Created template for quick search page

Fixed a couple bugs with quick_search_table.py

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 %}