLabID:
display = "inline"
else:
display = "none"
content += "<SELECT MULTIPLE id=\"lab_source_list_" + `labID` + "\" name=\"labSourceMembers_" + `labID` + "\" SIZE=\"10\" style=\"display:" + display + "\">"
for name in names:
uid = writersDict[name]
labID = writersObjDict[uid].getLab().getID()
if uid not in currReaderIDs and uid not in currWriterIDs:
#content += "<OPTION value=" + `uid` + ">" + name + "</OPTION>"
content += "<OPTION id=\"user_" + `uid` + "_lab_" + `labID` + "\" value=" + `uid` + ">" + name + "</OPTION>"
content += "</SELECT>"
content += '''
<BR/>
<INPUT TYPE="checkbox" style="margin-top:8px" onClick="selectAll(this.id, 'lab_source_list_' + getSelectedLab())" id="add_all_chkbx"> Select All Members</INPUT>
</TD>
<TD colspan="2" style="vertical-align:top">
Add selected members to:
<P style="font-size:9pt; margin-top:5px;">
<input type="radio" id="access_level_radio_read" name="access_levels" value="read" checked>Readers list</INPUT><BR/>
<input type="radio" id="access_level_radio_write" name="access_levels" value="write">Writers list</INPUT><BR/>
<input style="margin-top:8px" onclick="addMembers('lab_source_list_' + getSelectedLab(), getSelectedRole('1'))" value="Go" type="button"></INPUT>
<BR/>
</P>
</TD>
</TR>
</TABLE>
</FORM>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/project_request_handler.py", project.getNumber(), project.getNumber(), project.getName(), project.getDescription())
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def printSubmenuHeader(self, submenu_type):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
current_selection_names = [] # plain list of section names
current_selection_links = {} # dictionary, where section names are keys and their URLs are values
if submenu_type == "Location":
location_submenu_names = []
location_submenu_links = {}
location_submenu_names.append("Add container types")
location_submenu_links["Add container types"] = "../Location.php?View=6&Sub=3"
location_submenu_names.append("Add container sizes")
location_submenu_links["Add container sizes"] = "../Location.php?View=6&Sub=1"
location_submenu_names.append("Add containers")
location_submenu_links["Add containers"] = "../Location.php?View=6&Sub=3"
location_submenu_names.append("Search containers")
location_submenu_links["Search containers"] = "../Location.php?View=2"
current_selection_names = location_submenu_names
current_selection_links = location_submenu_links
elif submenu_type == "Reagent":
reagent_submenu_names = []
reagent_submenu_links = {}
reagent_submenu_names.append("Add reagents")
reagent_submenu_links["Add reagents"] = "../Reagent.php?View=2"
reagent_submenu_names.append("Search reagents")
reagent_submenu_links["Search reagents"] = "../search.php?View=1"
# June 3/09
reagent_submenu_names.append("Add reagent types")
reagent_submenu_links["Add reagent types"] = "../Reagent.php?View=3"
reagent_submenu_names.append("Search reagent types")
reagent_submenu_links["Search reagent types"] = "../Reagent.php?View=5"
current_selection_names = reagent_submenu_names
current_selection_links = reagent_submenu_links
elif submenu_type == "Chemical":
chemical_submenu_names = []
chemical_submenu_links = {}
chemical_submenu_names.append("Add Chemicals")
chemical_submenu_links["Add Chemicals"] = "../Chemical.php?View=2"
chemical_submenu_names.append("Search Chemicals")
chemical_submenu_links["Search Chemicals"] = "../Chemical.php?View=1"
current_selection_names = chemical_submenu_names
current_selection_links = chemical_submenu_links
elif submenu_type == "Prediction":
prediction_submenu_names = []
prediction_submenu_links = {}
prediction_submenu_names.append("Search predictions")
prediction_submenu_links["Search predictions"] = "../Prediction.php?View=1"
current_selection_names = prediction_submenu_names
current_selection_links = prediction_submenu_links
elif submenu_type == "Project":
project_submenu_names = []
project_submenu_links = {}
project_submenu_names.append("Add projects")
project_submenu_links["Add projects"] = "../Project.php?View=1"
project_submenu_names.append("Search projects")
project_submenu_links["Search projects"] = "../Project.php?View=2"
current_selection_names = project_submenu_names
current_selection_links = project_submenu_links
elif submenu_type == "User":
user_submenu_names = []
user_submenu_links = {}
user_submenu_names.append("Add users")
user_submenu_links["Add users"] = "../User.php?View=1"
user_submenu_names.append("Search users")
user_submenu_links["Search users"] = "../User.php?View=2"
user_submenu_names.append("Change your password")
user_submenu_links["Change your password"] = "******"
user_submenu_names.append("Personal page")
user_submenu_links["Personal page"] = "User.php?View=7"
user_submenu_names.append("View your orders")
user_submenu_links["View your orders"] = "../User.php?View=8"
current_selection_names = user_submenu_names
current_selection_links = user_submenu_links
elif submenu_type == "Lab":
lab_submenu_names = []
lab_submenu_links = {}
lab_submenu_names.append("Add laboratories")
lab_submenu_links["Add laboratories"] = "../User.php?View=3"
lab_submenu_names.append("Search laboratories")
lab_submenu_links["Search laboratories"] = "../User.php?View=4"
current_selection_names = lab_submenu_names
current_selection_links = lab_submenu_links
# There can be permission differentiations within a menu section as well (e.g. Projects - only Creators can create, buit Writers can view)
currUser = Session.getUser()
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
currUserCategory = category_Name_ID_Map[currUser.getCategory()]
allowedSections = uHandler.getAllowedSections(currUserCategory)
# print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
# print # DITTO
# print `allowedSections`
content = ""
for name in current_selection_names:
if name in allowedSections:
if name == "Personal page":
content += '<LI class="submenu">'
content += '<IMG SRC="../pictures/star_bullet.gif" WIDTH="10" HEIGHT="10" BORDER="0" ALT="plus" class="menu-leaf">'
content += (
'<span class="linkShow" style="font-size:9pt" onClick="redirectToCurrentUserDetailedView('
+ ` currUser.getUserID() `
+ ');">'
+ name
+ "</span>"
)
content += "</LI>"
content += '<form name="curr_user_form" style="display:none" method="post" action="user_request_handler.py">'
content += (
'<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username" VALUE="'
+ currUser.getFullName()
+ '">'
)
content += '<INPUT type="hidden" id="curr_user_hidden" name="view_user">'
content += "</FORM>"
else:
content += '<LI class="submenu">'
content += '<IMG SRC="../pictures/star_bullet.gif" WIDTH="10" HEIGHT="10" BORDER="0" ALT="plus" class="menu-leaf">'
content += '<a class="submenu" href="' + current_selection_links[name] + '">' + name + "</a>"
content += "</LI>"
return content
def drawMap():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
root_path = dbConn.getRootDir()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else:
#rID = 148913 # V4550
rID = 29125
#rID = 72
#rID = 309
#rID = 1901 # small feature labels @ start of seq. overlap
#rID = 36415
#print rID
reagentID = rHandler.convertDatabaseToReagentID(rID)
#print "Content-type:text/html"
#print
#print reagentID
namePropID = pHandler.findReagentPropertyInCategoryID(
prop_Name_ID_Map["name"],
prop_Category_Name_ID_Map["General Properties"])
rName = rHandler.findSimplePropertyValue(rID, namePropID)
#rName = rHandler.findSimplePropertyValue(rID, prop_Name_ID_Map["name"])
rTypeID = rHandler.findReagentTypeID(rID)
try:
os.remove(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
except OSError:
pass
#print root_path
c = Canvas(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
c.setPageSize((1000, 1000))
c.setStrokeColorRGB(0, 0, 0)
c.saveState()
# Draw circle
origin = 0
origin_x = 500
origin_y = 470
radius = 200
c.circle(origin_x, origin_y, radius)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print "Content-type:text/html"
#print
#print `rID`
unit_angle_measure = float(360) / float(seqLen)
#print unit_angle_measure
# Mark 1 on the circle - KEEP, Karen said!
c.setLineWidth(1)
c.setStrokeColor(black)
c.setFillColor(black)
c.saveState()
path = c.beginPath()
path.moveTo(origin_x, origin_y + radius + 7)
path.lineTo(origin_x - 5, origin_y + radius + 14)
path.lineTo(origin_x + 5, origin_y + radius + 14)
path.lineTo(origin_x, origin_y + radius + 7)
c.drawPath(path, True, True)
# label 1
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 16)
t.setTextOrigin(origin_x - 5, origin_y + radius + 19)
t.textOut("1")
c.drawText(t)
c.restoreState()
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
#print `sequenceFeatures`
# Draw legend
ox_legend = 800
oy_legend = 985
prev_legend = oy_legend
# draw frame
c.setStrokeColor(darkgray)
#c.setStrokeColor(white)
#c.setFillColor(lightgrey)
c.setFillColor(white)
c.saveState()
# Output the rest of the features in alphabetical order - Moved here Jan. 26/10
#featureNames = featureNameColorMap.keys()
#print `featureNameColorMap.keys()`
#print len(featureNameColorMap.keys())
#fnames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
#fnames.remove('expression system')
#fnames.remove('tag position')
#print `fnames`
#print len(fnames)
featureNames = rtPropHandler.findReagentTypeAttributeNamesByCategory(
rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
featureNames.sort()
#print `featureNames`
#print prev_legend-240
#print prev_legend-15-len(featureNames)*15
#c.rect(ox_legend-25, prev_legend-240, 215, 235, 1, 1)
#c.rect(ox_legend-25, prev_legend-15-len(featureNames)*15, 215, 10+len(featureNames)*15, 1, 1) # good for list of all db features
if len(featureNames) > 15:
origin_spacer = -19
coeff = 12
else:
origin_spacer = 65
coeff = 15
#origin_legend = prev_legend+65-len(featureNames)*15
origin_legend = prev_legend + origin_spacer - len(featureNames) * coeff
x = (990 - origin_legend) / len(featureNames)
#print x
if x < 12:
x = 12
legend_height = len(featureNames) * x + 15
#print legend_height
c.rect(ox_legend - 25, origin_legend - 17, 215, legend_height, 1,
1) # good for specific rtype attributes
c.restoreState()
# Order: 5' site, 3' site, 5' linker, 3' linker, then the rest
sites_color = featureNameColorMap["5' cloning site"] # same for 3' site
# 5' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
t.setStrokeColor(sites_color)
#t.setFillColor(black)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "5' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
# 3' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "3' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
# Show legend for linkers
linkers_color = featureNameColorMap["5' linker"]
# 5' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "5' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
# 3' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + "3' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
## Output the rest of the features in alphabetical order
#featureNames = featureNameColorMap.keys()
#featureNames.sort()
#print `featureNames`
for featureName in featureNames:
if featureNameColorMap.has_key(featureName):
color = featureNameColorMap[featureName]
#else:
#continue
if featureName != "5' cloning site" and featureName != "3' cloning site" and featureName != "5' linker" and featureName != "3' linker" and color != None:
#print featureName
c.setStrokeColor(color)
c.setFillColor(color)
c.saveState()
c.rect(ox_legend - 15, prev_legend - 20, 25, 8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(color)
t.setFillColor(color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend + 12, prev_legend - 20)
t.textOut(" - " + featureName.upper())
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
#print prev_legend
# Print reagent ID and size at the centre of the circle and print name at the top of the page
c.setFont("Helvetica-Bold", 32)
c.setFillColor(black)
c.saveState()
c.drawCentredString(origin_x, origin_y + 35, reagentID)
c.drawCentredString(origin_x, origin_y + 10, "nt 1 - " + ` seqLen `)
if rName:
c.setFillColor(blue)
c.drawCentredString(origin_x, 935, rName)
c.restoreState()
# SORT features by size, so that short features are not hidden behind the long ones
fSizes = []
sortedFeatures = []
for feature in sequenceFeatures:
fSize = int(feature.getFeatureSize())
if fSize > 0:
fSizes.append(fSize)
fSizes.sort(reverse=True)
#print `fSizes`
for fs in fSizes:
for feature in sequenceFeatures:
fSize = feature.getFeatureSize()
# added existence check July 17/08 - different features may have same sizes so end up with duplicate features in list (e.g. cloning sizes appeared twice on the map)
if fs == fSize and feature not in sortedFeatures:
sortedFeatures.append(feature)
#print `sortedFeatures`
ox_labels = 40
oy_labels = 910
prev_legend = oy_labels
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels, prev_legend - 15)
t.textOut("Features shorter than 150 nt:")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 18
#for feature in sequenceFeatures:
for feature in sortedFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fSize = feature.getFeatureSize()
#print fType
#print fValue
#print fSize
fColor = featureNameColorMap[fType]
if fType == 'cdna insert':
fValue = "cDNA Insert"
elif fType == 'promoter':
fValue = fValue + " " + fType
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
if fSize > 0:
f_start = fStart * unit_angle_measure
#print "Start " + `fStart`
#print "End " + `fEnd`
startAngle = 90 - f_start
#print "Start angle " + `startAngle`
f_end = fEnd * unit_angle_measure
endAngle = 90 - f_end
#print "End angle " + `endAngle`
extAngle = -1 * (f_end - f_start)
#print "Ext angle " + `extAngle`
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = c.beginPath()
#t = c.beginText()
c.setLineWidth(10)
c.setLineJoin(1)
fColor = featureNameColorMap[fType]
c.setStrokeColor(fColor)
c.saveState()
p.arc(x1, y1, x2, y2, startAngle, extAngle)
c.drawPath(p)
c.restoreState()
## jan. 27/10: this makes a contour for each arc
#p = c.beginPath()
#c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
#c.setStrokeColor(black)
#c.setFillColor(fColor)
#c.saveState()
#p.arc(x1+5, y1+5, x2-5, y2-5, startAngle, extAngle)
#c.drawPath(p)
##c.restoreState()
##c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
##c.setStrokeColor(black)
##c.setFillColor(fColor)
##c.saveState()
#p.arc(x1-5, y1-5, x2+5, y2+5, startAngle, extAngle)
#c.drawPath(p)
#c.restoreState() # jan. 27/10 modification ends here
# common to all
startAngle_rad = (startAngle * math.pi) / 180.0
endAngle_rad = (endAngle * math.pi) / 180.0
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 9)
c.saveState()
arc_x_start = origin_x + (radius + 5) * math.cos(startAngle_rad)
arc_y_start = origin_y + (radius + 5) * math.sin(startAngle_rad)
arc_x_end = origin_x + (radius + 5) * math.cos(endAngle_rad)
arc_y_end = origin_y + (radius + 5) * math.sin(endAngle_rad)
# draw label
c.setStrokeColorRGB(0, 0, 1)
c.setFillColorRGB(0, 0, 1)
c.setFont("Helvetica-Bold", 12)
c.saveState()
# draw line
delta = 45
# Rotate labels only for SMALL features (they can be crammed together)
#if fSize > 100:
#delta = 45
#else:
#delta = 32
if fStart < seqLen / 2:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
#if fSize <= 100:
#c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
#else:
# July 17/08: Show labels for long features only
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)))
c.restoreState()
# July 17/08: Show labels for long features only
if fSize > 150:
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(
arc_x_start + 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.restoreState()
else:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)))
#c.line(arc_x_start, arc_y_start, arc_x_start+10*math.fabs(math.sin(delta)), arc_y_start-10*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start + 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start,
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(
arc_x_start - 50 * math.fabs(math.sin(delta)),
arc_y_start - 55 * math.fabs(math.cos(delta)),
fValue + " (" + ` fStart ` + "-" + ` fEnd ` + ")")
c.restoreState()
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels + 5, prev_legend - 15, 15, 6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels + 25, prev_legend - 15)
t.textOut(fValue + " (" + ` fStart ` + "-" + ` fEnd ` +
")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend - 15
c.showPage()
c.save()
def drawMap2():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else:
#rID = 791
#print rID
rID = 154659
reagentID = rHandler.convertDatabaseToReagentID(rID)
d = Drawing(1000, 1000)
origin = 0
origin_x = 500
origin_y = 500
radius = 350
c = Circle(origin_x, origin_y, radius)
c.strokeColor = blue
c.fillColor = white
d.add(c)
c.line(origin_x, origin_y + radius - 7, origin_x - 7, origin_y + radius)
c.line(origin_x - 7, origin_y + radius, origin_x, origin_y + radius + 7)
c.line(origin_x, origin_y + radius + 7, origin_x + 7, origin_y + radius)
c.line(origin_x + 7, origin_y + radius, origin_x, origin_y + radius - 7)
p = c.beginPath()
c.setFillColor(black)
c.saveState()
p.moveTo(origin_x, origin_y + radius - 7)
p.lineTo(origin_x - 7, origin_y + radius)
p.lineTo(origin_x, origin_y + radius + 7)
p.lineTo(origin_x + 7, origin_y + radius)
p.close()
c.drawPath(p)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print seqLen
unit_angle_measure = float(360) / float(seqLen)
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
for feature in sequenceFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
f_start = fStart * unit_angle_measure
f_end = fEnd * unit_angle_measure
if fStart > 0 and fEnd > 0:
print "Start " + ` fStart `
print "End " + ` fEnd `
startAngle = 90 - f_start
extAngle = -1 * (f_end - f_start)
print "Angle " + ` extAngle `
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = ArcPath()
#p.dumpProperties()
p.strokeWidth = 15
p.strokeColor = black
p.fillColor = red
#p.addArc(x1, y1, x2, y2, startAngle, extAngle) # NO
d.add(p)
d.add(String(origin_x + fStart, origin_y + fStart, fValue))
renderPDF.drawToFile(d, "V7066_map.png")
#!/usr/local/bin/python
import cgi
import utils
from sequence_handler import DNAHandler
from database_conn import DatabaseConn
import Bio
from Bio.Seq import Seq
from Bio.Restriction import *
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
dnaHandler = DNAHandler(db, cursor)
form = cgi.FieldStorage()
lims_id = form.getvalue("limsID") # always exists
print "Content-type: application/octet-stream"
print "Content-Disposition: attachment; filename=" + lims_id + ".txt"
print "Pragma: no-cache"
print "Expires: 0"
#print "Content-type:text/html"
print
# sequence may be empty
if form.has_key("vector_sequence"):
def printUserInfo(self, cmd, user, errCode=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_ID_Name_Map = ucMapper.mapCategoryIDToName()
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
currUser = Session.getUser()
gOut = GeneralOutputClass()
if cmd =='create':
username = user.getUsername()
firstname = user.getFirstName()
lastname = user.getLastName()
email = user.getEmail()
passwd = user.getPassword()
lab = user.getLab()
uLabID = lab.getID()
uLabName = lab.getName()
labs = lHandler.findAllLabs()
# changed Aug. 18/08 - new format
#content = gOut.printHeader() + gOut.printMainMenu()
content = gOut.printHeader()
content += '''
<FORM NAME="create_user_form" METHOD="POST" ACTION="%s" onSubmit="return verifyAddUser();">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="760px" cellpadding="5" cellspacing="5">
<TH colspan="4" style="color:#0000FF; border-top:1px groove black; border-bottom: 1px groove black; padding-top: 10px; padding-top:5px;">
ADD NEW USER
<P style="color:#FF0000; font-weight:normal; font-size:8pt; margin-top:5px;">Fields in red marked with an asterisk (<span style="font-size:9pt; color:#FF0000;">*</span>) are mandatory</P>
</TH>
<TR>
<TD style="width:150px; vertical-align:top; padding-top:10px; color:#FF0000;">
Laboratory: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD style="vertical-align:top; padding-top:10px">
<SELECT id="labList" name="labs">
<OPTION>Select Lab</OPTION>
'''
# sort labs by name
labSortedDict = {} # will store (labName, labID) tuples
labNames = [] # just hold lab names
for labID in labs.keys():
labName = labs[labID]
labNames.append(labName)
labSortedDict[labName] = labID
labNames.sort()
#for labID in labs.keys():
for labName in labNames:
labID = labSortedDict[labName]
labName = labs[labID]
content += "<OPTION ID=\"" + `labID` + "\" NAME=\"lab_optn\" VALUE=\"" + `labID` + "\""
if labID == uLabID:
content += " SELECTED>" + labName
else:
content += ">" + labName
content += "</OPTION>"
content += '''
</SELECT>
<BR/>
<P id="lab_warning" style="color:#FF0000; display:none">Please select a laboratory name from the dropdown list above.</P>
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
Username: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColValue">
<INPUT TYPE="TEXT" SIZE="35px" id="user_name" NAME="username" VALUE="%s"/>
<BR/>
<!-- Warning anchor -->
<a name="w1" style="text-decoration:none; font-weight:normal; font-size:8pt">
<P id="dup_uname_warning" style="color:#FF0000; display:inline">This username already exists. Please specify a different username.</P>
</a>
</TD>
<TD style="font-size:8pt">
Alphanumeric string up to 10 characters used to log into the system.
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
Password: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColValue">
<INPUT TYPE="PASSWORD" SIZE="35px" id="passwd" NAME="password" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
First name: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColValue">
<INPUT TYPE="TEXT" SIZE="35px" id="first_name" NAME="firstName" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD class="createViewColName" style="color:#FF0000;">
Last name: <sup style="font-size:10pt; color:#FF0000;">*</sup>
</TD>
<TD class="createViewColName">
<INPUT TYPE="TEXT" SIZE="35px" id="last_name" NAME="lastName" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD class="createViewColName">
Email:
</TD>
<TD class="createViewColValue">
<INPUT TYPE="TEXT" SIZE="35px" id="e_mail" NAME="email" VALUE="%s"/>
</TD>
</TR>
<TR>
<TD>
Access Level:
</TD>
<TD class="createViewColName" colspan="3">
<INPUT TYPE="RADIO" name="system_access_level" value="Reader" style="margin-top:8px; font-size:9pt" checked>Reader<BR/>
<INPUT TYPE="RADIO" name="system_access_level" value="Writer" style="margin-top:8px; font-size:9pt">Writer<BR/>
<INPUT TYPE="RADIO" name="system_access_level" value="Creator" style="margin-top:8px; font-size:9pt">Creator<BR/>
<INPUT TYPE="RADIO" name="system_access_level" value="Admin" style="margin-top:8px; font-size:9pt">Admin<BR/>
</TD>
</TR>
<TR id="project_access">
<TD colspan="4">
<TABLE width="100%%">
<TR>
<TD colspan="4" style="border-top:1px groove black; border-bottom:1px groove black; padding-top:8px; font-size:8pt; font-weight:bold">
Grant project access permissions to this user:
</TD>
</TR>
<TR>
<TD style="width:210px">
<SELECT id="packetList" name="packets" multiple size="15">
'''
# PRINT PROJECT LIST
projects = pHandler.findAllProjects()
for project in projects:
projectNumber = project.getNumber()
projectName = project.getName()
tmpProject = `projectNumber` + ": " + projectName
content += "<OPTION value=\"" + `projectNumber` + "\">" + tmpProject + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT TYPE="checkbox" style="margin-top:10px; font-size:8pt;" onClick="selectAll(this.id, 'packetList')" id="add_all_chkbx"> Select All</INPUT>
</TD>
<TD style="vertical-align:top" colspan="3">
<span style="font-size:8pt; font-weight:bold">User's access level to selected projects:<BR/></span>
<input type="radio" id="access_level_radio_read" name="access_levels" value="read" style="margin-top:8px; font-size:9pt" checked>Read-Only <BR/>
<input type="radio" id="access_level_radio_write" name="access_levels" value="write" style="margin-top:5px; font-size:9pt">Write <BR/>
<input style="margin-top:8px" onclick="addProjects('packetList', getSelectedRole('1'))" value="Go" type="button"></INPUT>
<P style="font-size:8pt; border-top:1px groove black; padding-top:10px; padding-bottom:5px; margin-top:10px">
Access levels: <BR/>
<span style="font-size: 8pt; margin-left: 9px; font-weight:bold; ">- Read-Only:</span> May view reagents in a project but may NOT modify them or add new reagents<BR/>
<span style="font-size: 8pt; margin-left: 9px; font-weight:bold;">- Write:</span> May create and modify reagents in a project but may NOT change project details or add/remove members to/from the project<BR/>
</P>
</TD>
</TR>
<TR>
<TD colspan="4" style="border-top:1px groove black; border-bottom:1px groove black; font-size:8pt; font-weight:bold">
User's current project access privileges:
</TD>
</TR>
<TR>
<TD style="border-right:1px solid black; font-size:8pt">
<B>Read-Only</B><BR/>
<SELECT id="user_projects_readonly" name="userProjectsReadonly" style="margin-top:5px" multiple size="12">
'''
# August 10/07: Default reader access to all on public projects
publicProjects = pHandler.findAllProjects('FALSE')
for proj in publicProjects:
pID = proj.getNumber()
pName = proj.getName();
# concatenate project ID and name in the form '1:parent'
tmpDescr = `pID` + ": " + pName
content += "<OPTION VALUE=\"" + `pID` + "\">" + tmpDescr + "</OPTION>"
content += '''
</SELECT><BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'user_projects_readonly')" id="select_all_reader_chkbx"> Select All</INPUT>
</TD>
<TD style="text-align:center; width:100px; border-right: 1px solid black; padding-left:20px; padding-right:20px;">
<input onclick="addProjects('user_projects_readonly', 'write')" value=" Make Writeable >>" type="button"></INPUT><BR/>
<input style="margin-top:30px;" onclick="addProjects('user_projects_write', 'read')" value="<< Make Read-Only" type="button"></INPUT><BR/>
<input style="margin-top:30px;" onclick="addProjects('user_projects_write'); addProjects('user_projects_readonly')" value="Remove Selected" type="button"></INPUT>
</TD>
<TD style="padding-left:50px; font-size:8pt">
<B>Write</B><BR/>
<SELECT id="user_projects_write" name="userProjectsWrite" style="margin-top:5px" multiple size="12"></SELECT><BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'user_projects_write')" id="select_all_writer_chkbx"> Select All</INPUT>
</TD>
</TR>
</TABLE>
</TD>
</TR>
<TR>
<TD colspan="4" style="border-top:1px groove black; border-bottom:1px groove black">
<INPUT TYPE="SUBMIT" id="addUser" NAME="add_user" VALUE="Add User" onClick="selectAllElements('user_projects_readonly'); selectAllElements('user_projects_write');">
</TD>
</TR>
</TABLE>
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", username, passwd, firstname, lastname, email)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
elif cmd == 'view':
userID = user.getUserID()
username = user.getUsername()
firstname = user.getFirstName()
lastname = user.getLastName()
email = user.getEmail()
userCat = user.getCategory()
lab = user.getLab()
labID = lab.getID()
labName = lab.getName()
# Only allow modification by admin
modify_disabled = True
if (currUser.getCategory() == 'Admin'):
modify_disabled = False
content = gOut.printHeader()
#content += gOut.printMainMenu()
content += '''
<FORM name="user_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="767px" style="margin-left:2px" cellpadding="5px" cellspacing="5px" class="detailedView_tbl" border="1" frame="box" rules="none">
<TR>
<TD colspan="6" class="detailedView_heading" style="padding-left:265px">
USER DETAILS PAGE
'''
content += "<INPUT TYPE=\"submit\" style=\"margin-left:50px;\" name=\"modify_user\" value=\"Change User Details\""
if modify_disabled:
content += " disabled>"
else:
content += ">"
content += "<INPUT TYPE=\"submit\" style=\"margin-left:2px;\" name=\"delete_user\" value=\"Delete User\" onClick=\"return verifyDeleteUser();\""
if modify_disabled:
content += " disabled>"
else:
content += ">"
content += '''
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Username:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="username" value="%s">
<!-- user ID a hidden value -->
<INPUT TYPE="hidden" name="userID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
First Name:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="firstName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Last Name:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="lastName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Laboratory:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
'''
if modify_disabled:
content += labName
else:
content += "<span class=\"linkShow\" onClick=\"redirectToLabView(" + `labID` + ");\">" + labName + "</span>"
content += '''
<INPUT TYPE="hidden" name="labID" value="%d">
<INPUT type="hidden" id="view_lab_hidden" name="view_lab">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Email:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="email" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Access Level:
</TD>
<TD class="detailedView_value" colspan="2" style="width:400px">
%s
<INPUT TYPE="hidden" name="system_access_level" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" width="50px">
Projects:
</TD>
</TR>
<TR>
<TD style="font-weight:bold; font-size:8pt; width:250px" colspan="2">
Read-Only:
</TD>
<TD style="font-weight:bold; font-size:8pt">
Write:
</TD>
</TR>
<TR>
<TD style="vertical-align:top;" colspan="2">
<UL>
'''
# show projects for the user
publicProj = pHandler.findAllProjects("FALSE")
readOnlyProj = pHandler.findMemberProjects(userID, 'Reader')
readProj = utils.merge(publicProj, readOnlyProj)
writeProj = pHandler.findMemberProjects(userID, 'Writer')
# sort read projects
readKeys = []
readSorted = {}
for r in readProj:
rProjectID = r.getNumber()
readKeys.append(rProjectID)
readSorted[rProjectID] = r
readKeys = utils.unique(readKeys)
readKeys.sort()
#for r in readProj:
for rProjectID in readKeys:
#rProjectID = r.getNumber()
r = readSorted[rProjectID]
rProjectName = r.getName()
rProjectOwner = r.getOwner()
try:
rOwnerName = rProjectOwner.getLastName()
except AttributeError:
rOwnerName = ""
#content += "<LI>" + `rProjectID` + ": " + rOwnerName + ": " + rProjectName
content += "<LI>"
content += "<span class=\"linkShow\" onClick=\"redirectToProjectDetailedView(" + `rProjectID` + ");\">" + `rProjectID` + ": " + rOwnerName + ": " + rProjectName + "</span>"
content += "</LI>"
content += '''
</UL>
</TD>
<TD style="vertical-align:top;">
<UL>
'''
# sort write projects
writeKeys = []
writeSorted = {}
for w in writeProj:
wProjectID = w.getNumber()
writeKeys.append(wProjectID)
writeSorted[wProjectID] = w
writeKeys = utils.unique(writeKeys)
writeKeys.sort()
#for w in writeProj:
for wProjectID in writeKeys:
#wProjectID = w.getNumber()
w = writeSorted[wProjectID]
wProjectName = w.getName()
wProjectOwner = w.getOwner()
wOwnerName = wProjectOwner.getLastName()
#content += "<LI>" + `wProjectID` + ": " + wProjectName
content += "<LI>"
content += "<span class=\"linkShow\" onClick=\"redirectToProjectDetailedView(" + `wProjectID` + ");\">" + `wProjectID` + ": " + wOwnerName + ": " + wProjectName + "</span>"
content += "</LI>"
content += '''
</UL>
</TD>
</TR>
</TABLE>
</FORM>
<FORM id="viewProjectForm" method="POST" action="%s">
<INPUT type="hidden" id="view_packet_hidden" name="view_packet">
<INPUT type="hidden" ID="curr_userid_hidden" NAME="curr_user_id" value="%d">
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", username, username, userID, firstname, firstname, lastname, lastname, labID, email, email, userCat, category_Name_ID_Map[userCat], hostname + "cgi/project_request_handler.py", currUser.getUserID())
print "Content-type:text/html" #
print # DITTO
print page_content
elif cmd == 'edit':
userID = user.getUserID()
username = user.getUsername()
firstname = user.getFirstName()
lastname = user.getLastName()
email = user.getEmail()
passwd = user.getPassword()
userCat = user.getCategory()
lab = user.getLab()
uLabID = lab.getID()
labName = lab.getName()
labs = lHandler.findAllLabs()
if errCode == "Dup_un":
un_warn_display = "inline"
else:
un_warn_display = "none"
content = gOut.printHeader()
#content += gOut.printMainMenu()
content += '''
<FORM name="user_form" method="POST" action="%s" onSubmit="return verifyWriteProjects();">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="760px" cellpadding="5px" cellspacing="5px" style="border:1px solid black" frame="box" rules="rows">
<TR>
<TD colspan="3" style="padding-left:200px; text-align:center">
<span style="color:#0000FF; font-weight:bold">CHANGE USER INFORMATION</span>
<INPUT TYPE="submit" style="margin-left:50px;" name="save_user" value="Save" onClick="selectAllElements('user_projects_readonly'); selectAllElements('user_projects_write');">
<INPUT TYPE="submit" style="margin-left:20px;" name="cancel_user" value="Cancel">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Username:
</TD>
<TD class="detailedView_value" style="width:400px">
<INPUT TYPE="text" size="50px" name="username" value="%s">
<BR/>
<!-- Warning anchor -->
<a name="w1" style="text-decoration:none; font-weight:normal; font-size:8pt">
<P id="dup_uname_warning" style="color:#FF0000; display:%s">This username already exists. Please specify a different username.</P>
</a>
<!-- user ID hidden value -->
<INPUT TYPE="hidden" name="userID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Laboratory:
</TD>
<TD style="vertical-align:top; padding-top:10px">
<SELECT id="labList" name="labs">
'''
# sort labs by name
labSortedDict = {} # will store (labName, labID) tuples
labNames = [] # just hold lab names
for labID in labs.keys():
labName = labs[labID]
labNames.append(labName)
labSortedDict[labName] = labID
labNames.sort()
#for labID in labs.keys():
for labName in labNames:
labID = labSortedDict[labName]
labName = labs[labID]
content += "<OPTION ID=\"" + `labID` + "\" NAME=\"lab_optn\" VALUE=\"" + `labID` + "\""
if labID == uLabID:
content += " SELECTED>" + labName
else:
content += ">" + labName
content += "</OPTION>"
content += '''
</SELECT>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
First Name:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" name="firstName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Last Name:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" name="lastName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Email:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" name="email" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Access Level:
</TD>
<TD class="detailedView_value" colspan="2">
<SELECT ID="user_category" NAME="system_access_level">
'''
ucHandler = UserCategoryHandler(db, cursor)
categories = ucHandler.findAllCategories()
for cID in categories.keys():
if categories[cID] == userCat:
content += "<OPTION VALUE=\"" + `cID` + "\" SELECTED>" + categories[cID] + "</OPTION>"
else:
content += "<OPTION VALUE=\"" + `cID` + "\">" + categories[cID] + "</OPTION>"
# Don't allow addition of Writeable projects to Readers thru Modify view
if userCat == 'Reader':
write_disabled = True
else:
write_disabled = False
content += '''
</SELECT>
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Projects user has access to:
</TD>
</TR>
<TR>
<td colspan="3">
<table width="700px">
<tr>
<TD colspan="2" style="font-size:8pt; vertical-align:top"">
Read-Only
</TD>
<TD style="font-size:8pt; vertical-align:top">
'''
if not write_disabled:
content += "Write"
else:
content += " "
content += '''
</TD>
</TR>
<TR>
<TD style="">
<SELECT id="user_projects_readonly" name="userProjectsReadonly" style="margin-top:5px" multiple size="12">
'''
# show projects for the user
readProj = pHandler.findMemberProjects(userID, 'Reader')
writeProj = pHandler.findMemberProjects(userID, 'Writer')
for r in readProj:
rProjectID = r.getNumber()
rProjectName = r.getName()
content += "<OPTION name=\"project_read\" value=\"" + `rProjectID` + "\">" + `rProjectID` + ": " + rProjectName + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT TYPE="checkbox" style="margin-top:10px;" onClick="selectAll(this.id, 'user_projects_readonly')" id="select_all_reader_chkbx"> Select All</INPUT>
'''
if not write_disabled:
content += '''
</TD>
<TD style="text-align:center; padding-right:15px;">
<input onclick="addProjects('user_projects_readonly', 'write')" value=" Make Writeable >>" type="button"></INPUT><BR/>
<input style="margin-top:30px;" onclick="addProjects('user_projects_write', 'read')" value="<< Make Read-Only" type="button"></INPUT><BR/>
<input type="button" style="margin-top:30px;" value="Remove" onclick="removeUserProjects();"></INPUT>
</TD>
'''
else:
content += '''
<input type="button" value="Remove Selected" onclick="removeUserProjects();"></INPUT>
'''
if not write_disabled:
content += '''
<TD style="font-size:8pt">
<SELECT id="user_projects_write" name="userProjectsWrite" style="margin-top:5px" multiple size="12">
'''
for w in writeProj:
wProjectID = w.getNumber()
wProjectName = w.getName()
content += "<OPTION name=\"project_write\" value=\"" + `wProjectID` + "\">" + `wProjectID` + ": " + wProjectName + "</OPTION>"
content += '''
</SELECT><BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'user_projects_write')" id="select_all_writer_chkbx"> Select All</INPUT>
</TD>
'''
content += '''
</TR>
</table>
</td>
</tr>
<TR>
<TD class="detailedView_value" colspan="3">
Add new projects:
</TD>
</TR>
<TR>
<TD colspan="3">
<TABLE>
<TR>
<TD>
<SELECT multiple ID="packetList">
'''
# Fetch the list of read and write projects for this user and extract their IDs
readProjID = [] # list of numerical IDs of read projects
for r in readProj:
rNum = r.getNumber()
readProjID.append(rNum)
writeProjID = []
for w in writeProjID:
wNum = w.getNumber()
writeProjID.append(wNum)
allPackets = pHandler.findAllProjects()
for p in allPackets:
pID = p.getNumber()
pName = p.getName()
pOwner = p.getOwner()
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `pOwner`
# update March 11, 2011
try:
lastName = pOwner.getLastName()
except AttributeError:
lastName = ""
#pDesc = `pID` + " : " + pOwner + " : " + pName
pDesc = `pID` + " : " + lastName + " : " + pName
if not pID in readProjID and not pID in writeProjID:
content += "<OPTION VALUE=\"" + `pID` + "\">" + pDesc
content += '''
</SELECT>
<BR>
<INPUT TYPE="checkbox" style="margin-top:10px; font-size:8pt;" onClick="selectAll(this.id, 'packetList')" id="add_all_chkbx"> Select All</INPUT>
'''
if not write_disabled:
content += '''
</TD>
<TD style="vertical-align:top">
<span style="font-size:8pt; font-weight:bold">User's access level to selected projects:<BR/></span>
<input type="radio" id="access_level_radio_read" name="access_levels" value="read" style="margin-top:8px; font-size:9pt" checked>Read-Only <BR/>
<input type="radio" id="access_level_radio_write" name="access_levels" value="write" style="margin-top:5px; font-size:9pt">Write <BR/>
<input style="margin-top:8px" onclick="addProjects('packetList', getSelectedRole('1'))" value="Add project" type="button"></INPUT>
</TD>
</TABLE>
</TD>
</TR>
'''
else:
content += '''
<input style="margin-left:5px; margin-top:8px" onclick="addProjects('packetList', 'read')" value="Add project" type="button"></INPUT>
'''
content += '''
</TR>
</TABLE>
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", username, un_warn_display, userID, firstname, lastname, email)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def printProjectInfo(self, cmd, project):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
gOut = GeneralOutputClass()
currUser = Session.getUser()
if cmd == 'view':
projectID = project.getNumber()
projectOwner = project.getOwner()
ownerName = projectOwner.getFullName()
ownerID = projectOwner.getUserID()
projectName = project.getName()
projectDescr = project.getDescription()
# private or public
isPrivate = project.isPrivate()
if isPrivate:
accessType = 'Private'
else:
accessType = 'Public'
# Only allow modification by owner or admin AND disallow project deletion if there are reagents in it!!!
modify_disabled = True
delete_disabled = True
if (currUser.getUserID() == ownerID) or (currUser.getCategory()
== 'Admin'):
modify_disabled = False
if project.isEmpty():
delete_disabled = False
# Aug. 18/08: Changed b/c of new format
#content = gOut.printHeader() + gOut.printMainMenu()
content = gOut.printHeader()
content += '''
<FORM name="project_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="username_hidden" NAME="username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE height="100%%">
<TABLE width="770px" cellpadding="5px" cellspacing="5px" class="detailedView_tbl">
<TR>
<TD class="detailedView_heading" style="white-space:nowrap;">
PROJECT DETAILS PAGE
</TD>
<TD class="detailedView_heading" style="text-align:right">
'''
content += "<INPUT TYPE=\"submit\" name=\"modify_project\" value=\"Modify Project\""
if modify_disabled:
content += " disabled>"
else:
content += ">"
content += "<INPUT TYPE=\"submit\" style=\"margin-left:2px;\" name=\"delete_project\" value=\"Delete Project\" onClick=\"return confirmDeleteProject();\""
if modify_disabled or delete_disabled:
content += " disabled>"
else:
content += ">"
content += '''
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project #
</TD>
<TD class="detailedView_value" width="87%%">
%d
<INPUT TYPE="hidden" name="packetID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Owner:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="packetOwner" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Name:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="packetName" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Description:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="packetDescription" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Access type:
</TD>
<TD class="detailedView_value">
%s
<INPUT TYPE="hidden" name="private_or_public" value="%s">
</TD>
</TR>
<TR>
<TD colspan="2">
<HR/>
</TD>
</TR>
'''
# Now here, show or hide members section depending on the user's access level
# Condition is the same as for determining whether modification is allowed - so use 'modify_disabled' variable
if not modify_disabled:
content += '''
<TR>
<TD class="projectDetailedViewName">
Project Members:
</TD>
<TD> </TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="2">
<TABLE width="100%%">
<TR>
<TD style="font-weight:bold; padding-left:10px" width="30%%">
Readers:
</TD>
<TD style="font-weight:bold; padding-left:10px">
Writers:
</TD>
</TR>
<TR>
<TD class="detailedView_value" style="vertical-align:top">
<UL>
'''
if not isPrivate:
content += "All OpenFreezer Users"
else:
# maintain the indent
readers = project.getReaders()
# sort by labs
labs = []
rdrLabs = {}
# First, iterate over readers list to extract all the labs
for rdr in readers:
lab = rdr.getLab().getID()
if lab not in labs:
labs.append(lab)
# Now iterate over the list of labs and link its readers to it
for lab in labs:
tmpRdrs = [] # list of members in one lab
for rdr in readers:
tmpLab = rdr.getLab().getID()
if tmpLab == lab:
# append reader to list of members of this lab
if rdrLabs.has_key(lab):
tmpRdrs = rdrLabs[lab]
tmpRdrs.append(rdr)
rdrLabs[lab] = tmpRdrs
#for rdr in readers:
for lab_id in rdrLabs.keys():
rdrs = rdrLabs[lab_id] # list of objects!!
tmp_lab_name = lHandler.findLabName(lab_id)
# print out the lab name
if currUser.getCategory() == 'Admin':
content += "<span class=\"linkShow\" style=\"color:#2E8B57\" onClick=\"goToLabViewFromProject(" + ` lab_id ` + ");\">" + tmp_lab_name + "</span><BR/>"
else:
content += "<span style=\"color:#2E8B57\">" + tmp_lab_name + "</span><BR/>"
# print reader names
for rdr in rdrs:
content += "<INPUT TYPE=\"hidden\" name=\"projectReaders\" value=\"" + ` rdr.getUserID(
) ` + "\"></INPUT>"
# Only show hyperlinks if the viewer is an Admin; otherwise just output plain names
if currUser.getCategory() == 'Admin':
content += "<LI style=\"list-style:none; padding-left:6px;\">-- <span class=\"linkShow\" onClick=\"redirectToUserFromProject(" + ` rdr.getUserID(
) ` + ");\">" + rdr.getFullName(
) + "</span></LI>"
else:
content += "<LI style=\"list-style:none; padding-left:6px;\">-- " + rdr.getFullName(
) + "</LI>"
content += '''
</UL>
</TD>
<TD class="detailedView_value" style="width:250px; vertical-align:top">
<UL>
'''
writers = project.getWriters()
# sort them by lab too, same as for readers
labs = []
wrtrLabs = {}
# First, iterate over readers list to extract all the labs
for wrtr in writers:
lab = wrtr.getLab().getID()
if lab not in labs:
labs.append(lab)
# Now iterate over the list of labs and link its readers to it
for lab in labs:
tmpWrtrs = [] # list of members in one lab
for wrtr in writers:
tmpLab = wrtr.getLab().getID()
if tmpLab == lab:
# append reader to list of members of this lab
if wrtrLabs.has_key(lab):
tmpWrtrs = wrtrLabs[lab]
tmpWrtrs.append(wrtr)
wrtrLabs[lab] = tmpWrtrs
for lab_id in wrtrLabs.keys():
wrtrs = wrtrLabs[lab_id] # list of objects!!
tmp_lab_name = lHandler.findLabName(lab_id)
# print out the lab name
if currUser.getCategory() == 'Admin':
content += "<span class=\"linkShow\" style=\"color:#2E8B57\" onClick=\"goToLabViewFromProject(" + ` lab_id ` + ");\">" + tmp_lab_name + "</span><BR/>"
else:
content += "<span style=\"color:#2E8B57\" " + ` lab_id ` + ");\">" + tmp_lab_name + "</span><BR/>"
for wrtr in wrtrs:
content += "<INPUT TYPE=\"hidden\" name=\"projectWriters\" value=\"" + ` wrtr.getUserID(
) ` + "\">"
if currUser.getCategory() == 'Admin':
content += "<LI style=\"list-style:none; padding-left:6px;\">-- <span class=\"linkShow\" onClick=\"redirectToUserFromProject(" + ` wrtr.getUserID(
) ` + ");\">" + wrtr.getFullName() + "</span></LI>"
else:
content += "<LI style=\"list-style:none; padding-left:6px;\">-- " + wrtr.getFullName(
) + "</LI>"
content += '''
</UL>
</TD>
</TR>
</TABLE>
</TD>
</TR>
</TABLE>
</FORM>
<FORM id="viewUserForm" method="POST" action="%s">
<INPUT type="hidden" id="view_user_hidden" name="view_user">
<INPUT type="hidden" ID="curr_userid_hidden" NAME="curr_user_id" value="%d">
</FORM>
<FORM id="viewLabForm" method="POST" action="%s">
<INPUT type="hidden" ID="curr_userid_hidden" NAME="curr_user_id" value="%d">
<INPUT type="hidden" id="view_lab_hidden" name="view_lab">
</FORM>
</TABLE>
'''
content += gOut.printFooter()
else:
content += '''
</TABLE>
</FORM>
</TABLE>
'''
content += gOut.printFooter()
# and here, depending on what sections of the project view were printed, the number of arguments would vary
if not modify_disabled:
page_content = content % (
hostname + "cgi/project_request_handler.py", projectID,
projectID, ownerName, ownerID, projectName, projectName,
projectDescr, projectDescr, accessType, accessType,
hostname + "cgi/user_request_handler.py",
currUser.getUserID(), hostname +
"cgi/user_request_handler.py", currUser.getUserID())
else:
page_content = content % (
hostname + "cgi/project_request_handler.py", projectID,
projectID, ownerName, ownerID, projectName, projectName,
projectDescr, projectDescr, accessType, accessType)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
elif cmd == 'edit':
projectID = project.getNumber()
projectOwner = project.getOwner()
ownerName = projectOwner.getFullName()
ownerID = projectOwner.getUserID()
projectName = project.getName()
projectDescr = project.getDescription()
isPrivate = project.isPrivate()
content = gOut.printHeader()
#content += gOut.printMainMenu()
content += '''
<FORM name="project_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="username_hidden" NAME="username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="770px" cellpadding="5px" cellspacing="5px" style="border:1px solid black" frame="box" rules="rows">
<TR>
<TD colspan="3" style="padding-left:200px; text-align:center">
<span style="color:#0000FF; font-weight:bold">MODIFY PROJECT </span>
<span style="color:#FF0000; font-weight:bold">%d</span>
<INPUT TYPE="hidden" name="packetID" value="%d">
<INPUT TYPE="submit" style="margin-left:200px;" name="save_project" value="Save" onClick=\"alert('Please note: If your project writers list contains names of users who have read-only access to OpenFreezer, their names will be removed from the list during saving.'); addProjectOwnerToWritersList(); selectAllElements('readers_target_list'); selectAllElements('writers_target_list'); return verifyProjectOwner('projectOwnersList') && verifyProjectName('packet_name') && verifyProjectDescr('packet_descr') && verifyMembers('readers_target_list') && verifyMembers('writers_target_list');\">
<INPUT TYPE="submit" style="margin-left:20px;" name="cancel_project" value="Cancel">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Owner:
</TD>
<TD class="detailedView_value" colspan="2">
<SELECT ID="projectOwnersList" name="packetOwner">
'''
# Get list of all potential project owners - users with 'CREATOR' or higher privileges
# Returns list of User **objects**
creators = uHandler.findAllMembersInCategory(
'Creator', False, '<=')
creatorsDict = {} # name, uid
for creator in creators:
uid = creator.getUserID()
name = creator.getFullName()
creatorsDict[name] = uid
names = creatorsDict.keys()
names.sort()
#print "Content-type:text/html"
#print
for name in names:
#print name
uid = creatorsDict[name]
#print uid
#print ownerID
if uid == ownerID:
content += "<OPTION SELECTED value=" + ` uid ` + ">" + name + "</OPTION>"
else:
content += "<OPTION value=" + ` uid ` + ">" + name + "</OPTION>"
content += '''
</SELECT>
<DIV ID="projectOwnerWarning" STYLE="display:none; color:#FF0000; font-weight:normal;">
<BR>Please select a name from the list above.
</DIV>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Name:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" id="packet_name" name="packetName" value="%s">
<DIV ID="projectNameWarning" STYLE="display:none; color:#FF0000; font-weight:normal;">
<BR>Please provide a project name.
</DIV>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Description:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" id="packet_descr" name="packetDescription" value="%s">
<DIV ID="projectDescrWarning" STYLE="display:none; color:#FF0000; font-weight:normal;">
<BR>Please provide a project description.
</DIV>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Access type:
</TD>
<TD class="detailedView_value" style="width:400px">
'''
if not isPrivate:
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"public\" checked>Public "
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"private\">Private"
else:
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"public\">Public "
content += "<INPUT TYPE=\"RADIO\" NAME=\"private_or_public\" VALUE=\"private\" checked>Private"
content += '''
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Project Members:
</TD>
<TD class="detailedView_value" colspan="2">
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Edit existing project members lists:
</TD>
</TR>
<TR>
<TD style="width:100px">
<SELECT multiple size="10" id="readers_target_list" name="readersList">
'''
# Readers and writers associated with this project
currReaders = project.getReaders()
currWriters = project.getWriters()
# Since object comparison is done by reference, cannot check if a User object returned by findAllMembers is a member of this project by using 'in array'. Need to compare user IDs explicitly
currReaderIDs = []
currWriterIDs = []
currReaderNames = []
currWriterNames = []
currReadersDict = {} # name, id
currWritersDict = {}
# need lab IDs too - to match members to their labs when moved between lists, but having a 'memberID, labID' dictionary is too clumsy. Easiest approach: have 'memberID, Member Object' dictionary
currReaderObjDict = {} # id, User object
currWriterObjDict = {}
for r in currReaders:
rID = r.getUserID()
rName = r.getFullName()
# associate rID with its containing object
currReaderObjDict[rID] = r
currReaderIDs.append(rID)
currReaderNames.append(rName)
currReadersDict[rName] = rID
for w in currWriters:
wID = w.getUserID()
wName = w.getFullName()
currWriterObjDict[wID] = w
currWriterIDs.append(wID)
currWriterNames.append(wName)
currWritersDict[wName] = wID
currReaderNames.sort()
currWriterNames.sort()
for rName in currReaderNames:
rID = currReadersDict[rName]
rdr = currReaderObjDict[rID]
rdrLabID = rdr.getLab().getID()
#content += "<OPTION id=" + `rID` + " value=" + `rID` + ">" + rName + "</OPTION>"
# June 28/07: Include labID in the option id
content += "<OPTION id=\"user_" + ` rID ` + "_lab_" + ` rdrLabID ` + "\" value=" + ` rID ` + ">" + rName + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT TYPE="checkbox" style="margin-top:10px" onClick="selectAll(this.id, 'readers_target_list')" id="select_all_reader_chkbx"> Select All</INPUT>
</TD>
<TD width="30px">
<input onclick="addMembers('readers_target_list', 'write')" value=" Make Writer >>" type="button"></INPUT><BR/>
<input style="margin-top:10px;" onclick="addMembers('writers_target_list', 'read')" value="<< Make Reader" type="button"></INPUT><BR/>
<input style="margin-top:10px;" onclick="removeProjectMembers()" value="Remove Selected" type="button"></INPUT>
</TD>
<TD>
<SELECT multiple size="10" id="writers_target_list" name="writersList">
'''
for wName in currWriterNames:
wID = currWritersDict[wName]
wrtr = currWriterObjDict[wID]
wrtrLabID = wrtr.getLab().getID()
#content += "<OPTION id=" + `wID` + " value=" + `wID` + ">" + wName + "</OPTION>"
# June 28/07: Include labID in the option id
content += "<OPTION id=\"user_" + ` wID ` + "_lab_" + ` wrtrLabID ` + "\" value=" + ` wID ` + ">" + wName + "</OPTION>"
content += '''
</SELECT>
<BR/>
<INPUT style="margin-top:10px;" TYPE="checkbox" onClick="selectAll(this.id, 'writers_target_list')" id="select_all_writer_chkbx"> Select All</INPUT>
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Add new members to this project:
</TD>
</TR>
<TR>
<TD class="detailedView_value" colspan="3">
Laboratory:
<SELECT id="labList" name="labs" onChange="showLabMembersList()">
'''
# fetch lab list - Updated August 90/7: Fetch ALL labs, with any access - then if a read-only lab has members with higher access, would show these members in list
#labs = lHandler.findAllLabs('Writer', '<=')
labs = lHandler.findAllLabs()
# sort lab names alphabetically
labNames = []
labsDict = {} # name, id
for labID in labs.keys():
labName = labs[labID]
labNames.append(labName)
labsDict[labName] = labID
labNames.sort()
currLab = projectOwner.getLab()
currLabID = currLab.getID()
#for labID in labs.keys():
for labName in labNames:
#labName = labs[labID]
labID = labsDict[labName]
if labID == currLabID:
content += "<OPTION SELECTED id='" + ` labID ` + "' NAME='lab_optn' value=" + ` labName ` + ">" + labName + "</OPTION>"
else:
content += "<OPTION id='" + ` labID ` + "' NAME='lab_optn' value=" + ` labName ` + ">" + labName + "</OPTION>"
content += '''
</SELECT>
</TD>
</TR>
<TR>
<TD width="100px">
'''
# For each lab, print a list of its members
for labID in labs.keys():
# First, fetch a list of users
# These are **User instances** - need to get their names and IDs for comparison
# August 9/07: Don't fetch only writers, fetch readers too - it's up to the project owner to grant them access to the project
#writers = uHandler.findAllMembersInCategory('Writer', True, '<=', labID)
writers = uHandler.findAllMembersInCategory(
'Reader', True, '<=', labID)
writersDict = {} # name, uid
writersObjDict = {} # id, User object
# Fetch user IDs and sort their names alphabetically
for writer in writers:
name = writer.getFullName()
uid = writer.getUserID()
labID = (writer.getLab()).getID()
writersDict[name] = uid
writersObjDict[uid] = writer
names = writersDict.keys()
names.sort()
# Show members for one lab at a time
if labID == currLabID:
display = "inline"
else:
display = "none"
content += "<SELECT MULTIPLE id=\"lab_source_list_" + ` labID ` + "\" name=\"labSourceMembers_" + ` labID ` + "\" SIZE=\"10\" style=\"display:" + display + "\">"
for name in names:
uid = writersDict[name]
labID = writersObjDict[uid].getLab().getID()
if uid not in currReaderIDs and uid not in currWriterIDs:
#content += "<OPTION value=" + `uid` + ">" + name + "</OPTION>"
content += "<OPTION id=\"user_" + ` uid ` + "_lab_" + ` labID ` + "\" value=" + ` uid ` + ">" + name + "</OPTION>"
content += "</SELECT>"
content += '''
<BR/>
<INPUT TYPE="checkbox" style="margin-top:8px" onClick="selectAll(this.id, 'lab_source_list_' + getSelectedLab())" id="add_all_chkbx"> Select All Members</INPUT>
</TD>
<TD colspan="2" style="vertical-align:top">
Add selected members to:
<P style="font-size:9pt; margin-top:5px;">
<input type="radio" id="access_level_radio_read" name="access_levels" value="read" checked>Readers list</INPUT><BR/>
<input type="radio" id="access_level_radio_write" name="access_levels" value="write">Writers list</INPUT><BR/>
<input style="margin-top:8px" onclick="addMembers('lab_source_list_' + getSelectedLab(), getSelectedRole('1'))" value="Go" type="button"></INPUT>
<BR/>
</P>
</TD>
</TR>
</TABLE>
</FORM>
'''
content += gOut.printFooter()
page_content = content % (
hostname + "cgi/project_request_handler.py",
project.getNumber(), project.getNumber(), project.getName(),
project.getDescription())
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def rMap_specific(f_in, f_out, enz_list):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(
bioSeq,
linear=False) # linear = FALSE, we're dealing w/ VECTORS
analysis = Analysis(
enz_list, fSeq,
linear=False) # linear = FALSE again for VECTORS
result = analysis.full()
outfile.write(reagentID + ": " + '\n')
# calculate bandwidths
allSites = []
for enz in result.keys():
sites = result[enz]
if len(allSites) == 0:
allSites = sites
else:
# concatenate
for s in sites:
allSites.append(s)
allSites.sort()
if len(allSites) > 0:
# calculate distances between sites
bandSizes = []
i = 1
while i < len(allSites):
tmpLen = allSites[i] - allSites[i - 1]
bandSizes.append(tmpLen)
i += 1
# last band
tmpLen = len(mySeq) - allSites[i - 1] + allSites[0]
bandSizes.append(tmpLen)
bandSizes.sort()
outfile.write( ` bandSizes ` + '\n')
outfile.write('\n')
infile.close()
outfile.close()
cursor.close()
db.close()
def printReagentInfo(self, cmd, reagent, errMsg=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
gOut = GeneralOutputClass()
currUser = Session.getUser()
currUserID = currUser.getUserID()
sHandler = SystemSetHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
# print menu
content = gOut.printHeader() + gOut.printMainMenu()
# common to all reagent types
projectList = utils.unique(pHandler.findMemberProjects(currUserID, 'Writer') + pHandler.findMemberProjects(currUserID, 'Owner'))
# Differentiate other properties by reagent type
if reagent.getType() == 'Insert':
# Fetch dropdown list values to output on the form
iTypeList = sHandler.findAllSetValues("type of insert")
statusList = sHandler.findAllSetValues("status")
cloningMethodList = sHandler.findAllSetValues("insert cloning method")
fpcsList = sHandler.findAllSetValues("5' cloning site")
tpcsList = sHandler.findAllSetValues("3' cloning site")
tagTypeList = sHandler.findAllSetValues("tag")
tagPositionList = sHandler.findAllSetValues("tag position")
openClosedList = sHandler.findAllSetValues("open/closed")
speciesList = sHandler.findAllSetValues("species")
verificationList = sHandler.findAllSetValues("verification")
# Initialize property values
iType = ""
iName = ""
iStatus = ""
cloningMethod = ""
projectID = ""
fpcs = ""
tpcs = ""
tagType = ""
tagPosition = ""
openClosed = ""
species = ""
accession = ""
altID = ""
geneID = ""
ensemblID = ""
geneSymbol = ""
fp_start = ""
tp_stop = ""
fwd_linker = ""
rev_linker = ""
funcDescr = ""
verification = ""
expComm = ""
verComm = ""
sequence = ""
# Fetch POST values if available:
allProps = reagent.getProperties()
if allProps.has_key("type of insert"):
iType = allProps["type of insert"]
if allProps.has_key("name"):
iName = allProps["name"]
if allProps.has_key("status"):
iStatus = allProps["status"]
if allProps.has_key("insert cloning method"):
cloningMethod = allProps["insert cloning method"]
if allProps.has_key("packet id"):
projectID = int(allProps["packet id"])
if allProps.has_key("5' cloning site"):
fpcs = allProps["5' cloning site"]
if allProps.has_key("3' cloning site"):
tpcs = allProps["3' cloning site"]
if allProps.has_key("tag"):
tagType = allProps["tag"]
if allProps.has_key("tag position"):
tagPosition = allProps["tag position"]
if allProps.has_key("open/closed"):
openClosed = allProps["open/closed"]
if allProps.has_key("species"):
species = allProps["species"]
if allProps.has_key("accession number"):
accession = allProps["accession number"]
if allProps.has_key("alternate id"):
altID = allProps["alternate id"]
if allProps.has_key("entrez gene id"):
geneID = allProps["entrez gene id"]
if allProps.has_key("ensembl gene id"):
ensemblID = allProps["ensembl gene id"]
if allProps.has_key("official gene symbol"):
geneSymbol = allProps["official gene symbol"]
if allProps.has_key("5' start"):
fp_start = allProps["5' start"]
if allProps.has_key("3' stop"):
tp_stop = allProps["3' stop"]
if allProps.has_key("5' linker"):
fwd_linker = allProps["5' linker"]
if allProps.has_key("3' linker"):
rev_linker = allProps["3' linker"]
if allProps.has_key("description"):
funcDescr = allProps["description"]
if allProps.has_key("verification"):
verification = allProps["verification"]
if allProps.has_key("comments"):
expComm = allProps["comments"]
if allProps.has_key("verification comments"):
verComm = allProps["verification comments"]
if allProps.has_key("sequence"):
sequence = allProps["sequence"]
# associations
ipvID = ""
senseOligoID = ""
antisenseOligoID = ""
allAssoc = reagent.getAssociations()
'''
if allAssoc.has_key("insert_parent_vector"):
ipvID = allAssoc["insert_parent_vector"]
if allAssoc.has_key("sense_oligo"):
senseOligoID = allAssoc["sense_oligo"]
if allAssoc.has_key("antisense_oligo"):
antisenseOligoID = allAssoc["antisense_oligo"]
'''
# Action: Output form with POST values if set
if cmd == 'create':
content += '''
<div class="main">
<form NAME="create_insert_form" ACTION="%s" METHOD="POST" onSubmit="return validateInsert() && verifyParents();">
'''
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" value=\"" + currUser.getFullName() + "\">"
content += '''
<input type="hidden" name="reagent_type_hidden" value="Insert">
<table id="vector_insertproperty_table_id" border="1" width="780px" cellpadding="4" frame="box" rules="all">
'''
if errMsg != "":
content += "<th colspan=\"3\" style=\"color:#0000FF; text-align:left; font-weight:normal\">There was a problem:<br><P>" + errMsg + "<BR><BR></th>"
content += '''
<tr>
<td colspan="3" style="text-align:center">
<span style="color:#0000CD; font-size:13pt; font-weight:bold">
Insert Information
</span>
<br>
<span style="font-size:8pt; color:#FF0000">
Fields marked with a red asterisk (*) are mandatory
</span>
</td>
</tr>
<tr>
<td width="180px">
Type of Insert
<span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td width="275px">
<SELECT id="itype_list" size="1" NAME="INPUT_INSERT_info_insert_type_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for it in iTypeList:
content += "<OPTION VALUE=\"" + it + "\""
if it == iType:
content += " SELECTED>" + it + "</OPTION>"
else:
content += ">" + it + "</OPTION>"
content += '''
</SELECT>
</td>
<td>
Describes the type of insert. Users select from a pre-defined list. Designed to make insert use more apparent and searches easier.
</td>
</tr>
<tr>
<td>
Name
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_name_prop\" value=\"" + iName + "\">"
content += '''
</td>
<td>
Name that describes the reagent - free text field
</td>
</tr>
<tr>
<td>
Status
</td>
<td>
<SELECT id="status_list" name="INPUT_INSERT_info_status_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iStatus) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for s in statusList:
content += "<OPTION VALUE=\"" + s + "\""
if s == iStatus:
content += " SELECTED>" + s + "</OPTION>"
else:
content += ">" + s + "</OPTION>"
content += '''
</td>
<td>
Indicates the status and availability of the reagent. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Insert Cloning Method
</td>
<td>
<SELECT size="1" id="cm_list" name="INPUT_INSERT_info_cloning_method_prop" onChange="showCMText()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(cloningMethod) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for cm in cloningMethodList:
content += "<OPTION VALUE=\"" + cm + "\""
if cm == cloningMethod:
content += " SELECTED>" + cm + "</OPTION>"
else:
content += ">" + cm + "</OPTION>"
content += '''
</td>
<td>
Describes the method used to create the insert (e.g. PCR or RE (restriction enzyme)) and provides additional information for its cloning into a vector (eg. by RE, In Fusion or BP reaction)
</td>
</tr>
<tr>
<td>
Project ID <span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td>
<select id="packetList_insert" size="1" name="INPUT_INSERT_info_packet_id_prop">
'''
# need to sort projects
pNums = []
projects = {} # (pID, Packet)
for p in projectList:
pID = p.getNumber()
pNums.append(pID)
projects[pID] = p
pNums.sort()
for pID in pNums:
p = projects[pID]
content += "<OPTION VALUE=\"" + `p.getNumber()` + "\""
if p.getNumber() == projectID:
content += " SELECTED>" + `p.getNumber()` + ": " + p.getOwner().getLastName() + ": " + p.getName() + "</OPTION>"
else:
content += ">" + `p.getNumber()` + ": " + p.getOwner().getLastName() + ": " + p.getName() + "</OPTION>"
content += '''
</select>
<BR>
<div id="packet_warning_insert" style="display:none; color:#FF0000">Please select a Project ID from the dropdown list</div>
</td>
<td>
Indicates what person and project originally created the reagent.
</td>
</tr>
<tr>
<td>
5' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="fpcs_list" name="INPUT_INSERT_info_5_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(fpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for fps in fpcsList:
content += "<OPTION VALUE=\"" + fps + "\""
if fps == fpcs:
content += " SELECTED>" + fps + "</OPTION>"
else:
content += ">" + fps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 5' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
3' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="tpcs_list" name="INPUT_INSERT_info_3_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tps in tpcsList:
content += "<OPTION VALUE=\"" + tps + "\""
if tps == tpcs:
content += " SELECTED>" + tps + "</OPTION>"
else:
content += ">" + tps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 3' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag
</td>
<td>
<SELECT size="1" id="tag_list" name="INPUT_INSERT_info_tag_prop" onChange="showTagTypeBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tt in tagTypeList:
content += "<OPTION VALUE=\"" + tt + "\""
if tt == tagType:
content += " SELECTED>" + tt + "</OPTION>"
else:
content += ">" + tt + "</OPTION>"
content += '''
</td>
<td>
Indicates if the insert itself has a tag associated with it (outside of the backbone vector). Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag Position
</td>
<td>
<SELECT size="1" name="INPUT_INSERT_info_tag_position_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagPosition) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tp in tagPositionList:
content += "<OPTION VALUE=\"" + tp + "\""
if tp == tagPosition:
content += " SELECTED>" + tp + "</OPTION>"
else:
content += ">" + tp + "</OPTION>"
content += '''
</td>
<td>
Describes the position of the tag on the insert. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Open/Closed
</td>
<td>
<SELECT id="oc_list" size="1" name="INPUT_INSERT_info_open_closed_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(openClosed) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for oc in openClosedList:
content += "<OPTION VALUE=\"" + oc + "\""
if oc == openClosed:
content += " SELECTED>" + oc + "</OPTION>"
else:
content += ">" + oc + "</OPTION>"
content += '''
</td>
<td>
Indicates for an Open Reading Frame if there is a start codon (ATG) or stop codon (open - no stop codon, closed - stop codon).
</td>
</tr>
<tr>
<td>
Species
</td>
<td>
<SELECT size="1" style="color:000000" id = "species_list" name="INPUT_INSERT_info_species_prop" onChange="showSpeciesBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(species) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for sp in speciesList:
content += "<OPTION VALUE=\"" + sp + "\""
if sp == species:
content += " SELECTED>" + sp + "</OPTION>"
else:
content += ">" + sp + "</OPTION>"
content += '''
</td>
<td>
Indicates the species from which the Insert was derived. User selects species from a pre-defined list.
</td>
</tr>
<tr>
<td>
Accession Number
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_accession_number_prop\" value=\"" + accession + "\">"
content += '''
</td>
<td>
The Accession Number from which the insert was cloned or to which the sequence maps.
</td>
</tr>
<tr>
<td>
Alternate ID
</td>
<td>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="IMAGE" id="_alternate_id_IMAGE_checkbox" onClick="showAltIDTextBox('_alternate_id_IMAGE_checkbox', '_alternate_id_IMAGE_textbox')">IMAGE <INPUT style="display:none" id="_alternate_id_IMAGE_textbox" name="alternate_id_IMAGE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RIKEN" id="_alternate_id_RIKEN_checkbox" onClick="showAltIDTextBox('_alternate_id_RIKEN_checkbox', '_alternate_id_RIKEN_textbox')">RIKEN <INPUT style="display:none" id="_alternate_id_RIKEN_textbox" name="alternate_id_RIKEN_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="Kazusa" id="_alternate_id_Kazusa_checkbox" onClick="showAltIDTextBox('_alternate_id_Kazusa_checkbox', '_alternate_id_Kazusa_textbox')">Kazusa <INPUT style="display:none" id="_alternate_id_Kazusa_textbox" name="alternate_id_Kazusa_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="LIFESEQ" id="_alternate_id_LIFESEQ_checkbox" onClick="showAltIDTextBox('_alternate_id_LIFESEQ_checkbox', '_alternate_id_LIFESEQ_textbox')">LIFESEQ <INPUT style="display:none" id="_alternate_id_LIFESEQ_textbox" name="alternate_id_LIFESEQ_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RZPD" id="_alternate_id_RZPD_checkbox" onClick="showAltIDTextBox('_alternate_id_RZPD_checkbox', '_alternate_id_RZPD_textbox')">RZPD <INPUT style="display:none" id="_alternate_id_RZPD_textbox" name="alternate_id_RZPD_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="HIP" id="_alternate_id_HIP_checkbox" onClick="showAltIDTextBox('_alternate_id_HIP_checkbox', '_alternate_id_HIP_textbox')">HIP <INPUT style="display:none" id="_alternate_id_HIP_textbox" name="alternate_id_HIP_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="ADDGENE" id="_alternate_id_ADDGENE_checkbox" onClick="showAltIDTextBox('_alternate_id_ADDGENE_checkbox', '_alternate_id_ADDGENE_textbox')">ADDGENE <INPUT style="display:none" id="_alternate_id_ADDGENE_textbox" name="alternate_id_ADDGENE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="PMID" id="_alternate_id_PMID_checkbox" onClick="showAltIDTextBox('_alternate_id_PMID_checkbox', '_alternate_id_PMID_textbox')">PMID <INPUT style="display:none" id="_alternate_id_PMID_textbox" name="alternate_id_PMID_textbox_name" size="15"></INPUT><br>
<input type="checkbox" id="_other_Alt_ID_chkbx" name="INPUT_INSERT_info_alternate_id_prop[]" value="Other" onClick="showSpecificOtherCheckbox('_alternate_id_txt')">Other: <INPUT style="display:none" id="_alternate_id_txt" name="alternate_id_name_txt" size="15"></INPUT>
</td>
<td>
Indicates any other ID's that identify the insert, including but not limited to IMAGE, Kazusa, RIKEN, and other. <BR><BR><BR><BR>For 'Other', please enter the source name and ID separated by a semicolon (e.g. IMAGE:123456)
</td>
</tr>
<tr>
<td>
Entrez Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_id_prop\" value=\"" + geneID + "\">"
content += '''
</td>
<td>
The NCBI Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Ensembl Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_ensembl_gene_id_prop\" value=\"" + ensemblID + "\">"
content += '''
</td>
<td>
The Ensembl Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Official Gene Symbol
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_symbol_prop\" value=\"" + geneSymbol + "\">"
content += '''
</td>
<td>
The official gene symbol for this Insert.
</td>
</tr>
<tr>
<td>
5' Start
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_start_prop\" value=\"" + fp_start + "\">"
content += '''
</td>
<td>
Users can map the start of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence starts.
</td>
</tr>
<tr>
<td>
3' Stop
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_stop_prop\" value=\"" + tp_stop + "\">"
content += '''
</td>
<td>
Users can map the stop of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence stops
</td>
</tr>
<tr>
<td>
5' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_linker_prop\" value=\"" + fwd_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 5' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg kozak sequences, any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
3' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_linker_prop\" value=\"" + rev_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 3' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
Functional Description
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_description_prop\" value=\"" + funcDescr + "\">"
content += '''
</td>
<td>
Describes the purpose of the reagent and any information that may be key to working with the reagent.
</td>
</tr>
<tr>
<td>
Verification
</td>
<td>
<select size="1" name="INPUT_INSERT_info_verification_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(verification) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for v in verificationList:
content += "<OPTION VALUE=\"" + v + "\""
if v == verification:
content += " SELECTED>" + v + "</OPTION>"
else:
content += ">" + v + "</OPTION>"
content += '''
</select>
</td>
<td>
Indicates if the reagent has been verified and how. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Verification comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_verification_comments_prop\" value=\"" + verComm + "\">"
content += '''
</td>
<td>
Allows user to provide a description of the verification status - eg comments on sequence changes, expression levels.
</td>
</tr>
<tr>
<td>
Experimental comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_comments_prop\" value=\"" + expComm + "\">"
content += '''
</td>
<td>
Used to describe any information that descrbes how the reagent works in the experimental context - eg low expression, difficult to grow, etc.
</td>
</tr>
<tr>
<td>
Sequence
</td>
<td>
</td>
<td>
The sequence of the insert that corresponds to a cDNA or fragment of interest. Does include artificial start and stop codons. Does not include linker sequences as described above.
</td>
</tr>
<tr>
<td colspan="3">
<textarea rows="10" cols="93" id="dna_sequence" name="INPUT_INSERT_info_sequence_prop">
'''
content += sequence
content += '''
</textarea>
</td>
</tr>
'''
content += self.printParents('Insert', allAssoc)
content += '''
<tr>
<td colspan="3">
<hr><br>
<input type="submit" name="create_reagent" value="Create" onclick="document.pressed = this.value">
</td>
</tr>
</table>
</form>
</div>
'''
# Common to all
content += gOut.printFooter()
page_content = content % (hostname + "cgi/create.py")
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def printReagentInfo(self, cmd, reagent, errMsg=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
gOut = GeneralOutputClass()
currUser = Session.getUser()
currUserID = currUser.getUserID()
sHandler = SystemSetHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
# print menu
content = gOut.printHeader() + gOut.printMainMenu()
# common to all reagent types
projectList = utils.unique(
pHandler.findMemberProjects(currUserID, 'Writer') +
pHandler.findMemberProjects(currUserID, 'Owner'))
# Differentiate other properties by reagent type
if reagent.getType() == 'Insert':
# Fetch dropdown list values to output on the form
iTypeList = sHandler.findAllSetValues("type of insert")
statusList = sHandler.findAllSetValues("status")
cloningMethodList = sHandler.findAllSetValues(
"insert cloning method")
fpcsList = sHandler.findAllSetValues("5' cloning site")
tpcsList = sHandler.findAllSetValues("3' cloning site")
tagTypeList = sHandler.findAllSetValues("tag")
tagPositionList = sHandler.findAllSetValues("tag position")
openClosedList = sHandler.findAllSetValues("open/closed")
speciesList = sHandler.findAllSetValues("species")
verificationList = sHandler.findAllSetValues("verification")
# Initialize property values
iType = ""
iName = ""
iStatus = ""
cloningMethod = ""
projectID = ""
fpcs = ""
tpcs = ""
tagType = ""
tagPosition = ""
openClosed = ""
species = ""
accession = ""
altID = ""
geneID = ""
ensemblID = ""
geneSymbol = ""
fp_start = ""
tp_stop = ""
fwd_linker = ""
rev_linker = ""
funcDescr = ""
verification = ""
expComm = ""
verComm = ""
sequence = ""
# Fetch POST values if available:
allProps = reagent.getProperties()
if allProps.has_key("type of insert"):
iType = allProps["type of insert"]
if allProps.has_key("name"):
iName = allProps["name"]
if allProps.has_key("status"):
iStatus = allProps["status"]
if allProps.has_key("insert cloning method"):
cloningMethod = allProps["insert cloning method"]
if allProps.has_key("packet id"):
projectID = int(allProps["packet id"])
if allProps.has_key("5' cloning site"):
fpcs = allProps["5' cloning site"]
if allProps.has_key("3' cloning site"):
tpcs = allProps["3' cloning site"]
if allProps.has_key("tag"):
tagType = allProps["tag"]
if allProps.has_key("tag position"):
tagPosition = allProps["tag position"]
if allProps.has_key("open/closed"):
openClosed = allProps["open/closed"]
if allProps.has_key("species"):
species = allProps["species"]
if allProps.has_key("accession number"):
accession = allProps["accession number"]
if allProps.has_key("alternate id"):
altID = allProps["alternate id"]
if allProps.has_key("entrez gene id"):
geneID = allProps["entrez gene id"]
if allProps.has_key("ensembl gene id"):
ensemblID = allProps["ensembl gene id"]
if allProps.has_key("official gene symbol"):
geneSymbol = allProps["official gene symbol"]
if allProps.has_key("5' start"):
fp_start = allProps["5' start"]
if allProps.has_key("3' stop"):
tp_stop = allProps["3' stop"]
if allProps.has_key("5' linker"):
fwd_linker = allProps["5' linker"]
if allProps.has_key("3' linker"):
rev_linker = allProps["3' linker"]
if allProps.has_key("description"):
funcDescr = allProps["description"]
if allProps.has_key("verification"):
verification = allProps["verification"]
if allProps.has_key("comments"):
expComm = allProps["comments"]
if allProps.has_key("verification comments"):
verComm = allProps["verification comments"]
if allProps.has_key("sequence"):
sequence = allProps["sequence"]
# associations
ipvID = ""
senseOligoID = ""
antisenseOligoID = ""
allAssoc = reagent.getAssociations()
'''
if allAssoc.has_key("insert_parent_vector"):
ipvID = allAssoc["insert_parent_vector"]
if allAssoc.has_key("sense_oligo"):
senseOligoID = allAssoc["sense_oligo"]
if allAssoc.has_key("antisense_oligo"):
antisenseOligoID = allAssoc["antisense_oligo"]
'''
# Action: Output form with POST values if set
if cmd == 'create':
content += '''
<div class="main">
<form NAME="create_insert_form" ACTION="%s" METHOD="POST" onSubmit="return validateInsert() && verifyParents();">
'''
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" value=\"" + currUser.getFullName(
) + "\">"
content += '''
<input type="hidden" name="reagent_type_hidden" value="Insert">
<table id="vector_insertproperty_table_id" border="1" width="780px" cellpadding="4" frame="box" rules="all">
'''
if errMsg != "":
content += "<th colspan=\"3\" style=\"color:#0000FF; text-align:left; font-weight:normal\">There was a problem:<br><P>" + errMsg + "<BR><BR></th>"
content += '''
<tr>
<td colspan="3" style="text-align:center">
<span style="color:#0000CD; font-size:13pt; font-weight:bold">
Insert Information
</span>
<br>
<span style="font-size:8pt; color:#FF0000">
Fields marked with a red asterisk (*) are mandatory
</span>
</td>
</tr>
<tr>
<td width="180px">
Type of Insert
<span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td width="275px">
<SELECT id="itype_list" size="1" NAME="INPUT_INSERT_info_insert_type_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for it in iTypeList:
content += "<OPTION VALUE=\"" + it + "\""
if it == iType:
content += " SELECTED>" + it + "</OPTION>"
else:
content += ">" + it + "</OPTION>"
content += '''
</SELECT>
</td>
<td>
Describes the type of insert. Users select from a pre-defined list. Designed to make insert use more apparent and searches easier.
</td>
</tr>
<tr>
<td>
Name
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_name_prop\" value=\"" + iName + "\">"
content += '''
</td>
<td>
Name that describes the reagent - free text field
</td>
</tr>
<tr>
<td>
Status
</td>
<td>
<SELECT id="status_list" name="INPUT_INSERT_info_status_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iStatus) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for s in statusList:
content += "<OPTION VALUE=\"" + s + "\""
if s == iStatus:
content += " SELECTED>" + s + "</OPTION>"
else:
content += ">" + s + "</OPTION>"
content += '''
</td>
<td>
Indicates the status and availability of the reagent. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Insert Cloning Method
</td>
<td>
<SELECT size="1" id="cm_list" name="INPUT_INSERT_info_cloning_method_prop" onChange="showCMText()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(cloningMethod) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for cm in cloningMethodList:
content += "<OPTION VALUE=\"" + cm + "\""
if cm == cloningMethod:
content += " SELECTED>" + cm + "</OPTION>"
else:
content += ">" + cm + "</OPTION>"
content += '''
</td>
<td>
Describes the method used to create the insert (e.g. PCR or RE (restriction enzyme)) and provides additional information for its cloning into a vector (eg. by RE, In Fusion or BP reaction)
</td>
</tr>
<tr>
<td>
Project ID <span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td>
<select id="packetList_insert" size="1" name="INPUT_INSERT_info_packet_id_prop">
'''
# need to sort projects
pNums = []
projects = {} # (pID, Packet)
for p in projectList:
pID = p.getNumber()
pNums.append(pID)
projects[pID] = p
pNums.sort()
for pID in pNums:
p = projects[pID]
content += "<OPTION VALUE=\"" + ` p.getNumber() ` + "\""
if p.getNumber() == projectID:
content += " SELECTED>" + ` p.getNumber(
) ` + ": " + p.getOwner().getLastName(
) + ": " + p.getName() + "</OPTION>"
else:
content += ">" + ` p.getNumber() ` + ": " + p.getOwner(
).getLastName() + ": " + p.getName() + "</OPTION>"
content += '''
</select>
<BR>
<div id="packet_warning_insert" style="display:none; color:#FF0000">Please select a Project ID from the dropdown list</div>
</td>
<td>
Indicates what person and project originally created the reagent.
</td>
</tr>
<tr>
<td>
5' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="fpcs_list" name="INPUT_INSERT_info_5_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(fpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for fps in fpcsList:
content += "<OPTION VALUE=\"" + fps + "\""
if fps == fpcs:
content += " SELECTED>" + fps + "</OPTION>"
else:
content += ">" + fps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 5' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
3' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="tpcs_list" name="INPUT_INSERT_info_3_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tps in tpcsList:
content += "<OPTION VALUE=\"" + tps + "\""
if tps == tpcs:
content += " SELECTED>" + tps + "</OPTION>"
else:
content += ">" + tps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 3' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag
</td>
<td>
<SELECT size="1" id="tag_list" name="INPUT_INSERT_info_tag_prop" onChange="showTagTypeBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tt in tagTypeList:
content += "<OPTION VALUE=\"" + tt + "\""
if tt == tagType:
content += " SELECTED>" + tt + "</OPTION>"
else:
content += ">" + tt + "</OPTION>"
content += '''
</td>
<td>
Indicates if the insert itself has a tag associated with it (outside of the backbone vector). Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag Position
</td>
<td>
<SELECT size="1" name="INPUT_INSERT_info_tag_position_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagPosition) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tp in tagPositionList:
content += "<OPTION VALUE=\"" + tp + "\""
if tp == tagPosition:
content += " SELECTED>" + tp + "</OPTION>"
else:
content += ">" + tp + "</OPTION>"
content += '''
</td>
<td>
Describes the position of the tag on the insert. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Open/Closed
</td>
<td>
<SELECT id="oc_list" size="1" name="INPUT_INSERT_info_open_closed_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(openClosed) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for oc in openClosedList:
content += "<OPTION VALUE=\"" + oc + "\""
if oc == openClosed:
content += " SELECTED>" + oc + "</OPTION>"
else:
content += ">" + oc + "</OPTION>"
content += '''
</td>
<td>
Indicates for an Open Reading Frame if there is a start codon (ATG) or stop codon (open - no stop codon, closed - stop codon).
</td>
</tr>
<tr>
<td>
Species
</td>
<td>
<SELECT size="1" style="color:000000" id = "species_list" name="INPUT_INSERT_info_species_prop" onChange="showSpeciesBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(species) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for sp in speciesList:
content += "<OPTION VALUE=\"" + sp + "\""
if sp == species:
content += " SELECTED>" + sp + "</OPTION>"
else:
content += ">" + sp + "</OPTION>"
content += '''
</td>
<td>
Indicates the species from which the Insert was derived. User selects species from a pre-defined list.
</td>
</tr>
<tr>
<td>
Accession Number
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_accession_number_prop\" value=\"" + accession + "\">"
content += '''
</td>
<td>
The Accession Number from which the insert was cloned or to which the sequence maps.
</td>
</tr>
<tr>
<td>
Alternate ID
</td>
<td>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="IMAGE" id="_alternate_id_IMAGE_checkbox" onClick="showAltIDTextBox('_alternate_id_IMAGE_checkbox', '_alternate_id_IMAGE_textbox')">IMAGE <INPUT style="display:none" id="_alternate_id_IMAGE_textbox" name="alternate_id_IMAGE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RIKEN" id="_alternate_id_RIKEN_checkbox" onClick="showAltIDTextBox('_alternate_id_RIKEN_checkbox', '_alternate_id_RIKEN_textbox')">RIKEN <INPUT style="display:none" id="_alternate_id_RIKEN_textbox" name="alternate_id_RIKEN_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="Kazusa" id="_alternate_id_Kazusa_checkbox" onClick="showAltIDTextBox('_alternate_id_Kazusa_checkbox', '_alternate_id_Kazusa_textbox')">Kazusa <INPUT style="display:none" id="_alternate_id_Kazusa_textbox" name="alternate_id_Kazusa_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="LIFESEQ" id="_alternate_id_LIFESEQ_checkbox" onClick="showAltIDTextBox('_alternate_id_LIFESEQ_checkbox', '_alternate_id_LIFESEQ_textbox')">LIFESEQ <INPUT style="display:none" id="_alternate_id_LIFESEQ_textbox" name="alternate_id_LIFESEQ_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RZPD" id="_alternate_id_RZPD_checkbox" onClick="showAltIDTextBox('_alternate_id_RZPD_checkbox', '_alternate_id_RZPD_textbox')">RZPD <INPUT style="display:none" id="_alternate_id_RZPD_textbox" name="alternate_id_RZPD_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="HIP" id="_alternate_id_HIP_checkbox" onClick="showAltIDTextBox('_alternate_id_HIP_checkbox', '_alternate_id_HIP_textbox')">HIP <INPUT style="display:none" id="_alternate_id_HIP_textbox" name="alternate_id_HIP_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="ADDGENE" id="_alternate_id_ADDGENE_checkbox" onClick="showAltIDTextBox('_alternate_id_ADDGENE_checkbox', '_alternate_id_ADDGENE_textbox')">ADDGENE <INPUT style="display:none" id="_alternate_id_ADDGENE_textbox" name="alternate_id_ADDGENE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="PMID" id="_alternate_id_PMID_checkbox" onClick="showAltIDTextBox('_alternate_id_PMID_checkbox', '_alternate_id_PMID_textbox')">PMID <INPUT style="display:none" id="_alternate_id_PMID_textbox" name="alternate_id_PMID_textbox_name" size="15"></INPUT><br>
<input type="checkbox" id="_other_Alt_ID_chkbx" name="INPUT_INSERT_info_alternate_id_prop[]" value="Other" onClick="showSpecificOtherCheckbox('_alternate_id_txt')">Other: <INPUT style="display:none" id="_alternate_id_txt" name="alternate_id_name_txt" size="15"></INPUT>
</td>
<td>
Indicates any other ID's that identify the insert, including but not limited to IMAGE, Kazusa, RIKEN, and other. <BR><BR><BR><BR>For 'Other', please enter the source name and ID separated by a semicolon (e.g. IMAGE:123456)
</td>
</tr>
<tr>
<td>
Entrez Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_id_prop\" value=\"" + geneID + "\">"
content += '''
</td>
<td>
The NCBI Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Ensembl Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_ensembl_gene_id_prop\" value=\"" + ensemblID + "\">"
content += '''
</td>
<td>
The Ensembl Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Official Gene Symbol
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_symbol_prop\" value=\"" + geneSymbol + "\">"
content += '''
</td>
<td>
The official gene symbol for this Insert.
</td>
</tr>
<tr>
<td>
5' Start
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_start_prop\" value=\"" + fp_start + "\">"
content += '''
</td>
<td>
Users can map the start of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence starts.
</td>
</tr>
<tr>
<td>
3' Stop
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_stop_prop\" value=\"" + tp_stop + "\">"
content += '''
</td>
<td>
Users can map the stop of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence stops
</td>
</tr>
<tr>
<td>
5' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_linker_prop\" value=\"" + fwd_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 5' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg kozak sequences, any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
3' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_linker_prop\" value=\"" + rev_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 3' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
Functional Description
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_description_prop\" value=\"" + funcDescr + "\">"
content += '''
</td>
<td>
Describes the purpose of the reagent and any information that may be key to working with the reagent.
</td>
</tr>
<tr>
<td>
Verification
</td>
<td>
<select size="1" name="INPUT_INSERT_info_verification_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(verification) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for v in verificationList:
content += "<OPTION VALUE=\"" + v + "\""
if v == verification:
content += " SELECTED>" + v + "</OPTION>"
else:
content += ">" + v + "</OPTION>"
content += '''
</select>
</td>
<td>
Indicates if the reagent has been verified and how. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Verification comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_verification_comments_prop\" value=\"" + verComm + "\">"
content += '''
</td>
<td>
Allows user to provide a description of the verification status - eg comments on sequence changes, expression levels.
</td>
</tr>
<tr>
<td>
Experimental comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_comments_prop\" value=\"" + expComm + "\">"
content += '''
</td>
<td>
Used to describe any information that descrbes how the reagent works in the experimental context - eg low expression, difficult to grow, etc.
</td>
</tr>
<tr>
<td>
Sequence
</td>
<td>
</td>
<td>
The sequence of the insert that corresponds to a cDNA or fragment of interest. Does include artificial start and stop codons. Does not include linker sequences as described above.
</td>
</tr>
<tr>
<td colspan="3">
<textarea rows="10" cols="93" id="dna_sequence" name="INPUT_INSERT_info_sequence_prop">
'''
content += sequence
content += '''
</textarea>
</td>
</tr>
'''
content += self.printParents('Insert', allAssoc)
content += '''
<tr>
<td colspan="3">
<hr><br>
<input type="submit" name="create_reagent" value="Create" onclick="document.pressed = this.value">
</td>
</tr>
</table>
</form>
</div>
'''
# Common to all
content += gOut.printFooter()
page_content = content % (hostname + "cgi/create.py")
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def printMainMenu(self):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
# Aug. 20, 2010
pageMapper = SystemModuleMapper(db, cursor)
pageLinkMap = pageMapper.mapPageNameLink()
# Array of section names
currentSectionNames = []
# Dictionary of links to names, with names as dictionary keys and links as values
currentSectionLinks = {}
# Added Nov. 10/06 by Marina - Classify each header as to what OF section it belongs
menuTypes = {}
# June 04/07 - Differentiate between 'public' and 'private' pages
publicSectionNames = []
publicSectionLinks = []
publicSections = {}
# Feb. 2, 2010: change menu layout (reflect HeaderFunctions.php code changes Jan. 12/10)
submenu_links = {}
submenu_types = {}
menuitems = {}
# Home
currentSectionNames.append("Home")
currentSectionLinks["Home"] = "../index.php"
publicSections["Home"] = "index.php"
# Reagent
currentSectionNames.append("Reagent Tracker")
currentSectionLinks["Reagent Tracker"] = "../Reagent.php?View=1"
menuTypes["Reagent Tracker"] = "Reagent"
publicSections["Reagent Tracker"] = "../Reagent.php?View=1"
# Feb. 2, 2010
tmp_list = []
tmp_list.append("Reagents")
tmp_list.append("Reagent Types")
submenu_types["Reagent Tracker"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
tmp_order_list[2] = "Statistics"
submenu_order = {}
submenu_order["Reagents"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Reagent.php?View=2"
tmp_list["Search"] = "../search.php?View=1"
tmp_list["Statistics"] = "../Reagent.php?View=4"
submenu_links["Reagents"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add reagents"
tmp_list["Search"] = "Search reagents"
tmp_list["Statistics"] = "Statistics"
menuitems["Reagents"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Reagent Types"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Reagent.php?View=3"
tmp_list["Search"] = "../Reagent.php?View=5"
submenu_links["Reagent Types"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add reagent types"
tmp_list["Search"] = "Search reagent types"
menuitems["Reagent Types"] = tmp_list
# Locations
currentSectionNames.append("Location Tracker")
currentSectionLinks["Location Tracker"] = "../Location.php?View=1"
menuTypes["Location Tracker"] = "Location"
publicSections["Location Tracker"] = "../Location.php?View=1"
# Feb. 2/10
tmp_list = []
tmp_list.append("Containers")
tmp_list.append("Container Sizes")
tmp_list.append("Container Types")
submenu_types["Location Tracker"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Container Types"] = tmp_order_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
#tmp_order_list[1] = "Search"
submenu_order["Container Sizes"] = tmp_order_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Containers"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Location.php?View=6&Sub=2"
tmp_list["Search"] = "../Location.php?View=6&Sub=4"
submenu_links["Container Types"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add container types"
tmp_list["Search"] = "Search container types"
menuitems["Container Types"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../Location.php?View=6&Sub=1"
tmp_list["Search"] = "../Location.php?View=6&Sub=5"
submenu_links["Container Sizes"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add container sizes"
#tmp_list["Search"] = "Search container sizes"
menuitems["Container Sizes"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../Location.php?View=6&Sub=3"
tmp_list["Search"] = "../Location.php?View=2"
submenu_links["Containers"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add containers"
tmp_list["Search"] = "Search containers"
menuitems["Containers"] = tmp_list
# Projects
currentSectionNames.append("Project Management")
currentSectionLinks["Project Management"] = "../Project.php?View=1"
menuTypes["Project Management"] = "Project"
# Feb. 2/10
tmp_list = []
tmp_list.append("Projects")
submenu_types["Project Management"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Projects"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Project.php?View=1"
tmp_list["Search"] = "../Project.php?View=2"
submenu_links["Projects"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add projects"
tmp_list["Search"] = "Search projects"
menuitems["Projects"] = tmp_list
# Users and Labs
currentSectionNames.append("User Management")
currentSectionLinks["User Management"] = "../User.php"
menuTypes["User Management"] = "User"
currentSectionNames.append("Lab Management")
currentSectionLinks["Lab Management"] = "../User.php"
menuTypes["Lab Management"] = "Laboratories"
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Laboratories"] = tmp_order_list
# Jan. 7/09: Chemicals
currentSectionNames.append("Chemical Tracker")
currentSectionLinks["Chemical Tracker"] = "../Chemical.php?View=1"
menuTypes["Chemical Tracker"] = "Chemical"
# Feb. 2, 2010
tmp_list = []
tmp_list.append("Chemicals")
submenu_types["Chemical Tracker"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Chemicals"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Chemical.php?View=2"
tmp_list["Search"] = "../Chemical.php?View=1"
submenu_links["Chemicals"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add Chemicals"
tmp_list["Search"] = "Search Chemicals"
menuitems["Chemicals"] = tmp_list
# Feb. 2/10
tmp_list = []
tmp_list.append("Users")
submenu_types["User Management"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../User.php?View=1"
tmp_list["Search"] = "../User.php?View=2"
tmp_list["Change your password"] = "******"
tmp_list["Personal page"] = "../User.php?View=7"
tmp_list["View your orders"] = "../User.php?View=8"
submenu_links["Users"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
tmp_order_list[2] = "Change your password"
tmp_order_list[3] = "Personal page"
tmp_order_list[4] = "View your orders"
submenu_order["Users"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "Add users"
tmp_list["Search"] = "Search users"
tmp_list["Change your password"] = "******"
tmp_list["Personal page"] = "Personal page"
tmp_list["View your orders"] = "View your orders"
menuitems["Users"] = tmp_list
tmp_list = []
tmp_list.append("Laboratories")
submenu_types["Lab Management"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../User.php?View=3"
tmp_list["Search"] = "../User.php?View=4"
submenu_links["Laboratories"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Laboratories"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "Add laboratories"
tmp_list["Search"] = "Search laboratories"
menuitems["Laboratories"] = tmp_list
currentSectionNames.append("Documentation")
currentSectionLinks["Documentation"] = "../docs.php"
publicSections["Documentation"] = "docs.php"
currentSectionNames.append("Terms and Conditions")
currentSectionLinks["Terms and Conditions"] = "../copyright.php"
publicSections["Terms and Conditions"] = "copyright.php"
currentSectionNames.append("Help and Support")
currentSectionLinks["Help and Support"] = "../bugreport.php"
publicSections["Help and Support"] = "bugreport.php"
currentSectionNames.append("Contact Us")
currentSectionLinks["Contact Us"] = "../contacts.php"
publicSections["Contact Us"] = "contacts.php"
# Aug. 20/10: Quick links
tmp_ql = []
quickLinks = {}
tmp_ql.append("Add reagents")
tmp_ql.append("Search reagents")
quickLinks["Reagent Tracker"] = tmp_ql
tmp_ql = []
tmp_ql.append("Add containers")
tmp_ql.append("Search containers")
quickLinks["Location Tracker"] = tmp_ql
tmp_ql = []
tmp_ql.append("Add projects")
tmp_ql.append("Search projects")
quickLinks["Project Management"] = tmp_ql
tmp_ql = []
tmp_ql.append("Change your password")
tmp_ql.append("View your orders")
quickLinks["User Management"] = tmp_ql
content = '''
<div class="sidemenu" ID="mainMenu">
<div class="menu-content">
<ul class="menulist">
<!-- menu goes here -->
'''
# Output the menu link IFF the user is authorized to access that page
currUser = Session.getUser()
if currUser:
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
currUserCategory = category_Name_ID_Map[currUser.getCategory()]
#print "Content-type:text/html"
#print
allowedSections = uHandler.getAllowedSections(currUserCategory)
#print `allowedSections`
for name in currentSectionNames:
if name in allowedSections:
# added Jan. 7/09
if name in menuTypes:
#print "Content-type:text/html"
#print
#print name
content += "<DIV style=\"border-top:3px double #FFF8DC; border-right:6px double #FFF8DC; border-bottom:3px double #FFF8DC; border-left:6px double #FFF8DC; margin-top:2px; width:162px; padding-top:5px; padding-bottom:0;\">"
content += "<DIV style=\"background-image:url('../pictures/small_bg.png'); width:166px; height:30px;\">"
content += "<select style=\"cursor:pointer; width:150px; background:#FFF8DC; font-weight:bold; color:#555; font-size:9pt; margin-top:3px; margin-left:2px; font-family:Helvetica; border:0;\" onChange=\"openPage(this.options[this.options.selectedIndex]);\">"
content += "<option selected style=\"cursor:pointer; font-weight:bold; color:#555; font-size:9pt; border:0; font-family:Helvetica;\" value=\"\"> " + name + "</option>"
for st_val in submenu_types[name]:
numDisallowed = 0
# Jan. 13, 2010: Don't print category heading if user has no access to any of its subitems
for s_ord in submenu_order[st_val]:
linkName = submenu_order[st_val][s_ord]
linkURL = submenu_links[st_val][linkName]
if not menuitems[st_val][linkName] in allowedSections:
numDisallowed += 1
if numDisallowed == len(submenu_links[st_val]):
continue
#print st_val.upper()
content += "<option style=\"cursor:pointer; font-weight:bold; color:#555; background:#EFEFEF; font-size:9pt; border:0; font-family:Helvetica;\" onclick\"\"> " + st_val.upper() + "</option>"
# Now: since Python dictionaries are not ordered, arrays with > 2 items (e.g. Users - has more than 'add' and 'search') would appear scrambled. Use an 'order' array instead
for s_ord in submenu_order[st_val]:
linkName = submenu_order[st_val][s_ord]
linkURL = submenu_links[st_val][linkName]
#print st_val
#print linkName
if menuitems[st_val][linkName] in allowedSections:
content += "<option style=\"padding-left:15px; font-weight:bold; color:#555; font-size:8pt; border:0; font-family:Helvetica; cursor:pointer;\" value=\"" + linkURL + "\"> " + linkName + "</option>"
content += "</SELECT>"
content += "</DIV>"
# Quick links
if quickLinks.has_key(name):
content += "<div id=\"quick_links_" + name + "\" style=\"font-family:Helvetica; width:166px; padding-bottom:0; margin-top:0; padding-top:0; padding-left:2px;\">"
content += "<UL style=\"padding-bottom:2px; padding-top:2px; padding-left:10px; position:relative;\">"
for qlName in quickLinks[name]:
if qlName in allowedSections:
content += "<LI style=\"list-style:none;\"><img src=\"../pictures/silvermenubullet.png\" width=\"7\" height=\"6\" style=\"padding-bottom:2px;\"> <a style=\"font-weight:bold; font-size:8pt; font-family:Helvetica; text-decoration:none; color:#555; margin-left:2px;\" href=\"../" + pageLinkMap[qlName] + "\">" + qlName + "</a></LI>"
content += "</UL>"
content += "</DIV>"
content += "</DIV>"
else:
if name == "Home":
content += "<DIV style=\"background:url('../pictures/small_bg.png') repeat-y; padding-top:7px; margin-top:0; width:162px; border-top:6px double #FFF8DC; border-left:6px double #FFF8DC; border-right:6px double #FFF8DC; padding-bottom:8px;\">"
else:
content += "<DIV style=\"background:url('../pictures/small_bg.png') repeat-y; padding-top:7px; margin-top:2px; width:162px; border-left:6px double #FFF8DC; border-right:6px double #FFF8DC; padding-bottom:8px;\">"
content += "<img src=\"../pictures/silvermenubullet.png\" style=\"width:11px; height:9px; margin-left:5px;\">"
content += "<a style=\"font-weight:bold; color:#555; font-size:9pt; padding-left:3px; text-decoration:none;\" href=\"" + currentSectionLinks[name] + "\">" + name + "</a>"
content += "</DIV>"
else:
# WRITE THIS FUNCTION!!!!!!!!!!
#content += self.printGeneralMenu(publicSections)
print "Content-type:text/html"
print
print "Unknown user"
content += '''
</UL>
<!-- moved form down here on Aug. 20, 2010 -->
<form name="curr_user_form" style="display:none" method="post" action="user_request_handler.py">"
'''
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" VALUE=\"" + currUser.getFullName() + "\">"
content += "<INPUT TYPE=\"hidden\" id=\"curr_user_hidden\" name=\"view_user\" VALUE=\"" + `currUser.getUserID()` + "\">"
content += '''
</FORM>
<div class="login">
'''
content += self.printLoginBlock()
content += '''
</div>
</div>
</div>
'''
return content
def printSubmenuHeader(self, submenu_type):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
current_selection_names = [] # plain list of section names
current_selection_links = {} # dictionary, where section names are keys and their URLs are values
if submenu_type == "Location":
location_submenu_names = []
location_submenu_links = {}
location_submenu_names.append("Add container types")
location_submenu_links["Add container types"] = "../Location.php?View=6&Sub=3"
location_submenu_names.append("Add container sizes")
location_submenu_links["Add container sizes"] = "../Location.php?View=6&Sub=1"
location_submenu_names.append("Add containers")
location_submenu_links["Add containers"] = "../Location.php?View=6&Sub=3"
location_submenu_names.append("Search containers")
location_submenu_links["Search containers"] = "../Location.php?View=2"
current_selection_names = location_submenu_names
current_selection_links = location_submenu_links
elif submenu_type == "Reagent":
reagent_submenu_names = []
reagent_submenu_links = {}
reagent_submenu_names.append("Add reagents")
reagent_submenu_links["Add reagents"] = "../Reagent.php?View=2"
reagent_submenu_names.append("Search reagents")
reagent_submenu_links["Search reagents"] = "../search.php?View=1"
# June 3/09
reagent_submenu_names.append("Add reagent types")
reagent_submenu_links["Add reagent types"] = "../Reagent.php?View=3"
reagent_submenu_names.append("Search reagent types")
reagent_submenu_links["Search reagent types"] = "../Reagent.php?View=5"
current_selection_names = reagent_submenu_names
current_selection_links = reagent_submenu_links
elif submenu_type == "Chemical":
chemical_submenu_names = []
chemical_submenu_links = {}
chemical_submenu_names.append("Add Chemicals")
chemical_submenu_links["Add Chemicals"] = "../Chemical.php?View=2"
chemical_submenu_names.append("Search Chemicals")
chemical_submenu_links["Search Chemicals"] = "../Chemical.php?View=1"
current_selection_names = chemical_submenu_names
current_selection_links = chemical_submenu_links
elif submenu_type == "Prediction":
prediction_submenu_names = []
prediction_submenu_links = {}
prediction_submenu_names.append("Search predictions")
prediction_submenu_links["Search predictions"] = "../Prediction.php?View=1"
current_selection_names = prediction_submenu_names
current_selection_links = prediction_submenu_links
elif submenu_type == "Project":
project_submenu_names = []
project_submenu_links = {}
project_submenu_names.append("Add projects")
project_submenu_links["Add projects"] = "../Project.php?View=1"
project_submenu_names.append("Search projects")
project_submenu_links["Search projects"] = "../Project.php?View=2"
current_selection_names = project_submenu_names
current_selection_links = project_submenu_links
elif submenu_type == "User":
user_submenu_names = []
user_submenu_links = {}
user_submenu_names.append("Add users")
user_submenu_links["Add users"] = "../User.php?View=1"
user_submenu_names.append("Search users")
user_submenu_links["Search users"] = "../User.php?View=2"
user_submenu_names.append("Change your password")
user_submenu_links["Change your password"] = "******"
user_submenu_names.append("Personal page")
user_submenu_links["Personal page"] = "User.php?View=7"
user_submenu_names.append("View your orders")
user_submenu_links["View your orders"] = "../User.php?View=8"
current_selection_names = user_submenu_names
current_selection_links = user_submenu_links
elif submenu_type == "Lab":
lab_submenu_names = []
lab_submenu_links = {}
lab_submenu_names.append("Add laboratories")
lab_submenu_links["Add laboratories"] = "../User.php?View=3"
lab_submenu_names.append("Search laboratories")
lab_submenu_links["Search laboratories"] = "../User.php?View=4"
current_selection_names = lab_submenu_names
current_selection_links = lab_submenu_links
# There can be permission differentiations within a menu section as well (e.g. Projects - only Creators can create, buit Writers can view)
currUser = Session.getUser()
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
currUserCategory = category_Name_ID_Map[currUser.getCategory()]
allowedSections = uHandler.getAllowedSections(currUserCategory)
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `allowedSections`
content = ""
for name in current_selection_names:
if name in allowedSections:
if name == 'Personal page':
content += "<LI class=\"submenu\">"
content += "<IMG SRC=\"../pictures/star_bullet.gif\" WIDTH=\"10\" HEIGHT=\"10\" BORDER=\"0\" ALT=\"plus\" class=\"menu-leaf\">"
content += "<span class=\"linkShow\" style=\"font-size:9pt\" onClick=\"redirectToCurrentUserDetailedView(" + `currUser.getUserID()` + ");\">" + name + "</span>"
content += "</LI>"
content += "<form name=\"curr_user_form\" style=\"display:none\" method=\"post\" action=\"user_request_handler.py\">"
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" VALUE=\"" + currUser.getFullName() + "\">"
content += "<INPUT type=\"hidden\" id=\"curr_user_hidden\" name=\"view_user\">"
content += "</FORM>"
else:
content += "<LI class=\"submenu\">"
content += "<IMG SRC=\"../pictures/star_bullet.gif\" WIDTH=\"10\" HEIGHT=\"10\" BORDER=\"0\" ALT=\"plus\" class=\"menu-leaf\">"
content += "<a class=\"submenu\" href=\"" + current_selection_links[name] + "\">" + name + "</a>"
content += "</LI>"
return content
#!/usr/local/bin/python
import cgi
import utils
from sequence_handler import DNAHandler
from database_conn import DatabaseConn
import Bio
from Bio.Seq import Seq
from Bio.Restriction import *
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
dnaHandler = DNAHandler(db, cursor)
form = cgi.FieldStorage()
lims_id = form.getvalue("limsID") # always exists
print "Content-type: application/octet-stream"
print "Content-Disposition: attachment; filename=" + lims_id + ".txt"
print "Pragma: no-cache"
print "Expires: 0"
#print "Content-type:text/html"
print
# sequence may be empty
if form.has_key("vector_sequence"):
def update():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
print "Content-type:text/html" # REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
print # DITTO
#print `form`
# Aug 29/07
uHandler = UserHandler(db, cursor)
if form.has_key("curr_username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("curr_username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
#else: # debug
#currUname = 'Administrator'
#currUser = uHandler.getUserByDescription(currUname)
#Session.setUser(currUser)
if form.has_key("cloning_method"):
cloning_method = form.getvalue("cloning_method")
#else: # debug
#cloning_method = '1'
# Handlers and mappers
rHandler = ReagentHandler(db, cursor)
#sHandler = SystemSetHandler(db, cursor)
pHandler = ReagentPropertyHandler(db, cursor)
raHandler = ReagentAssociationHandler(db, cursor)
aHandler = AssociationHandler(db, cursor)
dnaHandler = DNAHandler(db, cursor)
commHandler = CommentHandler(db, cursor)
protHandler = ProteinHandler(db, cursor)
propMapper = ReagentPropertyMapper(db, cursor)
assocMapper = ReagentAssociationMapper(db, cursor)
# August 29/07: Restrict creation by user and project access
packetHandler = ProjectDatabaseHandler(db, cursor)
########################################################
# Various maps
########################################################
prop_Alias_ID_Map = propMapper.mapPropAliasID(
) # (propAlias, propID) - e.g. ('insert_type', '48') --> represents 'type of insert' property
prop_Name_Alias_Map = propMapper.mapPropNameAlias(
) # (propName, propAlias)
prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id)
# Restriction sites
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
newFivePrime = form.getvalue("fpcs")
newThreePrime = form.getvalue("tpcs")
gatewaySites = ['attb', 'attl', 'attp', 'attr'] # nov. 16/07
# resulting sequence
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj +
publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
# August 29/07: Need to verify parent project access AND (Sept. 12/07) reconstruct the sequence IFF parent values are changed
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(),
'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj +
publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
if form.has_key("PV"):
pvVal = form.getvalue("PV")
if len(pvVal) > 0:
pvID = rHandler.convertReagentToDatabaseID(pvVal)
try:
pvProjectID = int(
rHandler.findSimplePropertyValue(pvID, packetPropID))
pvSeqID = rHandler.findDNASequenceKey(
pvID) # get sequence for reconstitution later
except TypeError:
#pvProjectID = 0
e = PVProjectAccessException(
"You are not authorized to use this Parent Vector, since you do not have Read access to its project."
)
print ` e.err_code() `
else:
e = UnknownPVIDException("Unknown Parent Vector value")
print ` e.err_code() `
return
# else don't do anything, maybe want to delete parents!!!
#else:
#e = MissingPVException("No Parent Vector provided")
#print `e.err_code()`
if pvProjectID > 0 and currUser.getCategory(
) != 'Admin' and pvProjectID not in uPackets:
e = PVProjectAccessException("Not authorized to access parent")
print ` e.err_code() `
return
if cloning_method == '1':
# Non-recombination vector - Get the Insert
if form.has_key("I"):
insertVal = form.getvalue("I")
if len(insertVal) > 0:
insertID = rHandler.convertReagentToDatabaseID(insertVal)
insertSeqID = rHandler.findDNASequenceKey(
insertID) # fetch Insert sequence for reconstitution later
try:
insertProjectID = int(
rHandler.findSimplePropertyValue(
insertID, packetPropID))
except TypeError:
#insertProjectID = 0
e = InsertProjectAccessException(
"You are not authorized to use this Insert, since you do not have Read access to its project."
)
print ` e.err_code() `
else:
#insertID = -1
#insertProjectID = 0
#print "Invalid Insert value"
e = UnknownInsertIDException("Unknown Insert value")
print ` e.err_code() `
return
#else: # NO!!!!!!!!
#e = MissingInsertException("No Insert provided")
#print `e.err_code()`
if insertProjectID > 0 and currUser.getCategory(
) != 'Admin' and insertProjectID not in uPackets:
e = InsertProjectAccessException(
"You are not authorized to use this Insert, since you do not have Read access to its project."
)
print ` e.err_code() `
return
if pvID > 0 and insertID > 0:
# try to reconstruct sequence and issue warning if unable
if pvSeqID > 0 and insertSeqID > 0:
# fetch insert cloning sites
insertCloningSites = []
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
fp_insert_cs = rHandler.findSimplePropertyValue(
insertID, fpcs_prop_id)
tp_insert_cs = rHandler.findSimplePropertyValue(
insertID, tpcs_prop_id)
# Determine if this is a Gateway clone from sites
gwSites = False
if fp_insert_cs and tp_insert_cs and fp_insert_cs.lower(
) == 'attl' and tp_insert_cs.lower() == 'attl':
gwSites = True
elif not fp_insert_cs or not tp_insert_cs:
gwSites = True
# nov. 16/07: added this for check
elif fp_insert_cs.lower(
) in gatewaySites or tp_insert_cs.lower() in gatewaySites:
gwSites = True
else:
gwSites = False
if gwSites:
# this is a gateway clone
# if sites were changed to something other than gateway, clear sequence
if newFivePrime.lower() != 'attl' or newThreePrime.lower(
) != 'attl':
e = InsertSitesNotFoundOnParentSequenceException()
print ` e.err_code() `
return
else:
pvSeqKey = rHandler.findDNASequenceKey(pvID)
# For Gateway clones, linkers are found from primers - so find the sense and antisense Oligos for this Insert
insertLinkers = []
# Find Sense and Antisense Oligos for this Insert
# (not using antisense just yet - verify with Karen)
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insertID)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(
senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(
senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(
insertSeqID)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(
insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insertID, tpLinkerPropID)
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.entryVectorSequence(
pvSeqKey, insertSeqID, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException(
"Sites found more than once on parent vector sequence"
)
print ` e.err_code() `
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException(
"5' after 3'")
print ` e.err_code() `
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException(
"Gateway sites not found on parent vector sequence"
)
print ` e.err_code() `
else:
# Non-Gateway non-recombination Vector
fp_insert_cs = newFivePrime
tp_insert_cs = newThreePrime
if fp_insert_cs:
insertCloningSites.append(fp_insert_cs)
else:
insertCloningSites.append("")
if tp_insert_cs:
insertCloningSites.append(tp_insert_cs)
else:
insertCloningSites.append("")
# get linkers if there are any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insertID, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.constructNonRecombSequence(
pvSeqID, insertSeqID, insertCloningSites,
insertLinkers)
print newSeq
except (InsertSitesException):
e = InsertSitesException(
"Could not reconstitute sequence: Unknown sites on Insert."
)
print e.err_code()
except (InsertSitesNotFoundOnParentSequenceException):
e = InsertSitesNotFoundOnParentSequenceException(
"Could not reconstitute sequence: Parent vector sequence does not contain restriction sites."
)
print e.err_code()
except (MultipleSiteOccurrenceException):
e = MultipleSiteOccurrenceException(
"Could not reconstitute sequence: Restriction sites occur more than once on parent vector sequence"
)
print e.err_code()
except (HybridizationException):
e = HybridizationException(
"Could not reconstitute sequence: Restriction sites cannot be hybridized."
)
print e.err_code()
except (FivePrimeAfterThreePrimeException):
e = FivePrimeAfterThreePrimeException(
"Could not reconstitute sequence: 5' site occurs after 3' site on parent vector sequence."
)
print e.err_code()
else:
e = InvalidSequenceException("Invalid parent sequence")
print ` e.err_code() `
else:
e = UnknownPVIDException("Unknown PV ID")
print ` e.err_code() `
elif cloning_method == '2':
# Recombination vector - check IPV
ipvVal = form.getvalue("IPV")
if len(ipvVal) > 0:
ipvID = rHandler.convertReagentToDatabaseID(ipvVal)
ipvProjectID = int(
rHandler.findSimplePropertyValue(ipvID, packetPropID))
else:
e = UnknownIPVIDException("Unknown IPV ID")
print ` e.err_code() `
if ipvProjectID > 0 and currUser.getCategory(
) != 'Admin' and ipvProjectID not in uPackets:
e = IPVProjectAccessException("Not authorized to view IPV")
print ` e.err_code() `
if ipvID > 0 and pvID > 0:
# If restriction sites were modified to anything other than LoxP or gateway att sites, clear the sequence
if not (newFivePrime == newThreePrime and
(newFivePrime.lower() == 'loxp'
and newThreePrime.lower() == 'loxp') or
(newFivePrime.lower() == 'attb'
and newThreePrime.lower() == 'attb')):
e = InsertSitesNotFoundOnParentSequenceException(
"Invalid restriction sites for Non-Recombination Clone - must be LoxP only"
)
print ` e.err_code() `
else:
# get internal db IDs
pv_db_id = rHandler.convertReagentToDatabaseID(pvVal)
ipv_db_id = rHandler.convertReagentToDatabaseID(ipvVal)
# Get the Insert that belongs to the donor vector
ipvInsertAssocID = raHandler.findReagentAssociationID(
ipv_db_id)
insertAssocPropID = aHandler.findAssocPropID("insert id")
insert_db_id = aHandler.findAssocPropValue(
ipvInsertAssocID, insertAssocPropID)
# Construct a sequence for the new vector from the sequences of its parents
pvSeqKey = rHandler.findDNASequenceKey(pv_db_id)
#print "pv seq " + `pvSeqKey`
ipvSeqKey = rHandler.findDNASequenceKey(ipv_db_id)
#print "ipv seq " + `ipvSeqKey`
insertSeqKey = rHandler.findDNASequenceKey(insert_db_id)
#print "i seq " + `insertSeqKey`
if pvSeqKey > 0 and ipvSeqKey > 0 and insertSeqKey > 0:
# See if there are linkers, although there most likely aren't any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
# Differentiate by cloning sites whether this is a recombination vector or a Gateway Expression Vector
if newFivePrime == 'LoxP' and newThreePrime == 'LoxP':
# recombination
try:
newSeq = dnaHandler.constructRecombSequence(
pvSeqKey, ipvSeqKey, insertSeqKey,
insertLinkers)
newSeqID = dnaHandler.matchSequence(newSeq)
print newSeq
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException(
"LOXP sites not found on parent vector sequence"
)
print ` e.err_code() `
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException(
"LOXP found more than once on parent vector sequence"
)
print ` e.err_code() `
elif newFivePrime == 'attB' and newThreePrime == 'attB':
# Gateway Expression
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insert_db_id)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(
senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(
senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(
insertSeqKey)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(
insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(
insert_db_id, tpLinkerPropID)
if fp_insert_linker and len(
fp_insert_linker
) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.expressionVectorSequence(
pvSeqKey, insertSeqKey, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException(
"Sites found more than once on parent vector sequence"
)
print ` e.err_code() `
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException(
"5' after 3'")
print ` e.err_code() `
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException(
"Gateway sites not found on parent vector sequence"
)
print ` e.err_code() `
else:
e = InvalidSequenceException("Invalid parent sequence")
print ` e.err_code() `
else:
e = ReagentDoesNotExistException("Unknown parent values")
print ` e.err_code() `
def printMainMenu(self):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
# Aug. 20, 2010
pageMapper = SystemModuleMapper(db, cursor)
pageLinkMap = pageMapper.mapPageNameLink()
# Array of section names
currentSectionNames = []
# Dictionary of links to names, with names as dictionary keys and links as values
currentSectionLinks = {}
# Added Nov. 10/06 by Marina - Classify each header as to what OF section it belongs
menuTypes = {}
# June 04/07 - Differentiate between 'public' and 'private' pages
publicSectionNames = []
publicSectionLinks = []
publicSections = {}
# Feb. 2, 2010: change menu layout (reflect HeaderFunctions.php code changes Jan. 12/10)
submenu_links = {}
submenu_types = {}
menuitems = {}
# Home
currentSectionNames.append("Home")
currentSectionLinks["Home"] = "../index.php"
publicSections["Home"] = "index.php"
# Reagent
currentSectionNames.append("Reagent Tracker")
currentSectionLinks["Reagent Tracker"] = "../Reagent.php?View=1"
menuTypes["Reagent Tracker"] = "Reagent"
publicSections["Reagent Tracker"] = "../Reagent.php?View=1"
# Feb. 2, 2010
tmp_list = []
tmp_list.append("Reagents")
tmp_list.append("Reagent Types")
submenu_types["Reagent Tracker"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
tmp_order_list[2] = "Statistics"
submenu_order = {}
submenu_order["Reagents"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Reagent.php?View=2"
tmp_list["Search"] = "../search.php?View=1"
tmp_list["Statistics"] = "../Reagent.php?View=4"
submenu_links["Reagents"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add reagents"
tmp_list["Search"] = "Search reagents"
tmp_list["Statistics"] = "Statistics"
menuitems["Reagents"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Reagent Types"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Reagent.php?View=3"
tmp_list["Search"] = "../Reagent.php?View=5"
submenu_links["Reagent Types"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add reagent types"
tmp_list["Search"] = "Search reagent types"
menuitems["Reagent Types"] = tmp_list
# Locations
currentSectionNames.append("Location Tracker")
currentSectionLinks["Location Tracker"] = "../Location.php?View=1"
menuTypes["Location Tracker"] = "Location"
publicSections["Location Tracker"] = "../Location.php?View=1"
# Feb. 2/10
tmp_list = []
tmp_list.append("Containers")
tmp_list.append("Container Sizes")
tmp_list.append("Container Types")
submenu_types["Location Tracker"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Container Types"] = tmp_order_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
# tmp_order_list[1] = "Search"
submenu_order["Container Sizes"] = tmp_order_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Containers"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Location.php?View=6&Sub=2"
tmp_list["Search"] = "../Location.php?View=6&Sub=4"
submenu_links["Container Types"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add container types"
tmp_list["Search"] = "Search container types"
menuitems["Container Types"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../Location.php?View=6&Sub=1"
tmp_list["Search"] = "../Location.php?View=6&Sub=5"
submenu_links["Container Sizes"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add container sizes"
# tmp_list["Search"] = "Search container sizes"
menuitems["Container Sizes"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../Location.php?View=6&Sub=3"
tmp_list["Search"] = "../Location.php?View=2"
submenu_links["Containers"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add containers"
tmp_list["Search"] = "Search containers"
menuitems["Containers"] = tmp_list
# Projects
currentSectionNames.append("Project Management")
currentSectionLinks["Project Management"] = "../Project.php?View=1"
menuTypes["Project Management"] = "Project"
# Feb. 2/10
tmp_list = []
tmp_list.append("Projects")
submenu_types["Project Management"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Projects"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Project.php?View=1"
tmp_list["Search"] = "../Project.php?View=2"
submenu_links["Projects"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add projects"
tmp_list["Search"] = "Search projects"
menuitems["Projects"] = tmp_list
# Users and Labs
currentSectionNames.append("User Management")
currentSectionLinks["User Management"] = "../User.php"
menuTypes["User Management"] = "User"
currentSectionNames.append("Lab Management")
currentSectionLinks["Lab Management"] = "../User.php"
menuTypes["Lab Management"] = "Laboratories"
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Laboratories"] = tmp_order_list
# Jan. 7/09: Chemicals
currentSectionNames.append("Chemical Tracker")
currentSectionLinks["Chemical Tracker"] = "../Chemical.php?View=1"
menuTypes["Chemical Tracker"] = "Chemical"
# Feb. 2, 2010
tmp_list = []
tmp_list.append("Chemicals")
submenu_types["Chemical Tracker"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Chemicals"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "../Chemical.php?View=2"
tmp_list["Search"] = "../Chemical.php?View=1"
submenu_links["Chemicals"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "Add Chemicals"
tmp_list["Search"] = "Search Chemicals"
menuitems["Chemicals"] = tmp_list
# Feb. 2/10
tmp_list = []
tmp_list.append("Users")
submenu_types["User Management"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../User.php?View=1"
tmp_list["Search"] = "../User.php?View=2"
tmp_list["Change your password"] = "******"
tmp_list["Personal page"] = "../User.php?View=7"
tmp_list["View your orders"] = "../User.php?View=8"
submenu_links["Users"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
tmp_order_list[2] = "Change your password"
tmp_order_list[3] = "Personal page"
tmp_order_list[4] = "View your orders"
submenu_order["Users"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "Add users"
tmp_list["Search"] = "Search users"
tmp_list["Change your password"] = "******"
tmp_list["Personal page"] = "Personal page"
tmp_list["View your orders"] = "View your orders"
menuitems["Users"] = tmp_list
tmp_list = []
tmp_list.append("Laboratories")
submenu_types["Lab Management"] = tmp_list
tmp_list = {}
tmp_list["Add"] = "../User.php?View=3"
tmp_list["Search"] = "../User.php?View=4"
submenu_links["Laboratories"] = tmp_list
tmp_order_list = {}
tmp_order_list[0] = "Add"
tmp_order_list[1] = "Search"
submenu_order["Laboratories"] = tmp_order_list
tmp_list = {}
tmp_list["Add"] = "Add laboratories"
tmp_list["Search"] = "Search laboratories"
menuitems["Laboratories"] = tmp_list
currentSectionNames.append("Documentation")
currentSectionLinks["Documentation"] = "../docs.php"
publicSections["Documentation"] = "docs.php"
currentSectionNames.append("Terms and Conditions")
currentSectionLinks["Terms and Conditions"] = "../copyright.php"
publicSections["Terms and Conditions"] = "copyright.php"
currentSectionNames.append("Help and Support")
currentSectionLinks["Help and Support"] = "../bugreport.php"
publicSections["Help and Support"] = "bugreport.php"
currentSectionNames.append("Contact Us")
currentSectionLinks["Contact Us"] = "../contacts.php"
publicSections["Contact Us"] = "contacts.php"
# Aug. 20/10: Quick links
tmp_ql = []
quickLinks = {}
tmp_ql.append("Add reagents")
tmp_ql.append("Search reagents")
quickLinks["Reagent Tracker"] = tmp_ql
tmp_ql = []
tmp_ql.append("Add containers")
tmp_ql.append("Search containers")
quickLinks["Location Tracker"] = tmp_ql
tmp_ql = []
tmp_ql.append("Add projects")
tmp_ql.append("Search projects")
quickLinks["Project Management"] = tmp_ql
tmp_ql = []
tmp_ql.append("Change your password")
tmp_ql.append("View your orders")
quickLinks["User Management"] = tmp_ql
content = """
<div class="sidemenu" ID="mainMenu">
<div class="menu-content">
<ul class="menulist">
<!-- menu goes here -->
"""
# Output the menu link IFF the user is authorized to access that page
currUser = Session.getUser()
if currUser:
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
currUserCategory = category_Name_ID_Map[currUser.getCategory()]
# print "Content-type:text/html"
# print
allowedSections = uHandler.getAllowedSections(currUserCategory)
# print `allowedSections`
for name in currentSectionNames:
if name in allowedSections:
# added Jan. 7/09
if name in menuTypes:
# print "Content-type:text/html"
# print
# print name
content += '<DIV style="border-top:3px double #FFF8DC; border-right:6px double #FFF8DC; border-bottom:3px double #FFF8DC; border-left:6px double #FFF8DC; margin-top:2px; width:162px; padding-top:5px; padding-bottom:0;">'
content += "<DIV style=\"background-image:url('../pictures/small_bg.png'); width:166px; height:30px;\">"
content += '<select style="cursor:pointer; width:150px; background:#FFF8DC; font-weight:bold; color:#555; font-size:9pt; margin-top:3px; margin-left:2px; font-family:Helvetica; border:0;" onChange="openPage(this.options[this.options.selectedIndex]);">'
content += (
'<option selected style="cursor:pointer; font-weight:bold; color:#555; font-size:9pt; border:0; font-family:Helvetica;" value=""> '
+ name
+ "</option>"
)
for st_val in submenu_types[name]:
numDisallowed = 0
# Jan. 13, 2010: Don't print category heading if user has no access to any of its subitems
for s_ord in submenu_order[st_val]:
linkName = submenu_order[st_val][s_ord]
linkURL = submenu_links[st_val][linkName]
if not menuitems[st_val][linkName] in allowedSections:
numDisallowed += 1
if numDisallowed == len(submenu_links[st_val]):
continue
# print st_val.upper()
content += (
'<option style="cursor:pointer; font-weight:bold; color:#555; background:#EFEFEF; font-size:9pt; border:0; font-family:Helvetica;" onclick""> '
+ st_val.upper()
+ "</option>"
)
# Now: since Python dictionaries are not ordered, arrays with > 2 items (e.g. Users - has more than 'add' and 'search') would appear scrambled. Use an 'order' array instead
for s_ord in submenu_order[st_val]:
linkName = submenu_order[st_val][s_ord]
linkURL = submenu_links[st_val][linkName]
# print st_val
# print linkName
if menuitems[st_val][linkName] in allowedSections:
content += (
'<option style="padding-left:15px; font-weight:bold; color:#555; font-size:8pt; border:0; font-family:Helvetica; cursor:pointer;" value="'
+ linkURL
+ '"> '
+ linkName
+ "</option>"
)
content += "</SELECT>"
content += "</DIV>"
# Quick links
if quickLinks.has_key(name):
content += (
'<div id="quick_links_'
+ name
+ '" style="font-family:Helvetica; width:166px; padding-bottom:0; margin-top:0; padding-top:0; padding-left:2px;">'
)
content += '<UL style="padding-bottom:2px; padding-top:2px; padding-left:10px; position:relative;">'
for qlName in quickLinks[name]:
if qlName in allowedSections:
content += (
'<LI style="list-style:none;"><img src="../pictures/silvermenubullet.png" width="7" height="6" style="padding-bottom:2px;"> <a style="font-weight:bold; font-size:8pt; font-family:Helvetica; text-decoration:none; color:#555; margin-left:2px;" href="../'
+ pageLinkMap[qlName]
+ '">'
+ qlName
+ "</a></LI>"
)
content += "</UL>"
content += "</DIV>"
content += "</DIV>"
else:
if name == "Home":
content += "<DIV style=\"background:url('../pictures/small_bg.png') repeat-y; padding-top:7px; margin-top:0; width:162px; border-top:6px double #FFF8DC; border-left:6px double #FFF8DC; border-right:6px double #FFF8DC; padding-bottom:8px;\">"
else:
content += "<DIV style=\"background:url('../pictures/small_bg.png') repeat-y; padding-top:7px; margin-top:2px; width:162px; border-left:6px double #FFF8DC; border-right:6px double #FFF8DC; padding-bottom:8px;\">"
content += '<img src="../pictures/silvermenubullet.png" style="width:11px; height:9px; margin-left:5px;">'
content += (
'<a style="font-weight:bold; color:#555; font-size:9pt; padding-left:3px; text-decoration:none;" href="'
+ currentSectionLinks[name]
+ '">'
+ name
+ "</a>"
)
content += "</DIV>"
else:
# WRITE THIS FUNCTION!!!!!!!!!!
# content += self.printGeneralMenu(publicSections)
print "Content-type:text/html"
print
print "Unknown user"
content += """
</UL>
<!-- moved form down here on Aug. 20, 2010 -->
<form name="curr_user_form" style="display:none" method="post" action="user_request_handler.py">"
"""
content += (
'<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username" VALUE="'
+ currUser.getFullName()
+ '">'
)
content += (
'<INPUT TYPE="hidden" id="curr_user_hidden" name="view_user" VALUE="' + ` currUser.getUserID() ` + '">'
)
content += """
</FORM>
<div class="login">
"""
content += self.printLoginBlock()
content += """
</div>
</div>
</div>
"""
return content
from general_handler import * from reagent_handler import * from comment_handler import CommentHandler #from system_set_handler import SystemSetHandler from sequence_handler import DNAHandler, ProteinHandler from reagent import Reagent, Vector from sequence_feature import SequenceFeature # User and Project info from user_handler import UserHandler from project_database_handler import ProjectDatabaseHandler from session import Session # make global?? dbConn = DatabaseConn() db = dbConn.databaseConnect() hostname = dbConn.getHostname() cursor = db.cursor() # Handlers and Mappers aHandler = AssociationHandler(db, cursor) rHandler = ReagentHandler(db, cursor) iHandler = InsertHandler(db, cursor) raHandler = ReagentAssociationHandler(db, cursor) sHandler = DNAHandler(db, cursor) pHandler = ReagentPropertyHandler(db, cursor) packetHandler = ProjectDatabaseHandler(db, cursor) uHandler = UserHandler(db, cursor) rtPropHandler = ReagentTypePropertyHandler(db, cursor)
from general_handler import * from reagent_handler import * from sequence_handler import DNAHandler, ProteinHandler from comment_handler import CommentHandler #from system_set_handler import SystemSetHandler from sequence_handler import SequenceHandler from reagent import * import utils from user_handler import UserHandler from project_database_handler import ProjectDatabaseHandler from session import Session from exception import * dbConn = DatabaseConn() db = dbConn.databaseConnect() cursor = db.cursor() hostname = dbConn.getHostname() root_path = dbConn.getRootDir() dnaHandler = DNAHandler(db, cursor) protHandler = ProteinHandler(db, cursor) rHandler = ReagentHandler(db, cursor) oHandler = OligoHandler(db, cursor) propHandler = ReagentPropertyHandler(db, cursor) packetHandler = ProjectDatabaseHandler(db, cursor) propMapper = ReagentPropertyMapper(db, cursor) prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id)
def rMap_specific(f_in, f_out, enz_list):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(bioSeq, linear=False) # linear = FALSE, we're dealing w/ VECTORS
analysis = Analysis(enz_list, fSeq, linear=False) # linear = FALSE again for VECTORS
result = analysis.full()
outfile.write(reagentID + ": " + '\n')
# calculate bandwidths
allSites = []
for enz in result.keys():
sites = result[enz]
if len(allSites) == 0:
allSites = sites
else:
# concatenate
for s in sites:
allSites.append(s)
allSites.sort()
if len(allSites) > 0:
# calculate distances between sites
bandSizes = []
i = 1
while i < len(allSites):
tmpLen = allSites[i] - allSites[i-1]
bandSizes.append(tmpLen)
i += 1
# last band
tmpLen = len(mySeq) - allSites[i-1] + allSites[0]
bandSizes.append(tmpLen)
bandSizes.sort()
outfile.write(`bandSizes` + '\n')
outfile.write('\n')
infile.close()
outfile.close()
cursor.close()
db.close()
def drawMap2():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else:
#rID = 791
#print rID
rID = 154659
reagentID = rHandler.convertDatabaseToReagentID(rID)
d = Drawing(1000,1000)
origin = 0
origin_x = 500
origin_y = 500
radius = 350
c = Circle(origin_x, origin_y, radius)
c.strokeColor = blue
c.fillColor = white
d.add(c)
c.line(origin_x, origin_y+radius-7, origin_x-7, origin_y+radius)
c.line(origin_x-7, origin_y+radius, origin_x, origin_y+radius+7)
c.line(origin_x, origin_y+radius+7, origin_x+7, origin_y+radius)
c.line(origin_x+7, origin_y+radius, origin_x, origin_y+radius-7)
p = c.beginPath()
c.setFillColor(black)
c.saveState()
p.moveTo(origin_x, origin_y+radius-7)
p.lineTo(origin_x-7, origin_y+radius)
p.lineTo(origin_x, origin_y+radius+7)
p.lineTo(origin_x+7, origin_y+radius)
p.close()
c.drawPath(p)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print seqLen
unit_angle_measure = float(360) / float(seqLen)
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
for feature in sequenceFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
f_start = fStart * unit_angle_measure
f_end = fEnd * unit_angle_measure
if fStart > 0 and fEnd > 0:
print "Start " + `fStart`
print "End " + `fEnd`
startAngle = 90 - f_start
extAngle = -1*(f_end - f_start)
print "Angle " + `extAngle`
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = ArcPath()
#p.dumpProperties()
p.strokeWidth=15
p.strokeColor = black
p.fillColor = red
#p.addArc(x1, y1, x2, y2, startAngle, extAngle) # NO
d.add(p)
d.add(String(origin_x+fStart, origin_y+fStart, fValue))
renderPDF.drawToFile(d, "V7066_map.png")
def update():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
form = cgi.FieldStorage(keep_blank_values="True")
print "Content-type:text/html" # REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
print # DITTO
#print `form`
# Aug 29/07
uHandler = UserHandler(db, cursor)
if form.has_key("curr_username"):
# store the user ID for use throughout the session; add to other views in addition to create in PHP
currUname = form.getvalue("curr_username")
currUser = uHandler.getUserByDescription(currUname)
Session.setUser(currUser)
#else: # debug
#currUname = 'Administrator'
#currUser = uHandler.getUserByDescription(currUname)
#Session.setUser(currUser)
if form.has_key("cloning_method"):
cloning_method = form.getvalue("cloning_method")
#else: # debug
#cloning_method = '1'
# Handlers and mappers
rHandler = ReagentHandler(db, cursor)
#sHandler = SystemSetHandler(db, cursor)
pHandler = ReagentPropertyHandler(db, cursor)
raHandler = ReagentAssociationHandler(db, cursor)
aHandler = AssociationHandler(db, cursor)
dnaHandler = DNAHandler(db, cursor)
commHandler = CommentHandler(db, cursor)
protHandler = ProteinHandler(db, cursor)
propMapper = ReagentPropertyMapper(db, cursor)
assocMapper = ReagentAssociationMapper(db, cursor)
# August 29/07: Restrict creation by user and project access
packetHandler = ProjectDatabaseHandler(db, cursor)
########################################################
# Various maps
########################################################
prop_Alias_ID_Map = propMapper.mapPropAliasID() # (propAlias, propID) - e.g. ('insert_type', '48') --> represents 'type of insert' property
prop_Name_Alias_Map = propMapper.mapPropNameAlias() # (propName, propAlias)
prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id)
# Restriction sites
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
newFivePrime = form.getvalue("fpcs")
newThreePrime = form.getvalue("tpcs")
gatewaySites = ['attb', 'attl', 'attp', 'attr'] # nov. 16/07
# resulting sequence
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj + publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
# August 29/07: Need to verify parent project access AND (Sept. 12/07) reconstruct the sequence IFF parent values are changed
newSeq = ""
# Fetch projects the user has AT LEAST Read access to (i.e. if he is explicitly declared a Writer on a project but not declared a Reader, include that project, plus all public projects)
currReadProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Reader')
currWriteProj = packetHandler.findMemberProjects(currUser.getUserID(), 'Writer')
publicProj = packetHandler.findAllProjects(isPrivate="FALSE")
# list of Packet OBJECTS
currUserWriteProjects = utils.unique(currReadProj + currWriteProj + publicProj)
uPackets = []
for p in currUserWriteProjects:
uPackets.append(p.getNumber())
# Get project IDs of parents
packetPropID = pHandler.findPropID("packet id")
if form.has_key("PV"):
pvVal = form.getvalue("PV")
if len(pvVal) > 0:
pvID = rHandler.convertReagentToDatabaseID(pvVal)
try:
pvProjectID = int(rHandler.findSimplePropertyValue(pvID, packetPropID))
pvSeqID = rHandler.findDNASequenceKey(pvID) # get sequence for reconstitution later
except TypeError:
#pvProjectID = 0
e = PVProjectAccessException("You are not authorized to use this Parent Vector, since you do not have Read access to its project.")
print `e.err_code()`
else:
e = UnknownPVIDException("Unknown Parent Vector value")
print `e.err_code()`
return
# else don't do anything, maybe want to delete parents!!!
#else:
#e = MissingPVException("No Parent Vector provided")
#print `e.err_code()`
if pvProjectID > 0 and currUser.getCategory() != 'Admin' and pvProjectID not in uPackets:
e = PVProjectAccessException("Not authorized to access parent")
print `e.err_code()`
return
if cloning_method == '1':
# Non-recombination vector - Get the Insert
if form.has_key("I"):
insertVal = form.getvalue("I")
if len(insertVal) > 0:
insertID = rHandler.convertReagentToDatabaseID(insertVal)
insertSeqID = rHandler.findDNASequenceKey(insertID) # fetch Insert sequence for reconstitution later
try:
insertProjectID = int(rHandler.findSimplePropertyValue(insertID, packetPropID))
except TypeError:
#insertProjectID = 0
e = InsertProjectAccessException("You are not authorized to use this Insert, since you do not have Read access to its project.")
print `e.err_code()`
else:
#insertID = -1
#insertProjectID = 0
#print "Invalid Insert value"
e = UnknownInsertIDException("Unknown Insert value")
print `e.err_code()`
return
#else: # NO!!!!!!!!
#e = MissingInsertException("No Insert provided")
#print `e.err_code()`
if insertProjectID > 0 and currUser.getCategory() != 'Admin' and insertProjectID not in uPackets:
e = InsertProjectAccessException("You are not authorized to use this Insert, since you do not have Read access to its project.")
print `e.err_code()`
return
if pvID > 0 and insertID > 0 :
# try to reconstruct sequence and issue warning if unable
if pvSeqID > 0 and insertSeqID > 0:
# fetch insert cloning sites
insertCloningSites = []
fpcs_prop_id = pHandler.findPropID("5' cloning site")
tpcs_prop_id = pHandler.findPropID("3' cloning site")
fp_insert_cs = rHandler.findSimplePropertyValue(insertID, fpcs_prop_id)
tp_insert_cs = rHandler.findSimplePropertyValue(insertID, tpcs_prop_id)
# Determine if this is a Gateway clone from sites
gwSites = False;
if fp_insert_cs and tp_insert_cs and fp_insert_cs.lower() == 'attl' and tp_insert_cs.lower() == 'attl':
gwSites = True
elif not fp_insert_cs or not tp_insert_cs:
gwSites = True
# nov. 16/07: added this for check
elif fp_insert_cs.lower() in gatewaySites or tp_insert_cs.lower() in gatewaySites:
gwSites = True
else:
gwSites = False;
if gwSites:
# this is a gateway clone
# if sites were changed to something other than gateway, clear sequence
if newFivePrime.lower() != 'attl' or newThreePrime.lower() != 'attl':
e = InsertSitesNotFoundOnParentSequenceException()
print `e.err_code()`
return
else:
pvSeqKey = rHandler.findDNASequenceKey(pvID)
# For Gateway clones, linkers are found from primers - so find the sense and antisense Oligos for this Insert
insertLinkers = []
# Find Sense and Antisense Oligos for this Insert
# (not using antisense just yet - verify with Karen)
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insertID)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(insertSeqID)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insertID, tpLinkerPropID)
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.entryVectorSequence(pvSeqKey, insertSeqID, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException("Sites found more than once on parent vector sequence")
print `e.err_code()`
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException("5' after 3'")
print `e.err_code()`
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException("Gateway sites not found on parent vector sequence")
print `e.err_code()`
else:
# Non-Gateway non-recombination Vector
fp_insert_cs = newFivePrime
tp_insert_cs = newThreePrime
if fp_insert_cs:
insertCloningSites.append(fp_insert_cs)
else:
insertCloningSites.append("")
if tp_insert_cs:
insertCloningSites.append(tp_insert_cs)
else:
insertCloningSites.append("")
# get linkers if there are any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insertID, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insertID, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.constructNonRecombSequence(pvSeqID, insertSeqID, insertCloningSites, insertLinkers)
print newSeq
except (InsertSitesException):
e = InsertSitesException("Could not reconstitute sequence: Unknown sites on Insert.")
print e.err_code()
except (InsertSitesNotFoundOnParentSequenceException):
e = InsertSitesNotFoundOnParentSequenceException("Could not reconstitute sequence: Parent vector sequence does not contain restriction sites.")
print e.err_code()
except (MultipleSiteOccurrenceException):
e = MultipleSiteOccurrenceException("Could not reconstitute sequence: Restriction sites occur more than once on parent vector sequence")
print e.err_code()
except (HybridizationException):
e = HybridizationException("Could not reconstitute sequence: Restriction sites cannot be hybridized.")
print e.err_code()
except (FivePrimeAfterThreePrimeException):
e = FivePrimeAfterThreePrimeException("Could not reconstitute sequence: 5' site occurs after 3' site on parent vector sequence.")
print e.err_code()
else:
e = InvalidSequenceException("Invalid parent sequence")
print `e.err_code()`
else:
e = UnknownPVIDException("Unknown PV ID")
print `e.err_code()`
elif cloning_method == '2':
# Recombination vector - check IPV
ipvVal = form.getvalue("IPV")
if len(ipvVal) > 0:
ipvID = rHandler.convertReagentToDatabaseID(ipvVal)
ipvProjectID = int(rHandler.findSimplePropertyValue(ipvID, packetPropID))
else:
e = UnknownIPVIDException("Unknown IPV ID")
print `e.err_code()`
if ipvProjectID > 0 and currUser.getCategory() != 'Admin' and ipvProjectID not in uPackets:
e = IPVProjectAccessException("Not authorized to view IPV")
print `e.err_code()`
if ipvID > 0 and pvID > 0:
# If restriction sites were modified to anything other than LoxP or gateway att sites, clear the sequence
if not (newFivePrime == newThreePrime and (newFivePrime.lower() == 'loxp' and newThreePrime.lower() == 'loxp') or (newFivePrime.lower() == 'attb' and newThreePrime.lower() == 'attb')):
e = InsertSitesNotFoundOnParentSequenceException("Invalid restriction sites for Non-Recombination Clone - must be LoxP only")
print `e.err_code()`
else:
# get internal db IDs
pv_db_id = rHandler.convertReagentToDatabaseID(pvVal)
ipv_db_id = rHandler.convertReagentToDatabaseID(ipvVal)
# Get the Insert that belongs to the donor vector
ipvInsertAssocID = raHandler.findReagentAssociationID(ipv_db_id)
insertAssocPropID = aHandler.findAssocPropID("insert id")
insert_db_id = aHandler.findAssocPropValue(ipvInsertAssocID, insertAssocPropID)
# Construct a sequence for the new vector from the sequences of its parents
pvSeqKey = rHandler.findDNASequenceKey(pv_db_id)
#print "pv seq " + `pvSeqKey`
ipvSeqKey = rHandler.findDNASequenceKey(ipv_db_id)
#print "ipv seq " + `ipvSeqKey`
insertSeqKey = rHandler.findDNASequenceKey(insert_db_id)
#print "i seq " + `insertSeqKey`
if pvSeqKey > 0 and ipvSeqKey > 0 and insertSeqKey > 0:
# See if there are linkers, although there most likely aren't any
insertLinkers = []
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, tpLinkerPropID)
# sept. 3/07
fwd_linker = ""
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
# Differentiate by cloning sites whether this is a recombination vector or a Gateway Expression Vector
if newFivePrime == 'LoxP' and newThreePrime == 'LoxP':
# recombination
try:
newSeq = dnaHandler.constructRecombSequence(pvSeqKey, ipvSeqKey, insertSeqKey, insertLinkers)
newSeqID = dnaHandler.matchSequence(newSeq)
print newSeq
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException("LOXP sites not found on parent vector sequence")
print `e.err_code()`
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException("LOXP found more than once on parent vector sequence")
print `e.err_code()`
elif newFivePrime == 'attB' and newThreePrime == 'attB':
# Gateway Expression
iHandler = InsertHandler(db, cursor)
senseOligoID = iHandler.findSenseOligoID(insert_db_id)
#antisenseOligoID = iHandler.findAntisenseOligoID(insert_db_id)
# Find Oligo sequences
seqPropID = pHandler.findPropID("sequence")
senseOligoSeqID = rHandler.findIndexPropertyValue(senseOligoID, seqPropID)
senseOligoSequence = dnaHandler.findSequenceByID(senseOligoSeqID)
# Fetch Insert sequence and find linkers from Oligo and Insert sequences
insertSequence = dnaHandler.findSequenceByID(insertSeqKey)
attB_const = "ggggacaactttgtacaaaaaagttggc"
fwd_primer_seq = senseOligoSequence[len(attB_const):]
# First, find linkers from Oligos
fwd_linker = dnaHandler.linker_from_oligo(insertSequence, fwd_primer_seq)
#rev_linker = sHandler.linker_from_oligo(insertSequence, rev_primer_seq)
rev_linker = ""
# Now see if the Insert had its own linkers stored and append them to the Oligo linker
fpLinkerPropID = pHandler.findPropID("5' linker")
tpLinkerPropID = pHandler.findPropID("3' linker")
fp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, fpLinkerPropID)
tp_insert_linker = rHandler.findSimplePropertyValue(insert_db_id, tpLinkerPropID)
if fp_insert_linker and len(fp_insert_linker) > 0 and fp_insert_linker != 0 and fp_insert_linker != '0':
fp_insert_linker = fwd_linker + fp_insert_linker
else:
fp_insert_linker = fwd_linker
tp_insert_linker = rev_linker
insertLinkers.append(fp_insert_linker)
insertLinkers.append(tp_insert_linker)
try:
newSeq = dnaHandler.expressionVectorSequence(pvSeqKey, insertSeqKey, insertLinkers)
print newSeq
except MultipleSiteOccurrenceException:
e = MultipleSiteOccurrenceException("Sites found more than once on parent vector sequence")
print `e.err_code()`
except FivePrimeAfterThreePrimeException:
e = FivePrimeAfterThreePrimeException("5' after 3'")
print `e.err_code()`
except InsertSitesNotFoundOnParentSequenceException:
e = InsertSitesNotFoundOnParentSequenceException("Gateway sites not found on parent vector sequence")
print `e.err_code()`
else:
e = InvalidSequenceException("Invalid parent sequence")
print `e.err_code()`
else:
e = ReagentDoesNotExistException("Unknown parent values")
print `e.err_code()`
def printLabInfo(self, cmd, newLab, errCode=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
uHandler = UserHandler(db, cursor)
lHandler = LabHandler(db, cursor)
currUser = Session.getUser()
gOut = GeneralOutputClass()
if cmd == 'view':
labID = newLab.getID()
labHead = newLab.getLabHead()
labName = newLab.getName()
labCode = newLab.getLabCode()
labDescr = newLab.getDescription()
address = newLab.getAddress()
accessLevel = newLab.getDefaultAccessLevel()
# Determine if 'Delete' button should be disabled - if there are members in the lab, disallow deletion
labMembers = lHandler.findMembers(labID)
delete_disabled = True
if len(labMembers) == 0:
delete_disabled = False
# Only allow modification by admin
modify_disabled = True
# July 3/07: Can further disallow modification of labs other than the one currUser belongs to; however, this might be too restrictive. Keep it in the back of our minds but out of the website for now.
#if (currUser.getCategory() == 'Admin') and (currUser.getLab().getID() == labID):
if (currUser.getCategory() == 'Admin'):
modify_disabled = False
#content = gOut.printHeader() + gOut.printMainMenu()
content = gOut.printHeader()
content += '''
<FORM name="lab_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="775px" cellpadding="5px" cellspacing="5px" class="detailedView_tbl">
<TR>
<TD colspan="6" class="detailedView_heading" style="padding-left:250px">
LABORATORY DETAILS PAGE
'''
content += "<INPUT TYPE=\"submit\" style=\"margin-left:50px;\" name=\"modify_lab\" value=\"Change Lab Info\""
if modify_disabled:
content += " disabled>"
else:
content += ">"
content += "<INPUT TYPE=\"submit\" style=\"margin-left:2px;\" name=\"delete_lab\" value=\"Delete Lab\" onClick=\"return verifyDeleteLab()\""
if modify_disabled or delete_disabled:
content += " disabled>"
else:
content += ">"
content += '''
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Name:
</TD>
<TD class="detailedView_value" style="width:400px">
%s
<INPUT TYPE="hidden" name="labName" value="%s">
<!-- lab ID a hidden value -->
<INPUT TYPE="hidden" name="labID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Lab head:
</TD>
<TD class="detailedView_value" style="width:400px">
%s
<INPUT TYPE="hidden" name="labHead" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Lab ID:
</TD>
<TD class="detailedView_value" style="width:400px">
%s
<INPUT TYPE="hidden" name="labCode" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Description:
</TD>
<TD class="detailedView_value" style="width:400px">
%s
<INPUT TYPE="hidden" name="labDescription" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Location:
</TD>
<TD class="detailedView_value" style="width:400px">
%s
<INPUT TYPE="hidden" name="address" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName" style="white-space:nowrap">
Default access level:
</TD>
<TD class="detailedView_value" style="width:400px">
%s
<INPUT TYPE="hidden" name="access" value="%s">
</TD>
</TR>
<!-- Members -->
<TR>
<TD class="projectDetailedViewName">
Members:
</TD>
<TD class="detailedView_value" style="width:400px">
<UL>
'''
content += "<INPUT type=\"hidden\" id=\"view_user_hidden\" name=\"view_user\">"
for member in labMembers:
mName = member.getFullName()
memberID = member.getUserID()
#content += "<LI>" + mName
content += "<LI>"
content += "<span class=\"linkShow\" onClick=\"redirectToUserDetailedView(" + `memberID` + ");\">" + mName + "</span>"
content += "</LI>"
content += '''
</UL>
</TD>
</TR>
</TABLE>
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", labName, labName, labID, labHead, labHead, labCode, labCode, labDescr, labDescr, address, address, accessLevel, accessLevel)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
elif cmd == 'edit':
labID = newLab.getID()
labName = newLab.getName()
labHead = newLab.getLabHead()
labCode = newLab.getLabCode()
labDescr = newLab.getDescription()
address = newLab.getAddress()
accLev = newLab.getDefaultAccessLevel()
# Disable name modification if there are members in lab
labMembers = lHandler.findMembers(labID)
name_readonly = True
if len(labMembers) == 0:
name_readonly = False
# hide/show duplicate lab code warning
if errCode == 14:
dup_lab_code_warn_display = "inline"
else:
dup_lab_code_warn_display = "none"
#content = gOut.printHeader() + gOut.printMainMenu()
content = gOut.printHeader()
content += '''
<FORM name="user_form" method="POST" action="%s">
<!-- pass current user as hidden form field -->
<INPUT type="hidden" ID="curr_username_hidden" NAME="curr_username"'''
content += "value=\"" + currUser.getFullName() + "\">"
content += '''
<TABLE width="760px" cellpadding="5px" cellspacing="5px" style="border:1px solid black" frame="box" rules="rows">
<TR>
<TD colspan="3" style="padding-left:100px; text-align:center">
<span style="color:#0000FF; font-weight:bold">CHANGE LABORATORY INFORMATION</span>
<INPUT TYPE="submit" style="margin-left:180px;" name="save_lab" value="Save" onClick="selectAllElements('labMembersList'); return checkLab();">
<INPUT TYPE="submit" style="margin-left:20px;" name="cancel_lab" value="Cancel">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Name:
</TD>
<TD class="detailedView_value" style="width:400px" colspan="2">
'''
if name_readonly:
content += "<INPUT TYPE=\"text\" size=\"50px\" id=\"lab_name\" name=\"labName\" value=\"%s\" readonly>"
else:
content += "<INPUT TYPE=\"text\" size=\"50px\" id=\"lab_name\" name=\"labName\" value=\"%s\">"
content += '''
<!-- lab ID hidden value -->
<INPUT TYPE="hidden" name="labID" value="%d">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Lab head:
</TD>
<TD class="detailedView_value" style="width:400px" colspan="2">
<INPUT TYPE="text" size="50px" id="lab_head" name="labHead" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Lab ID:
</TD>
<TD class="detailedView_value" style="width:400px" colspan="2">
<INPUT TYPE="text" size="50px" id="lab_id" name="labCode" value="%s">
<BR>
<SPAN id="dup_labcode_warning" style="vertical-align:bottom; color:#FF0000; display:%s">This identifier already exists. Please specify a different lab ID.</SPAN>
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Description:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" id="lab_descr" name="description" value="%s">
</TD>
</TR>
<TR>
<TD class="projectDetailedViewName">
Location:
</TD>
<TD class="detailedView_value" colspan="2">
<INPUT TYPE="text" size="50px" id="lab_location" name="address" value="%s">
</TD>
</TR>
<TR>
<TD style="width:50px; vertical-align:top; padding-top:10px; white-space:nowrap; font-size:8pt">
Default access level:
</TD>
<TD style="font-size:8pt; vertical-align:top; width:50px;">
'''
# Determine which category radio button should be checked
ucHandler = UserCategoryHandler(db, cursor)
categories = ucHandler.findAllCategories()
for cID in categories.keys():
cat = categories[cID]
content += "<INPUT TYPE=\"RADIO\" name=\"system_access_level\" value=\"" + cat + "\" style=\"margin-top:8px; font-size:8pt\" onClick=\"showHideProjectAccess()\""
if cat == accLev:
content += " checked"
content += ">" + cat + "<BR/>"
content += '''
</TD>
</TR>
<!-- Members - allow deletion -->
<TR>
<TD style="width:50px; vertical-align:top; padding-top:10px; font-size:8pt">
<b>Members:</b>
<BR/><BR/>
Select one or more members to remove them from the system.<BR/><BR/>
(hold down CTRL key to select multiple names)
</TD>
<TD style="font-size:8pt; vertical-align:top; width:50px;">
<SELECT MULTIPLE SIZE="10" ID="labMembersList" NAME="labMembers">
'''
members = lHandler.findMembers(labID)
for member in members:
mName = member.getFullName()
memberID = member.getUserID()
content += "<OPTION value=\"" + `memberID` + "\">" + mName + "</OPTION>"
content += '''
</SELECT>
</TD>
<TD>
<INPUT TYPE=\"button\" onClick=\"removeLabMembers('labMembersList')\" value=\"Remove Selected Members\">
</TD>
</TR>
</TABLE>
</FORM>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
<blockquote> </blockquote>
</div>
'''
content += gOut.printFooter()
page_content = content % (hostname + "cgi/user_request_handler.py", labName, labID, labHead, labCode, dup_lab_code_warn_display, labDescr, address)
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def drawMap():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
root_path = dbConn.getRootDir()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else: # script executed from command line
# Worst-case scenarios
#rID = 260 # V260
#rID = 230 # V260
#rID = 80 # V80 - ok
#rID = 69661 # V2412 - not bad at all, just one of the oligos overlaps exactly with promoter (1 nt difference)
#rID = 23999 # V59541
rID = 97918
#print rID
if form.has_key("user_id_hidden"):
userID = form.getvalue("user_id_hidden")
else: # command-line execution
userID = 1 # debug
reagentID = rHandler.convertDatabaseToReagentID(rID)
uPackets = getCurrentUserProjects(userID)
#print "Content-type:text/html"
#print
#print reagentID
uPackets.sort()
#print `uPackets`
namePropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["name"], prop_Category_Name_ID_Map["General Properties"])
statusPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["status"], prop_Category_Name_ID_Map["General Properties"])
projectPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["packet id"], prop_Category_Name_ID_Map["General Properties"])
rName = rHandler.findSimplePropertyValue(rID, namePropID)
rTypeID = rHandler.findReagentTypeID(rID)
try:
os.remove(root_path + "Reagent/vector_maps/" + reagentID + "_Oligo_map.pdf")
except OSError:
pass
#print root_path
c = Canvas(root_path + "Reagent/vector_maps/" + reagentID + "_Oligo_map.pdf")
c.setPageSize((1500,1500))
c.setStrokeColorRGB(0,0,0)
c.saveState()
# Draw circle
origin = 0
origin_x = 750
origin_y = 750
radius = 200
c.circle(origin_x, origin_y, radius)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print "Content-type:text/html"
#print
#print `rID`
unit_angle_measure = float(360) / float(seqLen)
#print unit_angle_measure
# Mark 1 on the circle - KEEP, Karen said!
c.setLineWidth(1)
c.setStrokeColor(black)
c.setFillColor(black)
c.saveState()
path = c.beginPath()
# Draw a triangle pointing down above the circle
#path.moveTo(origin_x, origin_y+radius+7)
#path.lineTo(origin_x-5, origin_y+radius+14)
#path.lineTo(origin_x+5, origin_y+radius+14)
#path.lineTo(origin_x, origin_y+radius+7)
# Draw a triangle pointing up inside the circle
#path.moveTo(origin_x, origin_y+radius-10)
#path.lineTo(origin_x-5, origin_y+radius-14)
#path.lineTo(origin_x+5, origin_y+radius-14)
#path.lineTo(origin_x, origin_y+radius-10)
# Draw a triangle pointing right inside the circle
path.moveTo(origin_x, origin_y+radius-14)
path.lineTo(origin_x, origin_y+radius-28)
path.lineTo(origin_x+8, origin_y+radius-21)
path.lineTo(origin_x, origin_y+radius-14)
c.drawPath(path, True, True)
# label 1
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 16)
#t.setTextOrigin(origin_x-5, origin_y+radius+19) # above circle
t.setTextOrigin(origin_x-3, origin_y+radius-50) # above circle
t.textOut("1")
c.drawText(t)
c.restoreState()
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
#print `sequenceFeatures`
# Draw legend
ox_legend = 1280
oy_legend = 1465
prev_legend = oy_legend
# draw frame
c.setStrokeColor(darkgray)
c.setFillColor(white)
c.saveState()
featureNames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
featureNames.sort()
if len(featureNames) > 15:
origin_spacer = -19
coeff = 12
else:
origin_spacer = 65
coeff = 15
origin_legend = prev_legend+origin_spacer-len(featureNames)*coeff
x = (990 - origin_legend) / len(featureNames)
#print x
if x < 12:
x = 12
# WHEN WANT TO ADJUST LEGEND GREY BOX HEIGHT: UPDATE THE VALUE ADDED TO legend_height AND THE VALUE SUBTRACTED FROM origin_legend
legend_height = len(featureNames)*x + 55
c.rect(ox_legend-25, origin_legend-35, 215, legend_height, 1, 1) # good for specific rtype attributes
c.restoreState()
protocolPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["protocol"], prop_Category_Name_ID_Map["Classifiers"])
seqPropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["sequence"], prop_Category_Name_ID_Map["DNA Sequence"])
sequenceFeatures = rHandler.findAllReagentFeatures(Vector(rID), rID)
# Print reagent ID and size at the centre of the circle and print name at the top of the page
c.setFont("Helvetica-Bold", 32)
c.setFillColor(black)
c.saveState()
c.drawCentredString(origin_x, origin_y+35, reagentID)
c.drawCentredString(origin_x, origin_y+10, "nt 1 - " + `seqLen`)
if rName:
c.setFillColor(blue)
c.drawCentredString(origin_x, 1415, rName)
c.restoreState()
# find all Oligos whose protocol is 'sequencing'
# April 26, 2010: Do not include status in this query, as it might just not be recorded for the oligo at all (early entries)
cursor.execute("SELECT r.reagentID, r.groupID, s.sequence FROM Sequences_tbl s, ReagentPropList_tbl p1, ReagentPropList_tbl p2, Reagents_tbl r WHERE p1.propertyID=" + `protocolPropID` + " AND p1.propertyValue='sequencing' AND p1.reagentID=r.reagentID AND r.reagentTypeID='3' AND p1.reagentID=p2.reagentID AND p2.propertyID=" + `seqPropID` + " AND p2.propertyValue=s.seqID AND p1.status='ACTIVE' AND p2.status='ACTIVE' AND r.status='ACTIVE' AND s.status='ACTIVE'")
#print "SELECT r.reagentID, r.groupID, s.sequence FROM Sequences_tbl s, ReagentPropList_tbl p1, ReagentPropList_tbl p2, Reagents_tbl r WHERE p1.propertyID=" + `protocolPropID` + " AND p1.propertyValue='sequencing' AND p1.reagentID=r.reagentID AND r.reagentTypeID='3' AND p1.reagentID=p2.reagentID AND p2.propertyID=" + `seqPropID` + " AND p2.propertyValue=s.seqID AND p1.status='ACTIVE' AND p2.status='ACTIVE' AND r.status='ACTIVE' AND s.status='ACTIVE'"
results = cursor.fetchall()
rSeq = utils.squeeze(rSeq).lower()
#print rSeq
oligoFeatures = []
oligoIDsDict = {} # O123 => 123
oligoNamesDict = {} # 123 => "O123 Name"
oligoProjectDict = {} # 123 => 7
for result in results:
if result:
oligoID = int(result[0])
groupID = int(result[1])
oligo_lims_id = "O" + `groupID`
oligoIDsDict[oligo_lims_id] = oligoID
#print oligo_lims_id
oligoName = rHandler.findSimplePropertyValue(oligoID, namePropID)
# April 26, 2010, Karen's request: Ignore Oligos whose status is 'Failed' or 'Do Not Use'
oligoStatus = rHandler.findSimplePropertyValue(oligoID, statusPropID)
if oligoStatus:
#print oligoStatus
if oligoStatus.lower() == 'failed' or oligoStatus.lower() == 'do not use':
continue
if oligoName:
oligoNamesDict[oligoID] = oligoName
else:
oligoNamesDict[oligoID] = ""
#cursor.execute("SELECT propertyValue FROM ReagentPropList_tbl WHERE reagentID=" + `oligoID` + " AND propertyID=" + `namePropID` + " AND status='ACTIVE'")
#result2 = cursor.fetchone()
#if result2:
#oligoName = result2[0]
#oligoNamesDict[oligoID] = oligoName
#else:
#oligoNamesDict[oligoID] = ""
# PROJECT - MUST CAST TO INT
oligoPacket = int(rHandler.findSimplePropertyValue(oligoID, projectPropID))
#print oligoPacket
if oligoPacket:
if oligoPacket not in uPackets:
#print oligoPacket
continue
#cursor.execute("SELECT propertyValue FROM ReagentPropList_tbl WHERE reagentID=" + `oligoID` + " AND propertyID=" + `projectPropID` + " AND status='ACTIVE'")
#result3 = cursor.fetchone()
#if result3:
#oligoPacket = int(result3[0])
##print oligoPacket
#if oligoPacket not in uPackets:
##print oligoPacket
#continue
#oligoProjectDict[oligoID] = oligoPacket
#else:
#oligoProjectDict[oligoID] = 0
if len(result) == 3:
oligoSeq = result[2].strip().lower()
#print oligoSeq
tm = sHandler.calculateTm(oligoSeq)
# Changes made April 26, 2010: Karen caught that the sense/antisense check does not work for T3 and T7 vectors and said to check oligo sequence both ways
#if rSeq.find(oligoSeq) < 0:
#continue
if rSeq.find(oligoSeq) >= 0:
fStart = rSeq.find(oligoSeq) + 1
fEnd = fStart + len(oligoSeq) - 1
#if oHandler.isSenseOligo(oligoID):
oFeature = SequenceFeature("sequencing primer", oligo_lims_id, fStart, fEnd, 'forward', oligoSeq, tm)
#else:
#oFeature = SequenceFeature("sequencing primer", oligo_lims_id, fStart, fEnd, 'reverse', oligoSeq, tm)
else:
revSeq = sHandler.reverse_complement(oligoSeq)
if rSeq.find(revSeq) < 0:
continue
fStart = rSeq.find(revSeq) + 1
fEnd = fStart + len(revSeq)
# Note: start pos > end pos, as we're talking about reverse Oligo sequence
revStart = fEnd - 1
revEnd = fStart
# Still, record sense/antisense for displaying on the map ('forward' and 'reverse' here are just static values in Feature class, it doesn't reflect sequence orientation in our case - just use as a temporary placeholder)
#if oHandler.isSenseOligo(oligoID):
#oligoFeatures.append(oFeature)
#oFeature = SequenceFeature("sequencing primer", oligo_lims_id, revStart, revEnd, 'forward', oligoSeq, tm)
#else:
oFeature = SequenceFeature("sequencing primer", oligo_lims_id, revStart, revEnd, 'reverse', oligoSeq, tm)
oligoFeatures.append(oFeature)
sequenceFeatures.append(oFeature)
# SORT features by size, so that short features are not hidden behind the long ones
fSizes = []
sortedFeatures = []
fSortedPos = {}
fStartPos = []
fEndPos = []
for feature in sequenceFeatures:
fSize = int(feature.getFeatureSize())
if fSize > 0:
fSizes.append(fSize)
#if fSize > 150:
f_start_tmp = int(feature.getFeatureStartPos())
fStartPos.append(f_start_tmp)
fSortedPos[f_start_tmp] = feature
f_end_tmp = int(feature.getFeatureEndPos())
fEndPos.append(f_end_tmp)
fEndPos.sort()
fStartPos.sort()
#print `fStartPos`
#print `fEndPos`
fSizes.sort(reverse=True)
#print `fSizes`
for fs in fSizes:
for feature in sequenceFeatures:
fSize = feature.getFeatureSize()
# added existence check July 17/08 - different features may have same sizes so end up with duplicate features in list (e.g. cloning sizes appeared twice on the map)
if fs == fSize and feature not in sortedFeatures:
sortedFeatures.append(feature)
# Order: 5' site, 3' site, 5' linker, 3' linker, then the rest
sites_color = featureNameColorMap["5' cloning site"] # same for 3' site
# 5' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Show legend for linkers
linkers_color = featureNameColorMap["5' linker"]
# 5' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Output the rest of the features in alphabetical order
featureNames = featureNameColorMap.keys()
featureNames.sort()
#print `featureNames`
for featureName in featureNames:
#print featureName
if featureNameColorMap.has_key(featureName):
color = featureNameColorMap[featureName]
if featureName != "5' cloning site" and featureName != "3' cloning site" and featureName != "5' linker" and featureName != "3' linker" and color != None:
#print featureName
c.setStrokeColor(color)
c.setFillColor(color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(color)
t.setFillColor(color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + featureName.upper())
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Sequencing Primer
oligoColor = "#7cfc00"
c.setStrokeColor(oligoColor)
c.setFillColor(oligoColor)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(oligoColor)
t.setFillColor(oligoColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "SEQUENCING PRIMER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
ox_labels = 40
oy_labels = 40
#prev_legend = oy_labels
for feature in sortedFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fSize = feature.getFeatureSize()
#print fType
#print fValue
#print fSize
# color
if featureNameColorMap.has_key(fType):
fColor = featureNameColorMap[fType]
textColor = fColor
elif fType == 'sequencing primer':
fColor = "#7cfc00"
textColor = "black"
o_id = oligoIDsDict[fValue]
oligoName = oligoNamesDict[o_id]
if len(oligoName) > 0:
fValue += " " + oligoName
# property name
if fType == 'cdna insert':
fValue = "cDNA Insert"
elif fType == 'promoter':
fValue = fValue + " " + fType
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
# value
#if fType == 'sequencing primer':
#oligoDir = feature.getFeatureDirection()
#if oligoDir == 'forward':
#oligoType = 'Sense'
#else:
#oligoType = 'Antisense'
#fTxt = fValue + " (" + `fStart` + "-" + `fEnd` + "), " + oligoDir
#else:
fTxt = fValue + " (" + `fStart` + "-" + `fEnd` + ")"
if fSize > 0:
f_start = fStart * unit_angle_measure
#print "Start " + `fStart`
#print "End " + `fEnd`
startAngle = 90 - f_start
#print "Start angle " + `startAngle`
f_end = fEnd * unit_angle_measure
endAngle = 90 - f_end
#print "End angle " + `endAngle`
extAngle = -1*(f_end - f_start)
#print "Ext angle " + `extAngle`
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = c.beginPath()
c.setLineWidth(10)
c.setLineJoin(1)
c.setStrokeColor(fColor)
c.saveState()
p.arc(x1, y1, x2, y2, startAngle, extAngle)
c.drawPath(p)
c.restoreState()
# common to all
startAngle_rad = (startAngle * math.pi) / 180.0
endAngle_rad = (endAngle * math.pi) / 180.0
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 9)
c.saveState()
arc_x_start = origin_x + (radius+5)*math.cos(startAngle_rad)
arc_y_start = origin_y + (radius+5)*math.sin(startAngle_rad)
arc_x_end = origin_x+(radius+5)*math.cos(endAngle_rad)
arc_y_end = origin_y+(radius+5)*math.sin(endAngle_rad)
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 12)
c.saveState()
# draw line
delta = 45
if fStart < seqLen/2:
if arc_y_start > origin_y:
# THIS WORKS!!!!
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.line(arc_x_start, arc_y_start, arc_x_start+math.fabs(math.sin(delta))*(fInd*10), arc_y_start+math.fabs(math.cos(delta))*(fY*10))
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fInd*10)+2, arc_y_start+math.fabs(math.cos(delta))*(fY*10)-math.cos(delta)*0.9, fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fInd*10)+2, arc_y_start+math.fabs(math.cos(delta))*(fY*10)-math.cos(delta)*0.9, fTxt)
c.restoreState()
else:
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
c.line(arc_x_start, arc_y_start, arc_x_start+math.fabs(math.sin(delta))*(fY*10), arc_y_start-math.fabs(math.cos(delta))*(fInd*10))
c.restoreState()
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fY*10)+2, arc_y_start-math.fabs(math.cos(delta))*(fInd*10)-math.cos(delta)*13, fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawString(arc_x_start+math.fabs(math.sin(delta))*(fY*10)+2, arc_y_start-math.fabs(math.cos(delta))*(fInd*10)-math.cos(delta)*13, fTxt)
c.restoreState()
else:
if arc_y_start > origin_y:
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
c.line(arc_x_start, arc_y_start, arc_x_start-math.fabs(math.sin(delta)*(fY*10)), arc_y_start+math.fabs(math.cos(delta)*(fInd*10)))
c.restoreState()
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fY*10))+2, arc_y_start+math.fabs(math.cos(delta)*(fInd*10)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fY*10))+2, arc_y_start+math.fabs(math.cos(delta)*(fInd*10)), fTxt)
c.restoreState()
else:
fInd = fStartPos.index(fStart)
fY = len(fStartPos) - fInd
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
c.line(arc_x_start, arc_y_start, arc_x_start-math.fabs(math.sin(delta)*(fInd*10)), arc_y_start-math.fabs(math.cos(delta)*(fY*10)))
c.restoreState()
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(textColor)
c.setFillColor(textColor)
c.setFont("Helvetica-Bold", 8)
c.saveState()
#c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fInd*10))-2, arc_y_start-math.fabs(math.cos(delta)*(fY*10))-math.cos(delta)*12, fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawRightString(arc_x_start-math.fabs(math.sin(delta)*(fInd*10))-2, arc_y_start-math.fabs(math.cos(delta)*(fY*10))-math.cos(delta)*12, fTxt)
c.restoreState()
# print Oligo info
#prev_legend = prev_legend-10
prev_legend = 1365
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels, prev_legend-15)
t.textOut("Sequencing primers for " + reagentID + ":")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-18
fColor = "#7cfc00"
# sort oligos
tmp_oligos = {}
#print `oligoFeatures`
for oFeature in oligoFeatures:
oligoID = oFeature.getFeatureName()
#print oligoID
oligoStart = oFeature.getFeatureStartPos()
#print oligoStart
if tmp_oligos.has_key(oligoStart):
tmp_o_list = tmp_oligos[oligoStart]
else:
tmp_o_list = []
tmp_oligos[oligoStart] = oFeature
tmp_o_list.append(oFeature)
tmp_oligos[oligoStart] = tmp_o_list
oligoSeq = oFeature.getFeatureDescrType()
#print oligoSeq
#print `tmp_oligos`
for oligoStart in sorted(tmp_oligos.keys()):
oFeatures = tmp_oligos[oligoStart]
for oFeature in oFeatures:
oligoID = oFeature.getFeatureName()
#oligoSeq = oFeature.getFeatureDescrType()
oligoTm = oFeature.getFeatureDescrName()
oligoEnd = oFeature.getFeatureEndPos()
oligoDir = oFeature.getFeatureDirection()
o_rID = oligoIDsDict[oligoID]
oligoName = oligoNamesDict[o_rID]
#if oligoDir == 'forward':
#oligoType = 'Sense'
#else:
#oligoType = 'Antisense'
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
if len(oligoName) > 0:
#t.textOut(oligoID + ": " + oligoName + " (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoType)
t.textOut(oligoID + ": " + oligoName + " (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoDir)
else:
#t.textOut(oligoID + ": (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoType)
t.textOut(oligoID + ": (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoDir)
#print oligoID + ": (" + `oligoStart` + "-" + `oligoEnd` + ")" ", " + oligoType
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
c.showPage()
c.save()
from general_handler import * from reagent_handler import * from sequence_handler import DNAHandler, ProteinHandler from comment_handler import CommentHandler #from system_set_handler import SystemSetHandler from sequence_handler import SequenceHandler from reagent import * import utils from user_handler import UserHandler from project_database_handler import ProjectDatabaseHandler from session import Session from exception import * dbConn = DatabaseConn() db = dbConn.databaseConnect() cursor = db.cursor() hostname = dbConn.getHostname() root_path = dbConn.getRootDir() dnaHandler = DNAHandler(db, cursor) protHandler = ProteinHandler(db, cursor) rHandler = ReagentHandler(db, cursor) oHandler = OligoHandler(db, cursor) propHandler = ReagentPropertyHandler(db, cursor) packetHandler = ProjectDatabaseHandler(db, cursor) propMapper = ReagentPropertyMapper(db, cursor) prop_Name_ID_Map = propMapper.mapPropNameID() # (prop name, prop id)
from database_conn import DatabaseConn from exception import * from reagent import Reagent from user import User from reagent_handler import ReagentHandler from user_handler import UserHandler from location_database_handler import LocationHandler from general_handler import * from mapper import * from session import Session dbConn = DatabaseConn() db = dbConn.databaseConnect() cursor = db.cursor() hostname = dbConn.getHostname() rHandler = ReagentHandler(db, cursor) lHandler = LocationHandler(db, cursor) ################################################################################################################################### # This is an AJAX function invoked via Javascript from reagent search page # Written June 8, 2009, by Marina Olhovsky # Last modified June 8, 2009 ################################################################################################################################### def deleteReagent(form):
def drawMap():
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
hostname = dbConn.getHostname()
root_path = dbConn.getRootDir()
form = cgi.FieldStorage(keep_blank_values="True")
#print "Content-type:text/html"
#print
#print `form`
if form.has_key("rID"):
rID = form.getvalue("rID")
else:
#rID = 148913 # V4550
rID = 29125
#rID = 72
#rID = 309
#rID = 1901 # small feature labels @ start of seq. overlap
#rID = 36415
#print rID
reagentID = rHandler.convertDatabaseToReagentID(rID)
#print "Content-type:text/html"
#print
#print reagentID
namePropID = pHandler.findReagentPropertyInCategoryID(prop_Name_ID_Map["name"], prop_Category_Name_ID_Map["General Properties"])
rName = rHandler.findSimplePropertyValue(rID, namePropID)
#rName = rHandler.findSimplePropertyValue(rID, prop_Name_ID_Map["name"])
rTypeID = rHandler.findReagentTypeID(rID)
try:
os.remove(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
except OSError:
pass
#print root_path
c = Canvas(root_path + "Reagent/vector_maps/" + reagentID + "_map.pdf")
c.setPageSize((1000,1000))
c.setStrokeColorRGB(0,0,0)
c.saveState()
# Draw circle
origin = 0
origin_x = 500
origin_y = 470
radius = 200
c.circle(origin_x, origin_y, radius)
c.restoreState()
# Divide circle into 100-unit sectors
rSeqID = rHandler.findDNASequenceKey(rID)
rSeq = sHandler.findSequenceByID(rSeqID)
seqLen = len(rSeq)
#print "Content-type:text/html"
#print
#print `rID`
unit_angle_measure = float(360) / float(seqLen)
#print unit_angle_measure
# Mark 1 on the circle - KEEP, Karen said!
c.setLineWidth(1)
c.setStrokeColor(black)
c.setFillColor(black)
c.saveState()
path = c.beginPath()
path.moveTo(origin_x, origin_y+radius+7)
path.lineTo(origin_x-5, origin_y+radius+14)
path.lineTo(origin_x+5, origin_y+radius+14)
path.lineTo(origin_x, origin_y+radius+7)
c.drawPath(path, True, True)
# label 1
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 16)
t.setTextOrigin(origin_x-5, origin_y+radius+19)
t.textOut("1")
c.drawText(t)
c.restoreState()
# Calculate feature segment sizes
sequenceFeatures = rHandler.findReagentSequenceFeatures(rID)
#print `sequenceFeatures`
# Draw legend
ox_legend = 800
oy_legend = 985
prev_legend = oy_legend
# draw frame
c.setStrokeColor(darkgray)
#c.setStrokeColor(white)
#c.setFillColor(lightgrey)
c.setFillColor(white)
c.saveState()
# Output the rest of the features in alphabetical order - Moved here Jan. 26/10
#featureNames = featureNameColorMap.keys()
#print `featureNameColorMap.keys()`
#print len(featureNameColorMap.keys())
#fnames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
#fnames.remove('expression system')
#fnames.remove('tag position')
#print `fnames`
#print len(fnames)
featureNames = rtPropHandler.findReagentTypeAttributeNamesByCategory(rTypeID, prop_Category_Name_ID_Map["DNA Sequence Features"])
featureNames.sort()
#print `featureNames`
#print prev_legend-240
#print prev_legend-15-len(featureNames)*15
#c.rect(ox_legend-25, prev_legend-240, 215, 235, 1, 1)
#c.rect(ox_legend-25, prev_legend-15-len(featureNames)*15, 215, 10+len(featureNames)*15, 1, 1) # good for list of all db features
if len(featureNames) > 15:
origin_spacer = -19
coeff = 12
else:
origin_spacer = 65
coeff = 15
#origin_legend = prev_legend+65-len(featureNames)*15
origin_legend = prev_legend+origin_spacer-len(featureNames)*coeff
x = (990 - origin_legend) / len(featureNames)
#print x
if x < 12:
x = 12
legend_height = len(featureNames)*x + 15
#print legend_height
c.rect(ox_legend-25, origin_legend-17, 215, legend_height, 1, 1) # good for specific rtype attributes
c.restoreState()
# Order: 5' site, 3' site, 5' linker, 3' linker, then the rest
sites_color = featureNameColorMap["5' cloning site"] # same for 3' site
# 5' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
t.setStrokeColor(sites_color)
#t.setFillColor(black)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' site
c.setStrokeColor(sites_color)
c.setFillColor(sites_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(sites_color)
t.setFillColor(sites_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' CLONING SITE")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# Show legend for linkers
linkers_color = featureNameColorMap["5' linker"]
# 5' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "5' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
# 3' linker
c.setStrokeColor(linkers_color)
c.setFillColor(linkers_color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(linkers_color)
t.setFillColor(linkers_color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + "3' LINKER")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
## Output the rest of the features in alphabetical order
#featureNames = featureNameColorMap.keys()
#featureNames.sort()
#print `featureNames`
for featureName in featureNames:
if featureNameColorMap.has_key(featureName):
color = featureNameColorMap[featureName]
#else:
#continue
if featureName != "5' cloning site" and featureName != "3' cloning site" and featureName != "5' linker" and featureName != "3' linker" and color != None:
#print featureName
c.setStrokeColor(color)
c.setFillColor(color)
c.saveState()
c.rect(ox_legend-15, prev_legend-20, 25,8, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(color)
t.setFillColor(color)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_legend+12, prev_legend-20)
t.textOut(" - " + featureName.upper())
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
#print prev_legend
# Print reagent ID and size at the centre of the circle and print name at the top of the page
c.setFont("Helvetica-Bold", 32)
c.setFillColor(black)
c.saveState()
c.drawCentredString(origin_x, origin_y+35, reagentID)
c.drawCentredString(origin_x, origin_y+10, "nt 1 - " + `seqLen`)
if rName:
c.setFillColor(blue)
c.drawCentredString(origin_x, 935, rName)
c.restoreState()
# SORT features by size, so that short features are not hidden behind the long ones
fSizes = []
sortedFeatures = []
for feature in sequenceFeatures:
fSize = int(feature.getFeatureSize())
if fSize > 0:
fSizes.append(fSize)
fSizes.sort(reverse=True)
#print `fSizes`
for fs in fSizes:
for feature in sequenceFeatures:
fSize = feature.getFeatureSize()
# added existence check July 17/08 - different features may have same sizes so end up with duplicate features in list (e.g. cloning sizes appeared twice on the map)
if fs == fSize and feature not in sortedFeatures:
sortedFeatures.append(feature)
#print `sortedFeatures`
ox_labels = 40
oy_labels = 910
prev_legend = oy_labels
t = c.beginText()
t.setStrokeColor(black)
t.setFillColor(black)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels, prev_legend-15)
t.textOut("Features shorter than 150 nt:")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-18
#for feature in sequenceFeatures:
for feature in sortedFeatures:
fType = feature.getFeatureType()
fValue = feature.getFeatureName()
fSize = feature.getFeatureSize()
#print fType
#print fValue
#print fSize
fColor = featureNameColorMap[fType]
if fType == 'cdna insert':
fValue = "cDNA Insert"
elif fType == 'promoter':
fValue = fValue + " " + fType
fStart = feature.getFeatureStartPos()
fEnd = feature.getFeatureEndPos()
fDir = feature.getFeatureDirection()
if fSize > 0:
f_start = fStart * unit_angle_measure
#print "Start " + `fStart`
#print "End " + `fEnd`
startAngle = 90 - f_start
#print "Start angle " + `startAngle`
f_end = fEnd * unit_angle_measure
endAngle = 90 - f_end
#print "End angle " + `endAngle`
extAngle = -1*(f_end - f_start)
#print "Ext angle " + `extAngle`
x1 = origin_x - radius
y1 = origin_y - radius
x2 = origin_x + radius
y2 = origin_y + radius
p = c.beginPath()
#t = c.beginText()
c.setLineWidth(10)
c.setLineJoin(1)
fColor = featureNameColorMap[fType]
c.setStrokeColor(fColor)
c.saveState()
p.arc(x1, y1, x2, y2, startAngle, extAngle)
c.drawPath(p)
c.restoreState()
## jan. 27/10: this makes a contour for each arc
#p = c.beginPath()
#c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
#c.setStrokeColor(black)
#c.setFillColor(fColor)
#c.saveState()
#p.arc(x1+5, y1+5, x2-5, y2-5, startAngle, extAngle)
#c.drawPath(p)
##c.restoreState()
##c.setLineWidth(1)
##fColor = featureNameColorMap[fType]
##c.setStrokeColor(black)
##c.setFillColor(fColor)
##c.saveState()
#p.arc(x1-5, y1-5, x2+5, y2+5, startAngle, extAngle)
#c.drawPath(p)
#c.restoreState() # jan. 27/10 modification ends here
# common to all
startAngle_rad = (startAngle * math.pi) / 180.0
endAngle_rad = (endAngle * math.pi) / 180.0
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 9)
c.saveState()
arc_x_start = origin_x + (radius+5)*math.cos(startAngle_rad)
arc_y_start = origin_y + (radius+5)*math.sin(startAngle_rad)
arc_x_end = origin_x+(radius+5)*math.cos(endAngle_rad)
arc_y_end = origin_y+(radius+5)*math.sin(endAngle_rad)
# draw label
c.setStrokeColorRGB(0,0,1)
c.setFillColorRGB(0,0,1)
c.setFont("Helvetica-Bold", 12)
c.saveState()
# draw line
delta = 45
# Rotate labels only for SMALL features (they can be crammed together)
#if fSize > 100:
#delta = 45
#else:
#delta = 32
if fStart < seqLen/2:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
#if fSize <= 100:
#c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
#else:
# July 17/08: Show labels for long features only
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
c.restoreState()
# July 17/08: Show labels for long features only
if fSize > 150:
# draw label
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawString(arc_x_start+50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
else:
if arc_y_start > origin_y:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)))
#c.line(arc_x_start, arc_y_start, arc_x_start+10*math.fabs(math.sin(delta)), arc_y_start-10*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start+55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.restoreState()
else:
#c.setStrokeColor(black)
#c.setFillColor(black)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setLineWidth(1)
c.saveState()
if fSize > 150:
c.line(arc_x_start, arc_y_start, arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)))
c.restoreState()
# draw label
if fSize > 150:
#c.setStrokeColorRGB(0,0,1)
#c.setFillColorRGB(0,0,1)
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.setFont("Helvetica-Bold", 11)
c.saveState()
c.drawRightString(arc_x_start-50*math.fabs(math.sin(delta)), arc_y_start-55*math.fabs(math.cos(delta)), fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.restoreState()
else:
c.setStrokeColor(fColor)
c.setFillColor(fColor)
c.saveState()
c.rect(ox_labels+5, prev_legend-15, 15,6, 1, 1)
c.restoreState
t = c.beginText()
#t.setStrokeColor(black)
#t.setFillColor(black)
t.setStrokeColor(fColor)
t.setFillColor(fColor)
t.setFont("Helvetica-Bold", 10)
t.setTextOrigin(ox_labels+25, prev_legend-15)
t.textOut(fValue + " (" + `fStart` + "-" + `fEnd` + ")")
c.drawText(t)
c.restoreState
prev_legend = prev_legend-15
c.showPage()
c.save()