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authorzsloan2015-06-16 22:29:22 +0000
committerzsloan2015-06-16 22:29:22 +0000
commitf792574e8e07e684ec7501d7be7f4d2736a3b1cc (patch)
treea37dff06261f2f8de07723a111d88ab20dcdb0b8
parent29b51444acbc6fa7c839bb588d7985c79364dc3d (diff)
downloadgenenetwork2-f792574e8e07e684ec7501d7be7f4d2736a3b1cc.tar.gz
Finished adding all the extra tools/links below the trait details
-rwxr-xr-xwqflask/secure_server.py3
-rwxr-xr-xwqflask/wqflask/do_search.py10
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py59
-rwxr-xr-xwqflask/wqflask/templates/show_trait_details.html36
4 files changed, 64 insertions, 44 deletions
diff --git a/wqflask/secure_server.py b/wqflask/secure_server.py
index 975c97c0..fc258578 100755
--- a/wqflask/secure_server.py
+++ b/wqflask/secure_server.py
@@ -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,
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index ee85efb2..a42503c1 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -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)
@@ -456,9 +459,9 @@ class RifSearch(MrnaAssaySearch):
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)
@@ -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
@@ -478,9 +484,9 @@ class WikiSearch(MrnaAssaySearch):
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)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index adb12b7b..bd827086 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -225,7 +225,7 @@ class ShowTrait(object):
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")
@@ -299,7 +299,7 @@ class ShowTrait(object):
#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]
@@ -322,8 +322,8 @@ class ShowTrait(object):
#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"
@@ -377,18 +377,18 @@ class ShowTrait(object):
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)
@@ -396,7 +396,7 @@ class ShowTrait(object):
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;")
@@ -416,6 +416,7 @@ class ShowTrait(object):
#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)
@@ -423,7 +424,7 @@ class ShowTrait(object):
#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
@@ -462,14 +463,14 @@ class ShowTrait(object):
#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:
@@ -484,10 +485,10 @@ class ShowTrait(object):
# 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",\
@@ -497,13 +498,13 @@ class ShowTrait(object):
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"
@@ -519,7 +520,7 @@ class ShowTrait(object):
# 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", \
@@ -528,19 +529,19 @@ class ShowTrait(object):
# 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", \
@@ -643,13 +644,13 @@ class ShowTrait(object):
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:
@@ -895,7 +896,7 @@ class ShowTrait(object):
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':
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index c938c683..108fcd92 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -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
@@ -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>
+