From 9c8de54a30dc841dcabc43ef433102468746e285 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 22 Aug 2019 12:36:20 -0500 Subject: Changed header drop-down menu layout Added a couple new third party links Added link to GN1 trait page in trait pages Fixed gene global search table appearance --- wqflask/base/webqtlConfig.py | 2 ++ wqflask/wqflask/show_trait/show_trait.py | 7 ++++--- wqflask/wqflask/templates/base.html | 21 +++++++++++++-------- wqflask/wqflask/templates/gsearch_gene.html | 15 +++++++++------ wqflask/wqflask/templates/index_page_orig.html | 1 + wqflask/wqflask/templates/show_trait_details.html | 15 +++++++++------ 6 files changed, 38 insertions(+), 23 deletions(-) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index b9e6abd8..0b884815 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -54,6 +54,8 @@ EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s" WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s" ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s" DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s' +PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s" +OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s" # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 02c65d47..880a291f 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -255,7 +255,6 @@ class ShowTrait(object): self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if check_if_attr_exists(self.this_trait, 'pubmed_id') else None self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if check_if_attr_exists(self.this_trait, 'geneid') else None self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if check_if_attr_exists(self.this_trait, 'omim') else None - self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if check_if_attr_exists(self.this_trait, 'unigeneid') else None self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if check_if_attr_exists(self.this_trait, 'homologeneid') else None self.genbank_link = None @@ -265,14 +264,16 @@ class ShowTrait(object): genbank_id = genbank_id[0:-1] 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 = self.genemania_link = None + self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None + self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = self.ensembl_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 self.string_link = webqtlConfig.STRING_URL % self.this_trait.symbol self.panther_link = webqtlConfig.PANTHER_URL % self.this_trait.symbol self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol + self.protein_atlas_link = webqtlConfig.PROTEIN_ATLAS_URL % self.this_trait.symbol + self.open_targets_link = webqtlConfig.OPEN_TARGETS_URL % self.this_trait.symbol if self.dataset.group.species == "mouse" or self.dataset.group.species == "human": if self.dataset.group.species == "mouse": diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 2366bdec..f9bc1055 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -41,7 +41,12 @@ GeneNetwork
  • - Intro + +
  • @@ -56,7 +61,13 @@
  • - Submit Data + +
  • Collections @@ -67,9 +78,6 @@ {% endif %}
    • -
  • - SNP Browser -
  • {% if g.user_session.logged_in %} Sign out @@ -82,9 +90,6 @@ Use Staging Branch
    • --> -
  • - Use GN1 -
    • diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 0ee98972..1a4ff752 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -202,7 +202,8 @@ }, { 'title': "Location", - 'type': "natural", + 'type': "natural", + 'width': "100px", 'data': "location_repr" }, { @@ -212,19 +213,21 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS?", + 'title': "Max
    LRS?", 'type': "natural", 'data': "LRS_score_repr", 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS Location", - 'type': "natural", + 'title': "Max LRS
    Location", + 'type': "natural", + 'width': "100px", 'data': "max_lrs_text" }, { - 'title': "Additive Effect?", - 'type': "natural", + 'title': "Additive
    Effect?", + 'type': "natural", + 'width': "50px", 'data': "additive", 'orderSequence': [ "desc", "asc"] } diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index bdf51bf8..5706c870 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -191,6 +191,7 @@
  • Genome browser at UTHSC
  • Systems Genetics @ EPFL
  • UTHSC Bayesian Network Web Server
    • +
  • GeneNetwork 1
    • diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index bb0b62fe..63a87825 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -100,15 +100,15 @@    {% endif %} - {% if unigene_link %} - - UniGene + {% if protein_atlas_link %} + + Protein Atlas    {% endif %} - {% if genbank_link %} - - GenBank + {% if open_targets_link %} + + Open Targets    {% endif %} @@ -219,6 +219,9 @@ {% endif %} {% endif %} + + + -- cgit v1.2.3