diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 71 | ||||
| -rwxr-xr-x | wqflask/wqflask/search_results.py | 7 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/correlation_page.html | 8 |
3 files changed, 53 insertions, 33 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index f966b564..4cd87270 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -128,18 +128,24 @@ class MrnaAssaySearch(DoSearch): 'Additive Effect'] def get_where_clause(self): - where_clause = """(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 = %s - """ % (escape(self.search_term[0]), - escape(str(self.dataset.id))) + + if self.search_term[0] != "*": + match_clause = """(MATCH (ProbeSet.Name, + ProbeSet.description, + ProbeSet.symbol, + alias, + GenbankId, + UniGeneId, + Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE)) and + """ % (escape(self.search_term[0])) + else: + match_clause = "" + + where_clause = (match_clause + + """ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = %s + """ % (escape(str(self.dataset.id)))) return where_clause @@ -235,29 +241,40 @@ class PhenotypeSearch(DoSearch): # This adds a clause to the query that matches the search term # against each field in the search_fields tuple - fields_clause_list = [] + where_clause_list = [] for field in self.search_fields: - fields_clause_list.append('''%s REGEXP "%s"''' % (field, search_term)) - fields_clause = "(%s) " % ' OR '.join(fields_clause_list) + where_clause_list.append('''%s REGEXP "%s"''' % (field, search_term)) + where_clause = "(%s) " % ' OR '.join(where_clause_list) - return fields_clause + return where_clause def compile_final_query(self, from_clause = '', where_clause = ''): """Generates the final query string""" from_clause = self.normalize_spaces(from_clause) - query = (self.base_query + - """%s - WHERE %s - and PublishXRef.InbredSetId = %s - and PublishXRef.PhenotypeId = Phenotype.Id - and PublishXRef.PublicationId = Publication.Id - and PublishFreeze.Id = %s""" % ( - from_clause, - where_clause, - escape(str(self.dataset.group.id)), - escape(str(self.dataset.id)))) + if self.search_term[0] == "*": + query = (self.base_query + + """%s + WHERE PublishXRef.InbredSetId = %s + and PublishXRef.PhenotypeId = Phenotype.Id + and PublishXRef.PublicationId = Publication.Id + and PublishFreeze.Id = %s""" % ( + from_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) + else: + query = (self.base_query + + """%s + WHERE %s + and PublishXRef.InbredSetId = %s + and PublishXRef.PhenotypeId = Phenotype.Id + and PublishXRef.PublicationId = Publication.Id + and PublishFreeze.Id = %s""" % ( + from_clause, + where_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) print("query is:", pf(query)) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 6614520e..2e0299f2 100755 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -249,12 +249,7 @@ class SearchResultPage(object): search_type = {} search_type['dataset_type'] = self.dataset.type if a_search['key']: - search_type['key'] = a_search['key'].upper() - #search_type = a_search['key'].upper() - #else: - # # We fall back to the dataset type as the key to get the right object - # search_type = self.dataset.type - + search_type['key'] = a_search['key'].upper() print("search_type is:", pf(search_type)) search_ob = do_search.DoSearch.get_search(search_type) diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 74919c88..445ad428 100755 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -98,8 +98,16 @@ <td><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td> <td>{{ trait.num_overlap }}</td> <td>{{'%0.3e'|format(trait.sample_p)}}</td> + {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %} + <td>--</td> + {% else %} <td>{{'%0.3f'|format(trait.lit_corr)}}</td> + {% endif %} + {% if trait.tissue_corr == "" or trait.tissue_corr == 0.000 %} + <td>--</td> + {% else %} <td>{{'%0.3f'|format(trait.tissue_corr)}}</td> + {% endif %} <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td> {% elif target_dataset.type == "Publish" %} <td><a href="/show_trait?trait_id={{trait.name}}&dataset={{trait.dataset.name}}">{{ trait.name }}</a></td> |