diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_details.html | 6 |
5 files changed, 22 insertions, 7 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index b14cc4b0..a08acb0a 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -43,6 +43,7 @@ HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/homologene/?term=%s" GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s" GTEX_URL = "https://www.gtexportal.org/home/gene/%s" GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s" +GENEMANIA_URL = "https://genemania.org/search/%s/%s" UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s" STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s" @@ -87,4 +88,3 @@ if not valid_path(JSON_GENODIR): PORTADDR = "http://50.16.251.170" INFOPAGEHREF = '/dbdoc/%s.html' CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' -SCRIPTFILE = 'main.py' diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 66d3a448..e10b31c0 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -257,7 +257,7 @@ class ShowTrait(object): self.genbank_link = webqtlConfig.GENBANK_ID % genbank_id self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = None - self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = None + self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = None if self.this_trait.symbol: self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol self.gtex_link = webqtlConfig.GTEX_URL % self.this_trait.symbol @@ -266,7 +266,10 @@ class ShowTrait(object): self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol if self.dataset.group.species == "mouse" or self.dataset.group.species == "human": - self.genebridge_link = webqtlConfig.GENEBRIDGE_URL % (self.this_trait.symbol, self.dataset.group.species) + if self.dataset.group.species == "mouse": + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("mus-musculus", self.this_trait.symbol) + else: + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("homo-sapiens", self.this_trait.symbol) if self.dataset.group.species == "mouse": self.aba_link = webqtlConfig.ABA_URL % self.this_trait.symbol @@ -282,8 +285,10 @@ class ShowTrait(object): self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end) if self.dataset.group.species == "rat": + self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol) + query = """SELECT kgID, chromosome, txStart, txEnd - FROM GeneLink_rn33 + FROM GeneList_rn33 WHERE geneSymbol = '{}'""".format(self.this_trait.symbol) kgId, chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 8d22b2a8..7e1001fc 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -84,8 +84,8 @@ <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> - <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete From Collection</button> - <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy Record to Other Collection</button> + <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete Rows</button> + <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy to Other Collection</button> <br /> <br /> <form id="export_form" method="POST" action="/export_traits_csv"> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index e20ea2d3..bf434452 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -324,7 +324,11 @@ 'width': "500px", 'data': null, 'render': function(data, type, row, meta) { - return decodeURIComponent(escape(data.description)) + try { + return decodeURIComponent(escape(data.description)) + } catch { + return escape(data.description) + } } }, { diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 09f36021..43efa314 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -88,6 +88,12 @@ </a> {% endif %} + {% if genemania_link %} + <a href="{{ genemania_link }}" title="GeneMANIA"> + GeneMANIA + </a> + + {% endif %} {% if unigene_link %} <a href="{{ unigene_link }}" title="NCBI UniGene"> UniGene |