diff options
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 21 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_gene.html | 15 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 1 | ||||
| -rw-r--r-- | 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 @@ <a href="/" style="font-weight: bold;">GeneNetwork</a> </li> <li class=""> - <a href="/intro">Intro</a> + <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Intro <span class="caret"></a> + <ul class="dropdown-menu"> + <li><a href="/intro">Intro</a></li> + <li><a href="/submit_trait">Submit Trait</a></li> + <li><a href="http://genenetwork.org/webqtl/main.py?FormID=batSubmit">Batch Submission</a></li> + </ul> </li> <li class=""> <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Info <span class="caret"></a> @@ -56,7 +61,13 @@ </ul> </li> <li class=""> - <a href="/submit_trait">Submit Data</a> + <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Tools <span class="caret"></a> + <ul class="dropdown-menu"> + <li><a href="/snp_browser">Variant Browser</a></li> + <li><a href="http://bnw.genenetwork.org/BNW/sourcecodes/home.php">Bayesian Network Webserver</a></li> + <li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li> + <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li> + </ul> </li> <li class=""> <a href="/collections/list">Collections @@ -68,9 +79,6 @@ </a> </li> <li class=""> - <a href="/snp_browser">SNP Browser</a> - </li> - <li class=""> {% if g.user_session.logged_in %} <a id="login_out" title="Signed in as {{ g.user_session.user_name }}" href="/n/logout">Sign out</a> {% else %} @@ -82,9 +90,6 @@ <a href="http://gn2-staging.genenetwork.org" style="font-weight: bold;" >Use Staging Branch</a> </li> --> - <li style="margin-left: 20px;"> - <a href="http://www.genenetwork.org" style="font-weight: bold;" >Use GN1</a> - </li> </ul> </div> </div> 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<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Max<br>LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", 'type': "natural", 'data': "LRS_score_repr", 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS Location", - 'type': "natural", + 'title': "Max LRS<br>Location", + 'type': "natural", + 'width': "100px", 'data': "max_lrs_text" }, { - 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", - 'type': "natural", + 'title': "Additive<br>Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + '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 @@ <li><a href="http://ucscbrowser.genenetwork.org/">Genome browser</a> at UTHSC</li> <li><a href="https://systems-genetics.org/">Systems Genetics</a> @ EPFL</li> <li>UTHSC <a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a></li> + <li><a href="http://genenetwork.org">GeneNetwork 1</a></li> </ul> </div> </section> 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 @@ </a> {% endif %} - {% if unigene_link %} - <a href="{{ unigene_link }}" target="_blank" title="NCBI UniGene"> - UniGene + {% if protein_atlas_link %} + <a href="{{ protein_atlas_link }}" target="_blank" title="Human Protein Atlas"> + Protein Atlas </a> {% endif %} - {% if genbank_link %} - <a href="{{ genbank_link }}" target="_blank" title="Find the original GenBank sequence used to design the probes"> - GenBank + {% if open_targets_link %} + <a href="{{ open_targets_link }}" target="_blank" title="Open Targets"> + Open Targets </a> {% endif %} @@ -219,6 +219,9 @@ </a> {% endif %} {% endif %} + <a target="_blank" href="http://www.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}"> + <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button> + </a> </div> </div> |