diff options
| -rw-r--r-- | wqflask/maintenance/quick_search_table.py | 64 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/quick_search.html | 215 |
3 files changed, 256 insertions, 30 deletions
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py index a6ca6265..75bc7d00 100644 --- a/wqflask/maintenance/quick_search_table.py +++ b/wqflask/maintenance/quick_search_table.py @@ -24,6 +24,8 @@ from sqlalchemy.orm import scoped_session, sessionmaker, relationship, backref from sqlalchemy.orm.exc import NoResultFound from sqlalchemy.ext.declarative import declarative_base +from pprint import pformat as pf + import zach_settings as settings Engine = sa.create_engine(settings.SQLALCHEMY_DATABASE_URI, @@ -124,6 +126,7 @@ class PublishXRef(Base): "description", "lrs", "publication_id", + "pubmed_id", "year", "authors" ).from_statement( @@ -133,6 +136,7 @@ class PublishXRef(Base): "Phenotype.Original_description as description, " "PublishXRef.LRS as lrs, " "PublishXRef.PublicationId as publication_id, " + "Publication.PubMed_ID" "Publication.Year as year, " "Publication.Authors as authors " "FROM PublishXRef, " @@ -173,7 +177,7 @@ class PublishXRef(Base): return json_results class GenoXRef(Base): - __tablename__ = 'ProbeSetXRef' + __tablename__ = 'GenoXRef' GenoFreezeId = sa.Column(sa.Integer, primary_key=True) GenoId = sa.Column(sa.Integer, primary_key=True) @@ -191,14 +195,16 @@ class GenoXRef(Base): values['the_key'] = json.dumps([item.GenoId, item.GenoFreezeId]) values['terms'] = cls.get_unique_terms(item.GenoId) print("terms is:", values['terms']) - values['result_fields'] = cls.get_result_fields(item.GenoId, item.GenoFreezeId) - ins = QuickSearch.insert().values(**values) - conn.execute(ins) + if values['terms']: + values['result_fields'] = cls.get_result_fields(item.GenoId, item.GenoFreezeId) + ins = QuickSearch.insert().values(**values) + conn.execute(ins) counter += 1 print("Done:", counter) @staticmethod def get_unique_terms(geno_id): + print("geno_id: ", geno_id) results = Session.query( "name", "marker_name" @@ -208,23 +214,26 @@ class GenoXRef(Base): "FROM Geno " "WHERE Geno.Id = :geno_id ").params(geno_id=geno_id).all() + print("results: ", pf(results)) + unique = set() - for item in results[0]: - #print("locals:", locals()) - if not item: - continue - for token in item.split(): - if len(token) > 2: - try: - # This hopefully ensures that the token is utf-8 - token = token.encode('utf-8') - print(" ->", token) - except UnicodeDecodeError: - print("\n-- UDE \n") - # Can't get it into utf-8, we won't use it - continue - - unique.add(token) + if len(results): + for item in results[0]: + #print("locals:", locals()) + if not item: + continue + for token in item.split(): + if len(token) > 2: + try: + # This hopefully ensures that the token is utf-8 + token = token.encode('utf-8') + print(" ->", token) + except UnicodeDecodeError: + print("\n-- UDE \n") + # Can't get it into utf-8, we won't use it + continue + + unique.add(token) print("\nUnique terms are: {}\n".format(unique)) return " ".join(unique) @@ -233,18 +242,13 @@ class GenoXRef(Base): def get_result_fields(geno_id, dataset_id): results = Session.query( "name", - "species", + "marker_name", "group_name", + "species", "dataset", "dataset_name", - "symbol", - "description", "chr", "mb", - "lrs", - "genbank_id", - "gene_id", - "chip_id", - "chip_name" + "source" ).from_statement( "SELECT Geno.Name as name, " "Geno.Marker_Name as marker_name, " @@ -374,7 +378,7 @@ class ProbeSetXRef(Base): "symbol", "description", "chr", "mb", - "lrs", + "lrs", "mean", "genbank_id", "gene_id", "chip_id", @@ -390,6 +394,7 @@ class ProbeSetXRef(Base): "ProbeSet.Chr as chr, " "ProbeSet.Mb as mb, " "ProbeSetXRef.LRS as lrs, " + "ProbeSetXRef.mean as mean, " "ProbeSet.GenbankId as genbank_id, " "ProbeSet.GeneId as gene_id, " "ProbeSet.ChipId as chip_id, " @@ -463,6 +468,7 @@ def page_query(q): def main(): + GenoXRef.run() ProbeSetXRef.run() PublishXRef.run() diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 499782ac..dc872a8b 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -39,8 +39,13 @@ from utility import formatting #from base.JinjaPage import JinjaEnv, JinjaPage +#class QuickSearchResult(object): + #def __init__(self, key, result_fields): + # self.key = key + # self.result_fields = result_fields + -class SearchResultPage(): +class SearchResultPage(object): #maxReturn = 3000 diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html new file mode 100644 index 00000000..d50b4937 --- /dev/null +++ b/wqflask/wqflask/templates/quick_search.html @@ -0,0 +1,215 @@ +{% extends "base.html" %} +{% block title %}QuickSearch Results{% endblock %} +{% block content %} +<!-- Start of body --> + <header class="jumbotron subhead" id="overview"> + <div class="container"> + <h1>QuickSearch Results</h1> + <p class="lead"> + GeneNetwork found {{ numify(results|count, "record", "records") }}. + </p> + </div> + </header> + + <div class="container"> + <div class="page-header"> + <h1>Your Search</h1> + </div> + + <p>We across all data sets to find all records that match:</p> + + <ul> + {% if search_terms %} + <li> + {% for word in search_terms %} + <strong>{{word}}</strong> {% if not loop.last %} or {% endif %} + {% endfor %} + </li> + {% endif %} + </ul> + + <p>To study a record, click on its ID below.<br /> + Check records below and click Add button to add to selection.</p> + + <div class="tabbable"> <!-- Only required for left/right tabs --> + <ul class="nav nav-tabs"> + <li class="active"> <a href="#tab1" data-toggle="tab">Phenotype</a></li> + <li> <a href="#tab2" data-toggle="tab">mRNA Assay</a></li> + <li> <a href="#tab3" data-toggle="tab">Genotype</a></li> + </ul> + <div class="tab-content"> + <div class="tab-pane active" id="tab1"> + <table class="table table-hover"> + <thead> + <tr> + <!-- {% for key, _value in results.phenotype[0].result_fields.items() %} + <th>{{key}}</th> + {% endfor %}--> + <th>Id</th> + <th>Species</th> + <th>Group</th> + <th>Description</th> + <th>LRS</th> + <th>Year</th> + <th>Authors</th> + </tr> + </thead> + <tbody> + {% for result in results.phenotype %} + <tr> + {% for result in result.result_fields.items() %} + <td>{{ result['phenotype_id'] }}</td> + <td>{{ result['species'] }}</td> + <td>{{ result['group_name'] }}</td> + <td>{{ result['description'] }}</td> + <td>{{ result['lrs'] }}</td> + <td> + <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result['pubmed_id'] }}&dopt=Abstract"> + {{ result['year'] }} + </a> + </td> + <td>{{ result['authors'] }}</td> + {% endfor %} + </tr> + {% endfor %} + </tbody> + </table> + </div> + <div class="tab-pane" id="tab2"> + <table class="table table-hover"> + <thead> + <tr> + <th>Record ID</th> + <th>Species</th> + <th>Group</th> + <th>Data Set</th> + <th>Symbol</th> + <th>Description</th> + <th>Location</th> + <th>Mean Expr</th> + <th>Max LRS</th> + </tr> + </thead> + <tbody> + {% for result in results.mrna_assay %} + <tr> + {% for result in result.result_fields.items() %} + <td> + <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result['name'] }}&dataset={{ result['dataset'] }}" + {{ result['name'] }} + </a> + </td> + <td>{{ result['species'] }}</td> + <td>{{ result['group_name'] }}</td> + <td>{{ result['dataset_name'] }}</td> + <td>{{ result['symbol'] }}</td> + <td>{{ result['description'] }}</td> + <td>{{ result['chr'] }} : {{ result['mb'] }}</td> + <td>{{ result['mean'] }}</td> + <td>{{ result['lrs'] }}</td> + {% endfor %} + </tr> + {% endfor %} + </tbody> + </table> + </div> + <div class="tab-pane" id="tab3"> + <table class="table table-hover"> + <thead> + <tr> + <th>Marker</th> + <th>Species</th> + <th>Group</th> + <th>Data Set</th> + <th>Location</th> + </tr> + </thead> + <tbody> + {% for result in results.mrna_assay %} + <tr> + {% for result in result.result_fields.items() %} + <td> + <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result['marker_name'] }}&dataset={{ result['dataset'] }}"> + {{ result['marker_name'] }} + </a> + </td> + <td>{{ result['species'] }}</td> + <td>{{ result['group_name'] }}</td> + <td>{{ result['dataset_name'] }}</td> + <td>{{ result['chr'] }} : {{ result['mb'] }}</td> + {% endfor %} + </tr> + {% endfor %} + </tbody> + </table> + </div> + </div> + </div> + + + + <!--<div class="bs-docs-example"> + <table class="table table-hover"> + <thead> + <tr> + {% for header in header_fields %} + <th>{{header}}</th> + {% endfor %} + </tr> + </thead> + + <tbody> + {% for this_trait in trait_list %} + <TR id="{{ this_trait }}"> + <TD> + <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox" + VALUE="{{ this_trait }}"> + </TD> + <TD> + <a href="{{ url_for('show_trait_page', + trait_id = this_trait.name, + dataset = dataset.name + )}}"> + {{ this_trait.name }} + </a> + </TD> + {% if dataset.type == 'ProbeSet' %} + <TD>{{ this_trait.symbol }}</TD> + <TD>{{ this_trait.description_display }}</TD> + <TD>{{ this_trait.location_repr }}</TD> + <TD>{{ this_trait.mean }}</TD> + <TD>{{ this_trait.LRS_score_repr }}</TD> + <TD>{{ this_trait.LRS_location_repr }}</TD> + {% elif dataset.type == 'Publish' %} + <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> + {% elif dataset.type == 'Geno' %} + <TD>{{ this_trait.location_repr }}</TD> + {% endif %} + </TR> + {% endfor %} + </tbody> + + </table> + + <br /> + + <button class="btn"><i class="icon-ok"></i> Select</button> + <button class="btn"><i class="icon-remove"></i> Deselect</button> + <button class="btn"><i class="icon-resize-vertical"></i> Invert</button> + <button class="btn"><i class="icon-plus-sign"></i> Add</button> + <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button> + </div>--> + + </div> + +<!-- End of body --> + +{% endblock %} |