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 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 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 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 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 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