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Finished adding all the extra tools/links below the trait details
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@zsloan
zsloan committed Jun 16, 2015
1 parent 29b5144 commit f792574
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Showing 4 changed files with 64 additions and 44 deletions.
3 changes: 0 additions & 3 deletions wqflask/secure_server.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,11 +66,8 @@ def check_send_mail_running():
if __name__ == '__main__':
#create_user()



check_send_mail_running()


app.run(host='0.0.0.0',
port=5002,
use_debugger=True,
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10 changes: 8 additions & 2 deletions wqflask/wqflask/do_search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -448,6 +448,9 @@ class RifSearch(MrnaAssaySearch):

DoSearch.search_types['ProbeSet_RIF'] = "RifSearch"

def get_from_clause(self):
return ", GeneRIF_BASIC "

def get_where_clause(self):
where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and
MATCH (GeneRIF_BASIC.comment)
Expand All @@ -456,9 +459,9 @@ def get_where_clause(self):
return where_clause

def run(self):
from_clause = self.get_from_clause()
where_clause = self.get_where_clause()

from_clause = ", GeneRIF_BASIC "
query = self.compile_final_query(from_clause, where_clause)

return self.execute(query)
Expand All @@ -468,6 +471,9 @@ class WikiSearch(MrnaAssaySearch):

DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch"

def get_from_clause(self):
return ", GeneRIF "

def get_where_clause(self):
where_clause = """%s.symbol = GeneRIF.symbol
and GeneRIF.versionId=0 and GeneRIF.display>0
Expand All @@ -478,9 +484,9 @@ def get_where_clause(self):
return where_clause

def run(self):
from_clause = self.get_from_clause()
where_clause = self.get_where_clause()

from_clause = ", GeneRIF "
query = self.compile_final_query(from_clause, where_clause)

return self.execute(query)
Expand Down
59 changes: 30 additions & 29 deletions wqflask/wqflask/show_trait/show_trait.py
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,7 @@ def to_float(item):

def dispTraitInformation(self, args, title1Body, hddn, this_trait):

_Species = webqtlDatabaseFunction.retrieve_species(group=self.dataset.group.name)
self.species_name = webqtlDatabaseFunction.retrieve_species(group=self.dataset.group.name)

#tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1")

Expand Down Expand Up @@ -299,7 +299,7 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
#XZ: Gene Symbol
if this_trait.symbol:
#XZ: Show SNP Browser only for mouse
if _Species == 'mouse':
if self.species_name == 'mouse':
geneName = g.db.execute("SELECT geneSymbol FROM GeneList WHERE geneSymbol = %s", this_trait.symbol).fetchone()
if geneName:
snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0]
Expand All @@ -322,8 +322,8 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):

#XZ: display similar traits in other selected datasets
if this_trait and this_trait.dataset and this_trait.dataset.type=="ProbeSet" and this_trait.symbol:
if _Species in ("mouse", "rat", "human"):
similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.symbol, _Species)
if self.species_name in ("mouse", "rat", "human"):
similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.symbol, self.species_name)
similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl)
similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
similarText = "Find"
Expand Down Expand Up @@ -377,26 +377,26 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A'

#XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary.
if _Species == "rat":
if self.species_name == "rat":
self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence)
UTHSC_BLAT_URL = ""
elif _Species == "mouse":
self.UTHSC_BLAT_URL = ""
elif self.species_name == "mouse":
self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence)
UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence)
elif _Species == "human":
self.UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence)
elif self.species_name == "human":
self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
UTHSC_BLAT_URL = ""
self.UTHSC_BLAT_URL = ""
else:
self.UCSC_BLAT_URL = ""
UTHSC_BLAT_URL = ""
self.UTHSC_BLAT_URL = ""

if self.UCSC_BLAT_URL != "":
verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL)
verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ",
title=" Check probe locations at UCSC ", style="border:none;")
verifyButton.append(verifyButtonImg)
verifyText = 'Verify'
if UTHSC_BLAT_URL:
if self.UTHSC_BLAT_URL != "":
rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL)
rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ",
title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
Expand All @@ -416,14 +416,15 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
#query database for number of probes associated with trait; if count > 0, set probe tool button and text
probeResult = g.db.execute(query).fetchone()
if probeResult[0] > 0:
self.show_probes = "True"
probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&group=%s&incparentsf1=ON" \
% (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.dataset, this_trait.name, this_trait.cellid, self.dataset.group.name)
probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl)
probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
#probeButton.append(probeButton_img)
probeText = "Probes"

this_trait.species = _Species # We need this in the template, so we tuck it into this_trait
this_trait.species = self.species_name # We need this in the template, so we tuck it into this_trait
this_trait.database = this_trait.get_database()

#XZ: ID links
Expand Down Expand Up @@ -462,14 +463,14 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
#XZ,12/26/2008: Gene symbol may contain single quotation mark.
#For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948)
#I debug this by using double quotation marks.
if _Species == "rat":
if self.species_name == "rat":
result = g.db.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
if result != None:
kgId, chr, txst, txen = result[0], result[1], result[2], result[3]
if chr and txst and txen and kgId:
txst = int(txst*1000000)
txen = int(txen*1000000)
if _Species == "mouse":
if self.species_name == "mouse":
print("this_trait.symbol:", this_trait.symbol)
result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
if result != None:
Expand All @@ -484,10 +485,10 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
# url="http://symatlas.gnf.org/SymAtlas/bioentry?querytext=%s&query=14&species=%s&type=Expression" \
# % (this_trait.symbol,symatlas_species),Class="fs14 fwn", \
# title="Expression across many tissues and cell types"), style=linkStyle), " "*2)
if this_trait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"):
if this_trait.geneid and (self.species_name == "mouse" or self.species_name == "rat" or self.species_name == "human"):
#tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\
# url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \
# % (_Species, this_trait.geneid),Class="fs14 fwn", \
# % (self.species_name, this_trait.geneid),Class="fs14 fwn", \
# title="Expression across many tissues and cell types"), style=linkStyle), " "*2)
pass
#tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\
Expand All @@ -497,13 +498,13 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
if this_trait.symbol:
#ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input
#We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users
if _Species == "mouse":
if self.species_name == "mouse":
species_scientific = "Mus%20musculus"
elif _Species == "rat":
elif self.species_name == "rat":
species_scientific = "Rattus%20norvegicus"
elif _Species == "human":
elif self.species_name == "human":
species_scientific = "Homo%20sapiens"
elif _Species == "drosophila":
elif self.species_name == "drosophila":
species_scientific = "Drosophila%20melanogaster"
else:
species_scientific = "all"
Expand All @@ -519,7 +520,7 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
# url="http://bind.ca/?textquery=%s" \
# % this_trait.symbol,Class="fs14 fwn", \
# title="Protein interactions"), style=linkStyle), " "*2)
#if this_trait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"):
#if this_trait.geneid and (self.species_name == "mouse" or self.species_name == "rat" or self.species_name == "human"):
# tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\
# url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \
# % this_trait.geneid, Class="fs14 fwn", \
Expand All @@ -528,19 +529,19 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
# url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \
# % this_trait.symbol, Class="fs14 fwn", \
# title="Brain synapse database"), style=linkStyle), " "*2)
#if _Species == "mouse":
#if self.species_name == "mouse":
# tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
# url="http://mouse.brain-map.org/brain/%s.html" \
# % this_trait.symbol, Class="fs14 fwn", \
# title="Allen Brain Atlas"), style=linkStyle), " "*2)

if this_trait.geneid:
#if _Species == "mouse":
#if self.species_name == "mouse":
# tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
# url="http://www.brain-map.org/search.do?queryText=egeneid=%s" \
# % this_trait.geneid, Class="fs14 fwn", \
# title="Allen Brain Atlas"), style=linkStyle), " "*2)
if _Species == "human":
if self.species_name == "human":
#tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
# url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \
# % this_trait.geneid, Class="fs14 fwn", \
Expand Down Expand Up @@ -643,13 +644,13 @@ def dispTraitInformation(self, args, title1Body, hddn, this_trait):
location = "not available"

#if this_trait.sequence and len(this_trait.sequence) > 100:
# if _Species == "rat":
# if self.species_name == "rat":
# UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', this_trait.sequence)
# UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', this_trait.sequence)
# elif _Species == "mouse":
# elif self.species_name == "mouse":
# UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', this_trait.sequence)
# UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', this_trait.sequence)
# elif _Species == "human":
# elif self.species_name == "human":
# UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
# UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', this_trait.sequence)
# else:
Expand Down Expand Up @@ -895,7 +896,7 @@ def build_correlation_tools(self, this_trait):
def build_mapping_tools(self, this_trait):


_Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, group=fd.group)
#_Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, group=fd.group)

this_group = fd.group
if this_group[:3] == 'BXD':
Expand Down
36 changes: 26 additions & 10 deletions wqflask/wqflask/templates/show_trait_details.html
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Original file line number Diff line number Diff line change
Expand Up @@ -32,10 +32,12 @@
<dt>Resource Links</dt>
{% if this_trait.dataset.type == 'ProbeSet' %}
<dd>
{% if this_trait.symbol != None %}
<a href="http://bioinformatics-dev/Getd2g.pl?gene_list={{ this_trait.symbol }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
Genotation
</a>
&nbsp;&nbsp;
{% endif %}
{% if this_trait.geneid != None %}
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" target="_blank" title="Info from NCBI Entrez Gene">
Gene
Expand All @@ -59,41 +61,55 @@
</dl>



<div style="margin-bottom:15px;" class="btn-toolbar">
<div class="btn-group">
<a href="#redirect">
<button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">
<i class="icon-plus-sign icon-white"></i> Add
</button>
<a href="#redirect" onclick="window.open('http://www.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene=Shh&amp;alias=1&amp;species=mouse')">
</a>
{% if this_trait.dataset.type == 'ProbeSet' %}
{% if this_trait.symbol != None %}
<a href="#redirect" onclick="window.open('http://www.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ species_name }}')">
<button type="button" class="btn btn-default" title="Find similar expression data">
<i class="icon-search"></i> Find
</button>
</a>
{% endif %}
{% if UCSC_BLAT_URL != "" %}
<a href="#redirect" onclick="window.open('{{ UCSC_BLAT_URL }}')">
<button type="button" class="btn btn-default" title="Check probe locations at UCSC">
<i class="icon-ok"></i> Verify
</button>
</a>
</div>

<div class="btn-group">

{% endif %}
{% if this_trait.symbol != None %}
<a href="#redirect" onclick="window.open('http://genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}')">
<button type="button" class="btn btn-default" title="Write or review comments about this gene">
<i class="icon-edit"></i> GeneWiki
</button>

</a>
<a href="#redirect" onclick="window.open('http://genenetwork.org/webqtl/main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True&geneName={{ this_trait.symbol }}')">
<button type="button" class="btn btn-default" title="View SNPs and Indels">
<i class="icon-road"></i> SNPs
</button>

</a>
{% endif %}
{% if UTHSC_BLAT_URL != "" %}
<a href="#redirect" onclick="window.open('{{ UTHSC_BLAT_URL }}')">
<button type="button" class="btn btn-default" title="View probes, SNPs, and RNA-seq at UTHSC">
<i class="icon-eye-close"></i> RNA-seq
</button>

</a>
{% endif %}
{% if show_probes == "True" %}
<a href="#redirect" onclick="window.open('http://genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON')">
<button type="button" class="btn btn-default" title="Check sequence of probes">
<i class="icon-list"></i> Probes
</button>

</a>
{% endif %}
{% endif %}
</div>
</div>

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