diff options
| -rwxr-xr-x | wqflask/wqflask/gsearch.py | 21 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/gsearch_pheno.html | 38 |
2 files changed, 39 insertions, 20 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index dd0815b1..396da4cf 100755 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -1,6 +1,9 @@ from __future__ import absolute_import, print_function, division from flask import Flask, g +from base.data_set import create_dataset +from base.trait import GeneralTrait +from dbFunction import webqtlDatabaseFunction class GSearch(object): @@ -41,6 +44,7 @@ class GSearch(object): SELECT Species.`Name`, InbredSet.`Name`, + PublishFreeze.`Name`, PublishXRef.`Id`, Phenotype.`Post_publication_description`, Publication.`Authors`, @@ -48,8 +52,9 @@ class GSearch(object): PublishXRef.`LRS`, PublishXRef.`Locus`, PublishXRef.`additive` - FROM Species,InbredSet,PublishXRef,Phenotype,Publication + FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication WHERE PublishXRef.`InbredSetId`=InbredSet.`Id` + AND PublishFreeze.`InbredSetId`=InbredSet.`Id` AND InbredSet.`SpeciesId`=Species.`Id` AND PublishXRef.`PhenotypeId`=Phenotype.`Id` AND PublishXRef.`PublicationId`=Publication.`Id` @@ -63,6 +68,16 @@ class GSearch(object): OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]" OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]") - ORDER BY Species.`Name`, InbredSet.`Name`, Phenotype.`Post_publication_description` + ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id` + LIMIT 1000 """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms) - self.results = g.db.execute(sql).fetchall() + re = g.db.execute(sql).fetchall() + self.trait_list = [] + for line in re: + dataset = create_dataset(line[2], "Publish") + trait_id = line[3] + this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True) + self.trait_list.append(this_trait) + species = webqtlDatabaseFunction.retrieve_species(dataset.group.name) + dataset.get_trait_info([this_trait], species) + diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index f6b6efa3..8701673f 100755 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -23,33 +23,37 @@ <button class="btn btn-primary pull-right"><span class="glyphicon glyphicon-download"></span> Download Table</button> <br /> <br /> - <table class="table table-hover table-striped" id="trait_table"> + <table class="table table-hover table-striped" id='trait_table' style="float: left;"> <thead> <tr> - <th>Index</th> + <th>Index</th> <th>Species</th> <th>Group</th> - <th>Record ID</th> - <th>Phenotype</th> - <th>Authors</th> - <th>Year</th> - <th>Max LRS</th> - <th>Locus</th> - <th>Additive</th> + <th>Record</th> + <th>Description</th> + <th>Authors</th> + <th>Year</th> + <th style="text-align: right;">Max <br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th>Max LRS Location</th> + <th style="text-align: right;">Additive<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> </tr> </thead> - <tbody> - {% for this_trait in results %} - <TR> - <td><input type="checkbox">{{ loop.index }}</td> - {% for item in this_trait %} - <TD>{{ item }}</TD> - {% endfor %} + {% for this_trait in trait_list %} + <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}"> + <TD>{{ loop.index }}<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></TD> + <TD>{{ this_trait.dataset.group.species }}</TD> + <TD>{{ this_trait.dataset.group.name }}</TD> + <TD><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></TD> + <TD>{{ this_trait.description_display }}</TD> + <TD>{{ this_trait.authors }}</TD> + <TD><a href="{{ this_trait.pubmed_link }}">{{ this_trait.pubmed_text }}</a></TD> + <TD>{{ this_trait.LRS_score_repr }}</TD> + <TD>{{ this_trait.LRS_location_repr }}</TD> + <TD>{{ '%0.3f' % this_trait.additive|float }}</TD> </TR> {% endfor %} </tbody> - </table> </div> </div> |