def printReagentInfo(self, cmd, reagent, errMsg=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
gOut = GeneralOutputClass()
currUser = Session.getUser()
currUserID = currUser.getUserID()
sHandler = SystemSetHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
# print menu
content = gOut.printHeader() + gOut.printMainMenu()
# common to all reagent types
projectList = utils.unique(pHandler.findMemberProjects(currUserID, 'Writer') + pHandler.findMemberProjects(currUserID, 'Owner'))
# Differentiate other properties by reagent type
if reagent.getType() == 'Insert':
# Fetch dropdown list values to output on the form
iTypeList = sHandler.findAllSetValues("type of insert")
statusList = sHandler.findAllSetValues("status")
cloningMethodList = sHandler.findAllSetValues("insert cloning method")
fpcsList = sHandler.findAllSetValues("5' cloning site")
tpcsList = sHandler.findAllSetValues("3' cloning site")
tagTypeList = sHandler.findAllSetValues("tag")
tagPositionList = sHandler.findAllSetValues("tag position")
openClosedList = sHandler.findAllSetValues("open/closed")
speciesList = sHandler.findAllSetValues("species")
verificationList = sHandler.findAllSetValues("verification")
# Initialize property values
iType = ""
iName = ""
iStatus = ""
cloningMethod = ""
projectID = ""
fpcs = ""
tpcs = ""
tagType = ""
tagPosition = ""
openClosed = ""
species = ""
accession = ""
altID = ""
geneID = ""
ensemblID = ""
geneSymbol = ""
fp_start = ""
tp_stop = ""
fwd_linker = ""
rev_linker = ""
funcDescr = ""
verification = ""
expComm = ""
verComm = ""
sequence = ""
# Fetch POST values if available:
allProps = reagent.getProperties()
if allProps.has_key("type of insert"):
iType = allProps["type of insert"]
if allProps.has_key("name"):
iName = allProps["name"]
if allProps.has_key("status"):
iStatus = allProps["status"]
if allProps.has_key("insert cloning method"):
cloningMethod = allProps["insert cloning method"]
if allProps.has_key("packet id"):
projectID = int(allProps["packet id"])
if allProps.has_key("5' cloning site"):
fpcs = allProps["5' cloning site"]
if allProps.has_key("3' cloning site"):
tpcs = allProps["3' cloning site"]
if allProps.has_key("tag"):
tagType = allProps["tag"]
if allProps.has_key("tag position"):
tagPosition = allProps["tag position"]
if allProps.has_key("open/closed"):
openClosed = allProps["open/closed"]
if allProps.has_key("species"):
species = allProps["species"]
if allProps.has_key("accession number"):
accession = allProps["accession number"]
if allProps.has_key("alternate id"):
altID = allProps["alternate id"]
if allProps.has_key("entrez gene id"):
geneID = allProps["entrez gene id"]
if allProps.has_key("ensembl gene id"):
ensemblID = allProps["ensembl gene id"]
if allProps.has_key("official gene symbol"):
geneSymbol = allProps["official gene symbol"]
if allProps.has_key("5' start"):
fp_start = allProps["5' start"]
if allProps.has_key("3' stop"):
tp_stop = allProps["3' stop"]
if allProps.has_key("5' linker"):
fwd_linker = allProps["5' linker"]
if allProps.has_key("3' linker"):
rev_linker = allProps["3' linker"]
if allProps.has_key("description"):
funcDescr = allProps["description"]
if allProps.has_key("verification"):
verification = allProps["verification"]
if allProps.has_key("comments"):
expComm = allProps["comments"]
if allProps.has_key("verification comments"):
verComm = allProps["verification comments"]
if allProps.has_key("sequence"):
sequence = allProps["sequence"]
# associations
ipvID = ""
senseOligoID = ""
antisenseOligoID = ""
allAssoc = reagent.getAssociations()
'''
if allAssoc.has_key("insert_parent_vector"):
ipvID = allAssoc["insert_parent_vector"]
if allAssoc.has_key("sense_oligo"):
senseOligoID = allAssoc["sense_oligo"]
if allAssoc.has_key("antisense_oligo"):
antisenseOligoID = allAssoc["antisense_oligo"]
'''
# Action: Output form with POST values if set
if cmd == 'create':
content += '''
<div class="main">
<form NAME="create_insert_form" ACTION="%s" METHOD="POST" onSubmit="return validateInsert() && verifyParents();">
'''
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" value=\"" + currUser.getFullName() + "\">"
content += '''
<input type="hidden" name="reagent_type_hidden" value="Insert">
<table id="vector_insertproperty_table_id" border="1" width="780px" cellpadding="4" frame="box" rules="all">
'''
if errMsg != "":
content += "<th colspan=\"3\" style=\"color:#0000FF; text-align:left; font-weight:normal\">There was a problem:<br><P>" + errMsg + "<BR><BR></th>"
content += '''
<tr>
<td colspan="3" style="text-align:center">
<span style="color:#0000CD; font-size:13pt; font-weight:bold">
Insert Information
</span>
<br>
<span style="font-size:8pt; color:#FF0000">
Fields marked with a red asterisk (*) are mandatory
</span>
</td>
</tr>
<tr>
<td width="180px">
Type of Insert
<span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td width="275px">
<SELECT id="itype_list" size="1" NAME="INPUT_INSERT_info_insert_type_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for it in iTypeList:
content += "<OPTION VALUE=\"" + it + "\""
if it == iType:
content += " SELECTED>" + it + "</OPTION>"
else:
content += ">" + it + "</OPTION>"
content += '''
</SELECT>
</td>
<td>
Describes the type of insert. Users select from a pre-defined list. Designed to make insert use more apparent and searches easier.
</td>
</tr>
<tr>
<td>
Name
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_name_prop\" value=\"" + iName + "\">"
content += '''
</td>
<td>
Name that describes the reagent - free text field
</td>
</tr>
<tr>
<td>
Status
</td>
<td>
<SELECT id="status_list" name="INPUT_INSERT_info_status_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iStatus) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for s in statusList:
content += "<OPTION VALUE=\"" + s + "\""
if s == iStatus:
content += " SELECTED>" + s + "</OPTION>"
else:
content += ">" + s + "</OPTION>"
content += '''
</td>
<td>
Indicates the status and availability of the reagent. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Insert Cloning Method
</td>
<td>
<SELECT size="1" id="cm_list" name="INPUT_INSERT_info_cloning_method_prop" onChange="showCMText()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(cloningMethod) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for cm in cloningMethodList:
content += "<OPTION VALUE=\"" + cm + "\""
if cm == cloningMethod:
content += " SELECTED>" + cm + "</OPTION>"
else:
content += ">" + cm + "</OPTION>"
content += '''
</td>
<td>
Describes the method used to create the insert (e.g. PCR or RE (restriction enzyme)) and provides additional information for its cloning into a vector (eg. by RE, In Fusion or BP reaction)
</td>
</tr>
<tr>
<td>
Project ID <span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td>
<select id="packetList_insert" size="1" name="INPUT_INSERT_info_packet_id_prop">
'''
# need to sort projects
pNums = []
projects = {} # (pID, Packet)
for p in projectList:
pID = p.getNumber()
pNums.append(pID)
projects[pID] = p
pNums.sort()
for pID in pNums:
p = projects[pID]
content += "<OPTION VALUE=\"" + `p.getNumber()` + "\""
if p.getNumber() == projectID:
content += " SELECTED>" + `p.getNumber()` + ": " + p.getOwner().getLastName() + ": " + p.getName() + "</OPTION>"
else:
content += ">" + `p.getNumber()` + ": " + p.getOwner().getLastName() + ": " + p.getName() + "</OPTION>"
content += '''
</select>
<BR>
<div id="packet_warning_insert" style="display:none; color:#FF0000">Please select a Project ID from the dropdown list</div>
</td>
<td>
Indicates what person and project originally created the reagent.
</td>
</tr>
<tr>
<td>
5' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="fpcs_list" name="INPUT_INSERT_info_5_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(fpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for fps in fpcsList:
content += "<OPTION VALUE=\"" + fps + "\""
if fps == fpcs:
content += " SELECTED>" + fps + "</OPTION>"
else:
content += ">" + fps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 5' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
3' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="tpcs_list" name="INPUT_INSERT_info_3_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tps in tpcsList:
content += "<OPTION VALUE=\"" + tps + "\""
if tps == tpcs:
content += " SELECTED>" + tps + "</OPTION>"
else:
content += ">" + tps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 3' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag
</td>
<td>
<SELECT size="1" id="tag_list" name="INPUT_INSERT_info_tag_prop" onChange="showTagTypeBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tt in tagTypeList:
content += "<OPTION VALUE=\"" + tt + "\""
if tt == tagType:
content += " SELECTED>" + tt + "</OPTION>"
else:
content += ">" + tt + "</OPTION>"
content += '''
</td>
<td>
Indicates if the insert itself has a tag associated with it (outside of the backbone vector). Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag Position
</td>
<td>
<SELECT size="1" name="INPUT_INSERT_info_tag_position_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagPosition) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tp in tagPositionList:
content += "<OPTION VALUE=\"" + tp + "\""
if tp == tagPosition:
content += " SELECTED>" + tp + "</OPTION>"
else:
content += ">" + tp + "</OPTION>"
content += '''
</td>
<td>
Describes the position of the tag on the insert. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Open/Closed
</td>
<td>
<SELECT id="oc_list" size="1" name="INPUT_INSERT_info_open_closed_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(openClosed) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for oc in openClosedList:
content += "<OPTION VALUE=\"" + oc + "\""
if oc == openClosed:
content += " SELECTED>" + oc + "</OPTION>"
else:
content += ">" + oc + "</OPTION>"
content += '''
</td>
<td>
Indicates for an Open Reading Frame if there is a start codon (ATG) or stop codon (open - no stop codon, closed - stop codon).
</td>
</tr>
<tr>
<td>
Species
</td>
<td>
<SELECT size="1" style="color:000000" id = "species_list" name="INPUT_INSERT_info_species_prop" onChange="showSpeciesBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(species) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for sp in speciesList:
content += "<OPTION VALUE=\"" + sp + "\""
if sp == species:
content += " SELECTED>" + sp + "</OPTION>"
else:
content += ">" + sp + "</OPTION>"
content += '''
</td>
<td>
Indicates the species from which the Insert was derived. User selects species from a pre-defined list.
</td>
</tr>
<tr>
<td>
Accession Number
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_accession_number_prop\" value=\"" + accession + "\">"
content += '''
</td>
<td>
The Accession Number from which the insert was cloned or to which the sequence maps.
</td>
</tr>
<tr>
<td>
Alternate ID
</td>
<td>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="IMAGE" id="_alternate_id_IMAGE_checkbox" onClick="showAltIDTextBox('_alternate_id_IMAGE_checkbox', '_alternate_id_IMAGE_textbox')">IMAGE <INPUT style="display:none" id="_alternate_id_IMAGE_textbox" name="alternate_id_IMAGE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RIKEN" id="_alternate_id_RIKEN_checkbox" onClick="showAltIDTextBox('_alternate_id_RIKEN_checkbox', '_alternate_id_RIKEN_textbox')">RIKEN <INPUT style="display:none" id="_alternate_id_RIKEN_textbox" name="alternate_id_RIKEN_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="Kazusa" id="_alternate_id_Kazusa_checkbox" onClick="showAltIDTextBox('_alternate_id_Kazusa_checkbox', '_alternate_id_Kazusa_textbox')">Kazusa <INPUT style="display:none" id="_alternate_id_Kazusa_textbox" name="alternate_id_Kazusa_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="LIFESEQ" id="_alternate_id_LIFESEQ_checkbox" onClick="showAltIDTextBox('_alternate_id_LIFESEQ_checkbox', '_alternate_id_LIFESEQ_textbox')">LIFESEQ <INPUT style="display:none" id="_alternate_id_LIFESEQ_textbox" name="alternate_id_LIFESEQ_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RZPD" id="_alternate_id_RZPD_checkbox" onClick="showAltIDTextBox('_alternate_id_RZPD_checkbox', '_alternate_id_RZPD_textbox')">RZPD <INPUT style="display:none" id="_alternate_id_RZPD_textbox" name="alternate_id_RZPD_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="HIP" id="_alternate_id_HIP_checkbox" onClick="showAltIDTextBox('_alternate_id_HIP_checkbox', '_alternate_id_HIP_textbox')">HIP <INPUT style="display:none" id="_alternate_id_HIP_textbox" name="alternate_id_HIP_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="ADDGENE" id="_alternate_id_ADDGENE_checkbox" onClick="showAltIDTextBox('_alternate_id_ADDGENE_checkbox', '_alternate_id_ADDGENE_textbox')">ADDGENE <INPUT style="display:none" id="_alternate_id_ADDGENE_textbox" name="alternate_id_ADDGENE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="PMID" id="_alternate_id_PMID_checkbox" onClick="showAltIDTextBox('_alternate_id_PMID_checkbox', '_alternate_id_PMID_textbox')">PMID <INPUT style="display:none" id="_alternate_id_PMID_textbox" name="alternate_id_PMID_textbox_name" size="15"></INPUT><br>
<input type="checkbox" id="_other_Alt_ID_chkbx" name="INPUT_INSERT_info_alternate_id_prop[]" value="Other" onClick="showSpecificOtherCheckbox('_alternate_id_txt')">Other: <INPUT style="display:none" id="_alternate_id_txt" name="alternate_id_name_txt" size="15"></INPUT>
</td>
<td>
Indicates any other ID's that identify the insert, including but not limited to IMAGE, Kazusa, RIKEN, and other. <BR><BR><BR><BR>For 'Other', please enter the source name and ID separated by a semicolon (e.g. IMAGE:123456)
</td>
</tr>
<tr>
<td>
Entrez Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_id_prop\" value=\"" + geneID + "\">"
content += '''
</td>
<td>
The NCBI Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Ensembl Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_ensembl_gene_id_prop\" value=\"" + ensemblID + "\">"
content += '''
</td>
<td>
The Ensembl Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Official Gene Symbol
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_symbol_prop\" value=\"" + geneSymbol + "\">"
content += '''
</td>
<td>
The official gene symbol for this Insert.
</td>
</tr>
<tr>
<td>
5' Start
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_start_prop\" value=\"" + fp_start + "\">"
content += '''
</td>
<td>
Users can map the start of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence starts.
</td>
</tr>
<tr>
<td>
3' Stop
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_stop_prop\" value=\"" + tp_stop + "\">"
content += '''
</td>
<td>
Users can map the stop of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence stops
</td>
</tr>
<tr>
<td>
5' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_linker_prop\" value=\"" + fwd_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 5' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg kozak sequences, any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
3' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_linker_prop\" value=\"" + rev_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 3' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
Functional Description
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_description_prop\" value=\"" + funcDescr + "\">"
content += '''
</td>
<td>
Describes the purpose of the reagent and any information that may be key to working with the reagent.
</td>
</tr>
<tr>
<td>
Verification
</td>
<td>
<select size="1" name="INPUT_INSERT_info_verification_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(verification) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for v in verificationList:
content += "<OPTION VALUE=\"" + v + "\""
if v == verification:
content += " SELECTED>" + v + "</OPTION>"
else:
content += ">" + v + "</OPTION>"
content += '''
</select>
</td>
<td>
Indicates if the reagent has been verified and how. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Verification comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_verification_comments_prop\" value=\"" + verComm + "\">"
content += '''
</td>
<td>
Allows user to provide a description of the verification status - eg comments on sequence changes, expression levels.
</td>
</tr>
<tr>
<td>
Experimental comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_comments_prop\" value=\"" + expComm + "\">"
content += '''
</td>
<td>
Used to describe any information that descrbes how the reagent works in the experimental context - eg low expression, difficult to grow, etc.
</td>
</tr>
<tr>
<td>
Sequence
</td>
<td>
</td>
<td>
The sequence of the insert that corresponds to a cDNA or fragment of interest. Does include artificial start and stop codons. Does not include linker sequences as described above.
</td>
</tr>
<tr>
<td colspan="3">
<textarea rows="10" cols="93" id="dna_sequence" name="INPUT_INSERT_info_sequence_prop">
'''
content += sequence
content += '''
</textarea>
</td>
</tr>
'''
content += self.printParents('Insert', allAssoc)
content += '''
<tr>
<td colspan="3">
<hr><br>
<input type="submit" name="create_reagent" value="Create" onclick="document.pressed = this.value">
</td>
</tr>
</table>
</form>
</div>
'''
# Common to all
content += gOut.printFooter()
page_content = content % (hostname + "cgi/create.py")
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
def printReagentInfo(self, cmd, reagent, errMsg=""):
dbConn = DatabaseConn()
hostname = dbConn.getHostname() # to define form action URL
db = dbConn.databaseConnect()
cursor = db.cursor()
gOut = GeneralOutputClass()
currUser = Session.getUser()
currUserID = currUser.getUserID()
sHandler = SystemSetHandler(db, cursor)
pHandler = ProjectDatabaseHandler(db, cursor)
# print menu
content = gOut.printHeader() + gOut.printMainMenu()
# common to all reagent types
projectList = utils.unique(
pHandler.findMemberProjects(currUserID, 'Writer') +
pHandler.findMemberProjects(currUserID, 'Owner'))
# Differentiate other properties by reagent type
if reagent.getType() == 'Insert':
# Fetch dropdown list values to output on the form
iTypeList = sHandler.findAllSetValues("type of insert")
statusList = sHandler.findAllSetValues("status")
cloningMethodList = sHandler.findAllSetValues(
"insert cloning method")
fpcsList = sHandler.findAllSetValues("5' cloning site")
tpcsList = sHandler.findAllSetValues("3' cloning site")
tagTypeList = sHandler.findAllSetValues("tag")
tagPositionList = sHandler.findAllSetValues("tag position")
openClosedList = sHandler.findAllSetValues("open/closed")
speciesList = sHandler.findAllSetValues("species")
verificationList = sHandler.findAllSetValues("verification")
# Initialize property values
iType = ""
iName = ""
iStatus = ""
cloningMethod = ""
projectID = ""
fpcs = ""
tpcs = ""
tagType = ""
tagPosition = ""
openClosed = ""
species = ""
accession = ""
altID = ""
geneID = ""
ensemblID = ""
geneSymbol = ""
fp_start = ""
tp_stop = ""
fwd_linker = ""
rev_linker = ""
funcDescr = ""
verification = ""
expComm = ""
verComm = ""
sequence = ""
# Fetch POST values if available:
allProps = reagent.getProperties()
if allProps.has_key("type of insert"):
iType = allProps["type of insert"]
if allProps.has_key("name"):
iName = allProps["name"]
if allProps.has_key("status"):
iStatus = allProps["status"]
if allProps.has_key("insert cloning method"):
cloningMethod = allProps["insert cloning method"]
if allProps.has_key("packet id"):
projectID = int(allProps["packet id"])
if allProps.has_key("5' cloning site"):
fpcs = allProps["5' cloning site"]
if allProps.has_key("3' cloning site"):
tpcs = allProps["3' cloning site"]
if allProps.has_key("tag"):
tagType = allProps["tag"]
if allProps.has_key("tag position"):
tagPosition = allProps["tag position"]
if allProps.has_key("open/closed"):
openClosed = allProps["open/closed"]
if allProps.has_key("species"):
species = allProps["species"]
if allProps.has_key("accession number"):
accession = allProps["accession number"]
if allProps.has_key("alternate id"):
altID = allProps["alternate id"]
if allProps.has_key("entrez gene id"):
geneID = allProps["entrez gene id"]
if allProps.has_key("ensembl gene id"):
ensemblID = allProps["ensembl gene id"]
if allProps.has_key("official gene symbol"):
geneSymbol = allProps["official gene symbol"]
if allProps.has_key("5' start"):
fp_start = allProps["5' start"]
if allProps.has_key("3' stop"):
tp_stop = allProps["3' stop"]
if allProps.has_key("5' linker"):
fwd_linker = allProps["5' linker"]
if allProps.has_key("3' linker"):
rev_linker = allProps["3' linker"]
if allProps.has_key("description"):
funcDescr = allProps["description"]
if allProps.has_key("verification"):
verification = allProps["verification"]
if allProps.has_key("comments"):
expComm = allProps["comments"]
if allProps.has_key("verification comments"):
verComm = allProps["verification comments"]
if allProps.has_key("sequence"):
sequence = allProps["sequence"]
# associations
ipvID = ""
senseOligoID = ""
antisenseOligoID = ""
allAssoc = reagent.getAssociations()
'''
if allAssoc.has_key("insert_parent_vector"):
ipvID = allAssoc["insert_parent_vector"]
if allAssoc.has_key("sense_oligo"):
senseOligoID = allAssoc["sense_oligo"]
if allAssoc.has_key("antisense_oligo"):
antisenseOligoID = allAssoc["antisense_oligo"]
'''
# Action: Output form with POST values if set
if cmd == 'create':
content += '''
<div class="main">
<form NAME="create_insert_form" ACTION="%s" METHOD="POST" onSubmit="return validateInsert() && verifyParents();">
'''
content += "<INPUT type=\"hidden\" ID=\"curr_username_hidden\" NAME=\"curr_username\" value=\"" + currUser.getFullName(
) + "\">"
content += '''
<input type="hidden" name="reagent_type_hidden" value="Insert">
<table id="vector_insertproperty_table_id" border="1" width="780px" cellpadding="4" frame="box" rules="all">
'''
if errMsg != "":
content += "<th colspan=\"3\" style=\"color:#0000FF; text-align:left; font-weight:normal\">There was a problem:<br><P>" + errMsg + "<BR><BR></th>"
content += '''
<tr>
<td colspan="3" style="text-align:center">
<span style="color:#0000CD; font-size:13pt; font-weight:bold">
Insert Information
</span>
<br>
<span style="font-size:8pt; color:#FF0000">
Fields marked with a red asterisk (*) are mandatory
</span>
</td>
</tr>
<tr>
<td width="180px">
Type of Insert
<span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td width="275px">
<SELECT id="itype_list" size="1" NAME="INPUT_INSERT_info_insert_type_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for it in iTypeList:
content += "<OPTION VALUE=\"" + it + "\""
if it == iType:
content += " SELECTED>" + it + "</OPTION>"
else:
content += ">" + it + "</OPTION>"
content += '''
</SELECT>
</td>
<td>
Describes the type of insert. Users select from a pre-defined list. Designed to make insert use more apparent and searches easier.
</td>
</tr>
<tr>
<td>
Name
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_name_prop\" value=\"" + iName + "\">"
content += '''
</td>
<td>
Name that describes the reagent - free text field
</td>
</tr>
<tr>
<td>
Status
</td>
<td>
<SELECT id="status_list" name="INPUT_INSERT_info_status_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(iStatus) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for s in statusList:
content += "<OPTION VALUE=\"" + s + "\""
if s == iStatus:
content += " SELECTED>" + s + "</OPTION>"
else:
content += ">" + s + "</OPTION>"
content += '''
</td>
<td>
Indicates the status and availability of the reagent. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Insert Cloning Method
</td>
<td>
<SELECT size="1" id="cm_list" name="INPUT_INSERT_info_cloning_method_prop" onChange="showCMText()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(cloningMethod) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for cm in cloningMethodList:
content += "<OPTION VALUE=\"" + cm + "\""
if cm == cloningMethod:
content += " SELECTED>" + cm + "</OPTION>"
else:
content += ">" + cm + "</OPTION>"
content += '''
</td>
<td>
Describes the method used to create the insert (e.g. PCR or RE (restriction enzyme)) and provides additional information for its cloning into a vector (eg. by RE, In Fusion or BP reaction)
</td>
</tr>
<tr>
<td>
Project ID <span style="font-size:8pt; color:#FF0000; font-weight:bold">*</span>
</td>
<td>
<select id="packetList_insert" size="1" name="INPUT_INSERT_info_packet_id_prop">
'''
# need to sort projects
pNums = []
projects = {} # (pID, Packet)
for p in projectList:
pID = p.getNumber()
pNums.append(pID)
projects[pID] = p
pNums.sort()
for pID in pNums:
p = projects[pID]
content += "<OPTION VALUE=\"" + ` p.getNumber() ` + "\""
if p.getNumber() == projectID:
content += " SELECTED>" + ` p.getNumber(
) ` + ": " + p.getOwner().getLastName(
) + ": " + p.getName() + "</OPTION>"
else:
content += ">" + ` p.getNumber() ` + ": " + p.getOwner(
).getLastName() + ": " + p.getName() + "</OPTION>"
content += '''
</select>
<BR>
<div id="packet_warning_insert" style="display:none; color:#FF0000">Please select a Project ID from the dropdown list</div>
</td>
<td>
Indicates what person and project originally created the reagent.
</td>
</tr>
<tr>
<td>
5' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="fpcs_list" name="INPUT_INSERT_info_5_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(fpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for fps in fpcsList:
content += "<OPTION VALUE=\"" + fps + "\""
if fps == fpcs:
content += " SELECTED>" + fps + "</OPTION>"
else:
content += ">" + fps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 5' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
3' Cloning Site on Insert
</td>
<td>
<SELECT size="1" id="tpcs_list" name="INPUT_INSERT_info_3_prime_cloning_site_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tpcs) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tps in tpcsList:
content += "<OPTION VALUE=\"" + tps + "\""
if tps == tpcs:
content += " SELECTED>" + tps + "</OPTION>"
else:
content += ">" + tps + "</OPTION>"
content += '''
</td>
<td>
Indicates what 3' site on the insert was used to clone it into a vector. May not necessarily be the same as for the vector. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag
</td>
<td>
<SELECT size="1" id="tag_list" name="INPUT_INSERT_info_tag_prop" onChange="showTagTypeBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagType) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tt in tagTypeList:
content += "<OPTION VALUE=\"" + tt + "\""
if tt == tagType:
content += " SELECTED>" + tt + "</OPTION>"
else:
content += ">" + tt + "</OPTION>"
content += '''
</td>
<td>
Indicates if the insert itself has a tag associated with it (outside of the backbone vector). Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Tag Position
</td>
<td>
<SELECT size="1" name="INPUT_INSERT_info_tag_position_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(tagPosition) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for tp in tagPositionList:
content += "<OPTION VALUE=\"" + tp + "\""
if tp == tagPosition:
content += " SELECTED>" + tp + "</OPTION>"
else:
content += ">" + tp + "</OPTION>"
content += '''
</td>
<td>
Describes the position of the tag on the insert. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Open/Closed
</td>
<td>
<SELECT id="oc_list" size="1" name="INPUT_INSERT_info_open_closed_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(openClosed) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for oc in openClosedList:
content += "<OPTION VALUE=\"" + oc + "\""
if oc == openClosed:
content += " SELECTED>" + oc + "</OPTION>"
else:
content += ">" + oc + "</OPTION>"
content += '''
</td>
<td>
Indicates for an Open Reading Frame if there is a start codon (ATG) or stop codon (open - no stop codon, closed - stop codon).
</td>
</tr>
<tr>
<td>
Species
</td>
<td>
<SELECT size="1" style="color:000000" id = "species_list" name="INPUT_INSERT_info_species_prop" onChange="showSpeciesBox()">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(species) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for sp in speciesList:
content += "<OPTION VALUE=\"" + sp + "\""
if sp == species:
content += " SELECTED>" + sp + "</OPTION>"
else:
content += ">" + sp + "</OPTION>"
content += '''
</td>
<td>
Indicates the species from which the Insert was derived. User selects species from a pre-defined list.
</td>
</tr>
<tr>
<td>
Accession Number
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_accession_number_prop\" value=\"" + accession + "\">"
content += '''
</td>
<td>
The Accession Number from which the insert was cloned or to which the sequence maps.
</td>
</tr>
<tr>
<td>
Alternate ID
</td>
<td>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="IMAGE" id="_alternate_id_IMAGE_checkbox" onClick="showAltIDTextBox('_alternate_id_IMAGE_checkbox', '_alternate_id_IMAGE_textbox')">IMAGE <INPUT style="display:none" id="_alternate_id_IMAGE_textbox" name="alternate_id_IMAGE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RIKEN" id="_alternate_id_RIKEN_checkbox" onClick="showAltIDTextBox('_alternate_id_RIKEN_checkbox', '_alternate_id_RIKEN_textbox')">RIKEN <INPUT style="display:none" id="_alternate_id_RIKEN_textbox" name="alternate_id_RIKEN_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="Kazusa" id="_alternate_id_Kazusa_checkbox" onClick="showAltIDTextBox('_alternate_id_Kazusa_checkbox', '_alternate_id_Kazusa_textbox')">Kazusa <INPUT style="display:none" id="_alternate_id_Kazusa_textbox" name="alternate_id_Kazusa_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="LIFESEQ" id="_alternate_id_LIFESEQ_checkbox" onClick="showAltIDTextBox('_alternate_id_LIFESEQ_checkbox', '_alternate_id_LIFESEQ_textbox')">LIFESEQ <INPUT style="display:none" id="_alternate_id_LIFESEQ_textbox" name="alternate_id_LIFESEQ_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="RZPD" id="_alternate_id_RZPD_checkbox" onClick="showAltIDTextBox('_alternate_id_RZPD_checkbox', '_alternate_id_RZPD_textbox')">RZPD <INPUT style="display:none" id="_alternate_id_RZPD_textbox" name="alternate_id_RZPD_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="HIP" id="_alternate_id_HIP_checkbox" onClick="showAltIDTextBox('_alternate_id_HIP_checkbox', '_alternate_id_HIP_textbox')">HIP <INPUT style="display:none" id="_alternate_id_HIP_textbox" name="alternate_id_HIP_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="ADDGENE" id="_alternate_id_ADDGENE_checkbox" onClick="showAltIDTextBox('_alternate_id_ADDGENE_checkbox', '_alternate_id_ADDGENE_textbox')">ADDGENE <INPUT style="display:none" id="_alternate_id_ADDGENE_textbox" name="alternate_id_ADDGENE_textbox_name" size="15"></INPUT><br>
<input type="checkbox" name="INPUT_INSERT_info_alternate_id_prop[]" value="PMID" id="_alternate_id_PMID_checkbox" onClick="showAltIDTextBox('_alternate_id_PMID_checkbox', '_alternate_id_PMID_textbox')">PMID <INPUT style="display:none" id="_alternate_id_PMID_textbox" name="alternate_id_PMID_textbox_name" size="15"></INPUT><br>
<input type="checkbox" id="_other_Alt_ID_chkbx" name="INPUT_INSERT_info_alternate_id_prop[]" value="Other" onClick="showSpecificOtherCheckbox('_alternate_id_txt')">Other: <INPUT style="display:none" id="_alternate_id_txt" name="alternate_id_name_txt" size="15"></INPUT>
</td>
<td>
Indicates any other ID's that identify the insert, including but not limited to IMAGE, Kazusa, RIKEN, and other. <BR><BR><BR><BR>For 'Other', please enter the source name and ID separated by a semicolon (e.g. IMAGE:123456)
</td>
</tr>
<tr>
<td>
Entrez Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_id_prop\" value=\"" + geneID + "\">"
content += '''
</td>
<td>
The NCBI Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Ensembl Gene ID
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_ensembl_gene_id_prop\" value=\"" + ensemblID + "\">"
content += '''
</td>
<td>
The Ensembl Gene ID to which the sequence maps.
</td>
</tr>
<tr>
<td>
Official Gene Symbol
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_gene_symbol_prop\" value=\"" + geneSymbol + "\">"
content += '''
</td>
<td>
The official gene symbol for this Insert.
</td>
</tr>
<tr>
<td>
5' Start
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_start_prop\" value=\"" + fp_start + "\">"
content += '''
</td>
<td>
Users can map the start of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence starts.
</td>
</tr>
<tr>
<td>
3' Stop
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_stop_prop\" value=\"" + tp_stop + "\">"
content += '''
</td>
<td>
Users can map the stop of the sequence onto its accession number by indicating at what nucleotide position on the accession number that the sequence stops
</td>
</tr>
<tr>
<td>
5' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_5_prime_linker_prop\" value=\"" + fwd_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 5' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg kozak sequences, any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
3' Linker
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_3_prime_linker_prop\" value=\"" + rev_linker + "\">"
content += '''
</td>
<td>
Indicates any sequence added to the 3' end of an insert that does not map to a cDNA sequence but should be included as part of the insert - eg any nucleotides added to maintain frame.
</td>
</tr>
<tr>
<td>
Functional Description
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_description_prop\" value=\"" + funcDescr + "\">"
content += '''
</td>
<td>
Describes the purpose of the reagent and any information that may be key to working with the reagent.
</td>
</tr>
<tr>
<td>
Verification
</td>
<td>
<select size="1" name="INPUT_INSERT_info_verification_prop">
'''
# default option
content += "<OPTION VALUE=\"\" "
if len(verification) == 0:
content += "SELECTED></OPTION>"
else:
content += "></OPTION>"
for v in verificationList:
content += "<OPTION VALUE=\"" + v + "\""
if v == verification:
content += " SELECTED>" + v + "</OPTION>"
else:
content += ">" + v + "</OPTION>"
content += '''
</select>
</td>
<td>
Indicates if the reagent has been verified and how. Users select from a pre-defined list.
</td>
</tr>
<tr>
<td>
Verification comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_verification_comments_prop\" value=\"" + verComm + "\">"
content += '''
</td>
<td>
Allows user to provide a description of the verification status - eg comments on sequence changes, expression levels.
</td>
</tr>
<tr>
<td>
Experimental comments
</td>
<td>
'''
content += "<INPUT type=\"text\" name=\"INPUT_INSERT_info_comments_prop\" value=\"" + expComm + "\">"
content += '''
</td>
<td>
Used to describe any information that descrbes how the reagent works in the experimental context - eg low expression, difficult to grow, etc.
</td>
</tr>
<tr>
<td>
Sequence
</td>
<td>
</td>
<td>
The sequence of the insert that corresponds to a cDNA or fragment of interest. Does include artificial start and stop codons. Does not include linker sequences as described above.
</td>
</tr>
<tr>
<td colspan="3">
<textarea rows="10" cols="93" id="dna_sequence" name="INPUT_INSERT_info_sequence_prop">
'''
content += sequence
content += '''
</textarea>
</td>
</tr>
'''
content += self.printParents('Insert', allAssoc)
content += '''
<tr>
<td colspan="3">
<hr><br>
<input type="submit" name="create_reagent" value="Create" onclick="document.pressed = this.value">
</td>
</tr>
</table>
</form>
</div>
'''
# Common to all
content += gOut.printFooter()
page_content = content % (hostname + "cgi/create.py")
print "Content-type:text/html" # THIS IS PERMANENT; DO NOT REMOVE
print # DITTO
print page_content
