Changed global gene search to no longer use server-side processing

4 files changed, 123 insertions, 215 deletions

diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 4f9dc316..4cd3874c 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,94 +1,94 @@
 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
+from base.data_set import create_dataset
+from base.trait import GeneralTrait
+from dbFunction import webqtlDatabaseFunction
 
-#from utility.benchmark import Bench
+from utility.benchmark import Bench
 
 class GSearch(object):
 
     def __init__(self, kw):
         self.type = kw['type']
         self.terms = kw['terms']
-        # if self.type == "gene":
-            # sql = """
-                # SELECT
-                # Species.`Name` AS species_name,
-                # InbredSet.`Name` AS inbredset_name,
-                # Tissue.`Name` AS tissue_name,
-                # ProbeSetFreeze.Name AS probesetfreeze_name,
-                # ProbeSet.Name AS probeset_name,
-                # ProbeSet.Symbol AS probeset_symbol,
-                # ProbeSet.`description` AS probeset_description,
-                # ProbeSet.Chr AS chr,
-                # ProbeSet.Mb AS mb,
-                # ProbeSetXRef.Mean AS mean,
-                # ProbeSetXRef.LRS AS lrs,
-                # ProbeSetXRef.`Locus` AS locus,
-                # ProbeSetXRef.`pValue` AS pvalue,
-                # ProbeSetXRef.`additive` AS additive
-                # FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
-                # WHERE InbredSet.`SpeciesId`=Species.`Id`
-                # AND ProbeFreeze.InbredSetId=InbredSet.`Id`
-                # AND ProbeFreeze.`TissueId`=Tissue.`Id`
-                # AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
-                # AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
-                # AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
-                # AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
-                # AND ProbeSetFreeze.public > 0
-                # ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
-                # LIMIT 6000
-                # """ % (self.terms)
-            # with Bench("Running query"):
-                # re = g.db.execute(sql).fetchall()
-            # self.trait_list = []
-            # with Bench("Creating trait objects"):
-                # for line in re:
-                    # dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
-                    # trait_id = line[4]
-                    # with Bench("Building trait object"):
-                    # this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
-                    # self.trait_list.append(this_trait)
+        if self.type == "gene":
+            sql = """
+                SELECT
+                Species.`Name` AS species_name,
+                InbredSet.`Name` AS inbredset_name,
+                Tissue.`Name` AS tissue_name,
+                ProbeSetFreeze.Name AS probesetfreeze_name,
+                ProbeSet.Name AS probeset_name,
+                ProbeSet.Symbol AS probeset_symbol,
+                ProbeSet.`description` AS probeset_description,
+                ProbeSet.Chr AS chr,
+                ProbeSet.Mb AS mb,
+                ProbeSetXRef.Mean AS mean,
+                ProbeSetXRef.LRS AS lrs,
+                ProbeSetXRef.`Locus` AS locus,
+                ProbeSetXRef.`pValue` AS pvalue,
+                ProbeSetXRef.`additive` AS additive
+                FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
+                WHERE InbredSet.`SpeciesId`=Species.`Id`
+                AND ProbeFreeze.InbredSetId=InbredSet.`Id`
+                AND ProbeFreeze.`TissueId`=Tissue.`Id`
+                AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
+                AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
+                AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
+                AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
+                AND ProbeSetFreeze.public > 0
+                ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
+                LIMIT 6000
+                """ % (self.terms)
+            with Bench("Running query"):
+                re = g.db.execute(sql).fetchall()
+            self.trait_list = []
+            with Bench("Creating trait objects"):
+                for line in re:
+                    dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
+                    trait_id = line[4]
+                    #with Bench("Building trait object"):
+                    this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                    self.trait_list.append(this_trait)
 
-        # elif self.type == "phenotype":
-            # sql = """
-                # SELECT
-                # Species.`Name`,
-                # InbredSet.`Name`,
-                # PublishFreeze.`Name`,
-                # PublishXRef.`Id`,
-                # Phenotype.`Post_publication_description`,
-                # Publication.`Authors`,
-                # Publication.`Year`,
-                # PublishXRef.`LRS`,
-                # PublishXRef.`Locus`,
-                # PublishXRef.`additive`
-                # 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`
-                # AND	  (Phenotype.Post_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Phenotype.Pre_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Phenotype.Lab_code REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Publication.PubMed_ID REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Publication.Abstract REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" 
-                    # OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]")
-                # ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
-                # LIMIT 6000
-                # """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
-            # re = g.db.execute(sql).fetchall()
-            # self.trait_list = []
-            # with Bench("Creating trait objects"):
-                # 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, get_sample_info=False)
-                    # self.trait_list.append(this_trait)
+        elif self.type == "phenotype":
+            sql = """
+                SELECT
+                Species.`Name`,
+                InbredSet.`Name`,
+                PublishFreeze.`Name`,
+                PublishXRef.`Id`,
+                Phenotype.`Post_publication_description`,
+                Publication.`Authors`,
+                Publication.`Year`,
+                PublishXRef.`LRS`,
+                PublishXRef.`Locus`,
+                PublishXRef.`additive`
+                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`
+                AND	  (Phenotype.Post_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Pre_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Lab_code REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.PubMed_ID REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.Abstract REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]")
+                ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
+                LIMIT 6000
+                """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
+            re = g.db.execute(sql).fetchall()
+            self.trait_list = []
+            with Bench("Creating trait objects"):
+                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, get_sample_info=False)
+                    self.trait_list.append(this_trait)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 9941a4d3..8a0485b3 100755..100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -63,40 +63,29 @@ class SearchResultPage(object):
         #    self.dataset_group_ids = map(lambda x: x[2], results)
         #else:
 
-        self.quick = False
-
         self.uc_id = uuid.uuid4()
         print("uc_id:", self.uc_id)
 
-        if 'q' in kw:
-            self.results = {}
-            self.quick = True
-            self.search_terms = kw['q']
-            print("self.search_terms is: ", self.search_terms)
-            self.trait_type = kw['trait_type']
-            self.quick_search()
+        print("kw is:", kw)
+        if kw['search_terms_or']:
+            self.and_or = "or"
+            self.search_terms = kw['search_terms_or']
         else:
-            print("kw is:", kw)
-            if kw['search_terms_or']:
-                self.and_or = "or"
-                self.search_terms = kw['search_terms_or']
-            else:
-                self.and_or = "and"
-                self.search_terms = kw['search_terms_and']
-            self.search_term_exists = True
-            self.results = []
-            if kw['type'] == "Phenotypes":
-                dataset_type = "Publish"
-            elif kw['type'] == "Genotypes":
-                dataset_type = "Geno"
-            else:
-                dataset_type = "ProbeSet"
-            self.dataset = create_dataset(kw['dataset'], dataset_type)
-            print("KEYWORD:", self.search_terms)
-            self.search()
-            if self.search_term_exists:
-                self.gen_search_result()
-
+            self.and_or = "and"
+            self.search_terms = kw['search_terms_and']
+        self.search_term_exists = True
+        self.results = []
+        if kw['type'] == "Phenotypes":
+            dataset_type = "Publish"
+        elif kw['type'] == "Genotypes":
+            dataset_type = "Geno"
+        else:
+            dataset_type = "ProbeSet"
+        self.dataset = create_dataset(kw['dataset'], dataset_type)
+        print("KEYWORD:", self.search_terms)
+        self.search()
+        if self.search_term_exists:
+            self.gen_search_result()
 
 
     def gen_search_result(self):
@@ -124,56 +113,6 @@ class SearchResultPage(object):
             self.trait_list.append(this_trait)
 
         self.dataset.get_trait_info(self.trait_list, species)
-
-    def quick_search(self):
-        #search_terms = ""
-        #for term in self.search_terms.split():
-        #    search_terms += '+{} '.format(term)
-            
-        search_terms = ' '.join('+{}'.format(escape(term)) for term in self.search_terms.split())
-        print("search_terms are:", search_terms)
-        
-        query = """ SELECT table_name, the_key, result_fields
-                    FROM QuickSearch
-                    WHERE MATCH (terms)
-                          AGAINST ('{}' IN BOOLEAN MODE) """.format(search_terms)
-        
-        with Bench("Doing QuickSearch Query: "):
-            dbresults = g.db.execute(query, no_parameters=True).fetchall()
-        #print("results: ", pf(results))
-        
-        self.results = collections.defaultdict(list)
-        
-        type_dict = {'PublishXRef': 'phenotype',
-                   'ProbeSetXRef': 'mrna_assay',
-                   'GenoXRef': 'genotype'}
-        
-        self.species_groups = {}
-        
-        for dbresult in dbresults:
-            this_result = {}
-            this_result['table_name'] = dbresult.table_name
-            if self.trait_type == type_dict[dbresult.table_name] or self.trait_type == 'all':
-                this_result['key'] = dbresult.the_key
-                this_result['result_fields'] = json.loads(dbresult.result_fields)
-                this_species = this_result['result_fields']['species']
-                this_group = this_result['result_fields']['group_name']
-                if this_species not in self.species_groups:
-                    self.species_groups[this_species] = {}
-                if type_dict[dbresult.table_name] not in self.species_groups[this_species]:
-                    self.species_groups[this_species][type_dict[dbresult.table_name]] = []
-                if this_group not in self.species_groups[this_species][type_dict[dbresult.table_name]]:
-                    self.species_groups[this_species][type_dict[dbresult.table_name]].append(this_group)
-                #if type_dict[dbresult.table_name] not in self.species_groups:
-                #    self.species_groups[type_dict[dbresult.table_name]] = {}
-                #if this_species not in self.species_groups[type_dict[dbresult.table_name]]:
-                #    self.species_groups[type_dict[dbresult.table_name]][this_species] = []
-                #if this_group not in self.species_groups[type_dict[dbresult.table_name]][this_species]:
-                #    self.species_groups[type_dict[dbresult.table_name]][this_species].append(this_group)
-                self.results[type_dict[dbresult.table_name]].append(this_result)
-            
-        import redis
-        Redis = redis.Redis()
         
     #def get_group_species_tree(self):
     #    self.species_groups = collections.default_dict(list)
@@ -183,43 +122,6 @@ class SearchResultPage(object):
     #                                        item['result_fields']['group_name'])
 
 
-    #def quick_search(self):
-    #    self.search_terms = parser.parse(self.search_terms)
-    #
-    #    search_types = ["quick_mrna_assay", "quick_phenotype"]
-    #
-    #    for search_category in search_types:
-    #        these_results = []
-    #        search_ob = do_search.DoSearch.get_search(search_category)
-    #        search_class = getattr(do_search, search_ob)
-    #        for a_search in self.search_terms:
-    #            search_term = a_search['search_term']
-    #            the_search = search_class(search_term)
-    #            these_results.extend(the_search.run())
-    #            print("in the search results are:", self.results)
-    #        self.results[search_category] = these_results
-    #
-    #    #for a_search in self.search_terms:
-    #    #    search_term = a_search['search_term']
-    #    #
-    #    #    #Do mRNA assay search
-    #    #    search_ob = do_search.DoSearch.get_search("quick_mrna_assay")
-    #    #    search_class = getattr(do_search, search_ob)
-    #    #    the_search = search_class(search_term)
-    #    #    
-    #    #    self.results.extend(the_search.run())
-    #    #    print("in the search results are:", self.results)
-    #
-    #
-    #    #return True
-    #
-    #    #search_gene
-    #    #search_geno
-    #    #search_pheno
-    #    #search_mrn
-    #    #search_publish
-
-
     def search(self):
         self.search_terms = parser.parse(self.search_terms)
         print("After parsing:", self.search_terms)
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 92b0b411..37e26817 100755
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -43,6 +43,25 @@
                     <th>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 trait_list %}
+                  <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
+                    <td><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td>
+                    <td>{{ loop.index }}</td>
+                    <td>{{ this_trait.dataset.group.species }}</td>
+                    <td>{{ this_trait.dataset.group.name }}</td>
+                    <td>{{ this_trait.dataset.tissue }}</td>
+                    <td>{{ this_trait.dataset.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.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>
+                    <td>{{ this_trait.additive }}</td>
+                  </tr>
+                  {% endfor %}
               </table>
             </div>
         </div>
@@ -135,18 +154,7 @@
 
             console.time("Creating table");
             $('#trait_table').DataTable( {
-                "processing": true,
-                "serverSide": true,
                 "paging": false,
-                "ajax": {
-                    "url": "/gsearch_updating?terms={{ terms }}&type={{ type }}",
-                    "type": "POST",
-                    "dataType": "json",
-                    "contentType": "application/json; charset=utf-8",
-                    "data": function ( args ) {
-                         return { "args": JSON.stringify( args ) };
-                    }
-                },
                 "buttons": [
                     {
                        extend: 'csvHtml5',
@@ -174,7 +182,7 @@
                     { "data": "max_lrs_location", "orderable" : true },
                     { "data": "additive_effect", "orderable" : true }
                 ],
-                "sDom": "Bfrti",
+                "sDom": "RZBtir",
                 "autoWidth": false,
                 "scrollY": "800px",
                 "bDeferRender": true
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7854b0df..b7fcfa1d 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -155,9 +155,7 @@ def search_page():
             Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
             Redis.expire(key, 60*60)
 
-        if result['quick']:
-            return render_template("quick_search.html", **result)
-        elif result['search_term_exists']:
+        if result['search_term_exists']:
             return render_template("search_result_page.html", **result)
         else:
             return render_template("search_error.html")