diff options
| -rwxr-xr-x | wqflask/secure_server.py | 3 | ||||
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 10 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 59 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_details.html | 36 |
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> + {% 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&gene=Shh&alias=1&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&gene={{ this_trait.symbol }}&alias=1&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> + |