Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

1 files changed, 255 insertions, 0 deletions

diff --git a/gn2/wqflask/templates/show_trait_details.html b/gn2/wqflask/templates/show_trait_details.html
new file mode 100644
index 00000000..9c12393d
--- /dev/null
+++ b/gn2/wqflask/templates/show_trait_details.html
@@ -0,0 +1,255 @@
+<table class="table">
+    <tr>
+        <td><b>Group</b></td>
+        <td>{{ this_trait.dataset.group.species[0]|upper }}{{ this_trait.dataset.group.species[1:] }}: {{ this_trait.dataset.group.name }} group</td>
+    </tr>
+    {% if this_trait.dataset.type == 'Publish' %}
+    <tr>
+        <td><b>Phenotype</b></td>
+        <td><div>{{ this_trait.description_fmt }}</div></td>
+    </tr>
+    <tr>
+        <td><b>Authors</b></td>
+        <td><div>{{ this_trait.authors }}</div></td>
+    </tr>
+    <tr>
+        <td><b>Title</b></td>
+        <td><div>{{ this_trait.title }}</div></td>
+    </tr>
+    <tr>
+        <td><b>Journal</b></td>
+        <td>{{ this_trait.journal }} ({% if this_trait.pubmed_id %}<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" target="_blank" title="PubMed">{{ this_trait.year }}</a>{% else %}{{ this_trait.year }}{% endif %})</td>
+    </tr>
+    {% elif this_trait.dataset.type == 'ProbeSet' %}
+    <tr>
+        <td><b>Tissue</b></td>
+        <td>{{ this_trait.dataset.tissue }}</td>
+    </tr>
+    {% endif %}
+    {% if this_trait.dataset.type == 'ProbeSet' %}
+    {% if this_trait.symbol != None %}
+    <tr>
+        <td><b>Gene Symbol</b></td>
+        <td>{{ this_trait.symbol }}</td>
+    </tr>
+    {% endif %}
+    <tr>
+        <td><b>Aliases</b></td>
+        <td>Wikidata: {{ this_trait.wikidata_alias_fmt|replace(",",";") }}</td>
+    </tr>
+    {% if this_trait.alias_fmt != "Not Available" %}
+    <tr>
+        <td></td>
+        <td>GeneNetwork: {{ this_trait.alias_fmt|replace(",",";") }}</td>
+    </tr>
+    {% endif %}
+    {% endif %}
+    {% if this_trait.dataset.type != 'Publish' %}
+    <tr>
+        <td><b>Location</b></td>
+        <td>{{ this_trait.location_fmt }}</td>
+    </tr>
+    {% endif %}
+    {% if ncbi_summary != None and ncbi_summary != "" %}
+    <tr>
+        <td><b>Summary</b></td>
+        <td>{{ ncbi_summary }}</td>
+    </tr>
+    {% endif %}
+    <tr>
+        <td><b>Database</b></td>
+        <td>
+            <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}" target="_blank">
+                {{ dataset.fullname }}
+            </a>
+	    <br/>
+	    <a href="{{ url_for('get_dataset', name=dataset.name) }}" target="_blank">
+                GN2 Link: {{ dataset.fullname }}
+            </a>
+        </td>
+    </tr>
+    {% if this_trait.probe_set_specificity %}
+    <tr>
+        <td><b>Target Score</b></td>
+        <td>
+            <a href="http://gn1.genenetwork.org/blatInfo.html" target="_blank" title="Values higher than 2 for the specificity are good">
+                BLAT Specificity
+            </a>: 
+            {{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}
+            &nbsp;&nbsp;
+            {% if this_trait.probe_set_blat_score %}
+            Score: {{ "%0.3f" | format(this_trait.probe_set_blat_score|float) }}
+            {% endif %}
+        </td>
+    </tr>
+    {% endif %}
+    {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %}
+    <tr>
+        <td><b>Resource Links</b></td>
+        <td>
+            {% if pubmed_link %}
+            <a href="{{ pubmed_link }}" target="_blank" title="PubMed">
+                PubMed
+            </a>
+            {% endif %}
+            {% if ncbi_gene_link %}
+            <a href="{{ ncbi_gene_link }}" target="_blank" title="Info from NCBI Entrez Gene">
+                Gene
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if omim_link %}
+            <a href="{{ omim_link }}" target="_blank" title="Summary from On Mendelion Inheritance in Man">
+                OMIM
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if genemania_link %}
+            <a href="{{ genemania_link }}" target="_blank" title="GeneMANIA">
+                GeneMANIA
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if protein_atlas_link %}
+            <a href="{{ protein_atlas_link }}" target="_blank" title="Human Protein Atlas">
+                    Protein Atlas
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if open_targets_link %}
+            <a href="{{ open_targets_link }}" target="_blank" title="Open Targets">
+                Open Targets
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if homologene_link %}
+            <a href="{{ homologene_link }}" target="_blank" title="Find similar genes in other species">
+                HomoloGene
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if this_trait.symbol %}
+            <!--
+            <a href="{{ genotation_link }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
+                Genotation
+            </a>
+            &nbsp;&nbsp;
+            -->
+            {% if rgd_link %}
+            <a href="{{ rgd_link }}" target="_blank">
+                Rat Genome DB
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            <a href="{{ gtex_link }}" target="_blank" title="GTEx Portal">
+                GTEx Portal
+            </a>
+            &nbsp;&nbsp;
+            {% if phenogen_link %}
+            <a href="{{ phenogen_link }}" target="_blank">
+                PhenoGen
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if genebridge_link %}
+            <a href="{{ genebridge_link }}" target="_blank">
+                GeneBridge
+            </a>
+            {% endif %}
+            {% endif %}
+            <br>
+            {% if ucsc_blat_link %}
+            <a href="{{ ucsc_blat_link }}" target="_blank" title="Info from UCSC Genome Browser">
+                UCSC
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if biogps_link %}
+            <a href="{{ biogps_link }}" target="_blank" title="Expression across many tissues and cell types">
+                BioGPS
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if string_link %}
+            <a href="{{ string_link }}" target="_blank" title="Protein interactions: known and inferred">
+                STRING
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if panther_link %}
+            <a href="{{ panther_link }}" target="_blank" title="Gene and protein data resources from Celera-ABI">
+                PANTHER
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if gemma_link %}
+            <a href="{{ gemma_link }}" target="_blank" title="Meta-analysis of gene expression data">
+                Gemma
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if aba_link %}
+            <a href="{{ aba_link }}" target="_blank" title="Allen Brain Atlas">
+                ABA
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if ebi_gwas_link %}
+            <a href="{{ ebi_gwas_link }}" target="_blank" title="EBI GWAS">
+                EBI GWAS
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if wiki_pi_link %}
+            <a href="{{ wiki_pi_link }}" target="_blank" title="Wiki-Pi">
+                Wiki-Pi
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if uniprot_link %}
+            <a href="{{ uniprot_link }}" target="_blank" title="UniProt">
+                UniProt
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+        </td>
+    </tr>
+    {% endif %}
+</table>
+
+<div class="btn-toolbar">
+    <div class="btn-group">
+        <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
+        {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
+        {% if this_trait.symbol != None %}
+        <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}', '_blank')">Find</button>
+        {% endif %}
+        {% if UCSC_BLAT_URL != "" %}
+        <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button>
+        {% endif %}
+        {% if this_trait.symbol != None %}
+	<button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">(GN1) GeneWiki</button>
+        {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
+        <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
+        {% endif %}
+        {% endif %}
+        {% if show_probes == "True" %}
+        <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.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', '_blank')">Probes</button>
+        {% endif %}
+        {% endif %}
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
+        {% if this_trait.dataset.type == 'Publish' %}
+        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/datasets/{{ this_trait.dataset.group.id }}/traits/{{ this_trait.name }}?resource-id={{ resource_id }}&dataset_name={{this_trait.dataset.name}}', '_blank')">Edit</button>
+        {% endif %}
+
+        {% if this_trait.dataset.type == 'ProbeSet' %}
+        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/datasets/traits/{{ this_trait.name }}?resource-id={{ resource_id }}&dataset_name={{this_trait.dataset.name}}', '_blank')">Edit</button>
+        {% endif %}
+    </div>
+    {%if "group:resource:edit-resource" in trait_privileges%}
+    <div class="btn-group">
+        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Privileges" onclick="window.open('{{url_for('oauth2.resource.view_resource', resource_id=resource_id)}}', '_blank')">Edit Privileges</button>
+    </div>
+    {% endif %}
+</div>
+