diff options
| -rw-r--r-- | doc/database.org | 2 | ||||
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 26 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/collect.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 2 |
6 files changed, 29 insertions, 36 deletions
diff --git a/doc/database.org b/doc/database.org index 753179e6..c20e4564 100644 --- a/doc/database.org +++ b/doc/database.org @@ -727,7 +727,7 @@ User selection - retained * Fetching Data -** Menu +** Search What happens at the main search menu can be emulated with curl. diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 5511af06..e99ef7b5 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -92,24 +92,22 @@ class MrnaAssayTissueData(object): def get_symbol_values_pairs(self): id_list = [self.data[symbol].data_id for symbol in self.data] - print("id_list:", id_list) - symbol_values_dict = {} - query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value - FROM TissueProbeSetXRef, TissueProbeSetData - WHERE TissueProbeSetData.Id IN {} and - TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) + if len(id_list) > 0: + query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value + FROM TissueProbeSetXRef, TissueProbeSetData + WHERE TissueProbeSetData.Id IN {} and + TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) - print("TISSUE QUERY:", query) - logger.sql(query) + logger.sql('tissue query',query) - results = g.db.execute(query).fetchall() - for result in results: - if result.Symbol.lower() not in symbol_values_dict: - symbol_values_dict[result.Symbol.lower()] = [result.value] - else: - symbol_values_dict[result.Symbol.lower()].append(result.value) + results = g.db.execute(query).fetchall() + for result in results: + if result.Symbol.lower() not in symbol_values_dict: + symbol_values_dict[result.Symbol.lower()] = [result.value] + else: + symbol_values_dict[result.Symbol.lower()].append(result.value) #for symbol in self.data: # data_id = self.data[symbol].data_id diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index afde3dbe..9566c192 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -82,13 +82,7 @@ class GeneralTrait(object): dataset=self.dataset.name, description=self.description_display, mean=self.mean) - - - def get_info(self): - """For lots of traits just use get_trait_info in dataset instead...that will be way - more efficient""" - self.dataset.get_trait_info([self], - webqtlDatabaseFunction.retrieve_species(self.dataset.group.name)) + def get_name(self): stringy = "" diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 958a1e43..4ea8407c 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -297,13 +297,13 @@ def view_collection(): params = request.args print("PARAMS in view collection:", params) - if "uc_id" in params: - uc_id = params['uc_id'] - uc = model.UserCollection.query.get(uc_id) - traits = json.loads(uc.members) - print("traits are:", traits) - else: - traits = AnonCollection().get_traits() + #if "uc_id" in params: + uc_id = params['uc_id'] + uc = model.UserCollection.query.get(uc_id) + traits = json.loads(uc.members) + print("traits are:", traits) + #else: + # traits = AnonCollection().get_traits() print("in view_collection traits are:", traits) @@ -316,7 +316,6 @@ def view_collection(): trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name) trait_ob.retrieve_info(get_qtl_info=True) - trait_ob.get_info() trait_obs.append(trait_ob) json_version.append(trait_ob.jsonable()) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 71f03d05..401059fd 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -167,9 +167,13 @@ class CorrelationResults(object): self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol") tissue_corr_data = self.do_tissue_correlation_for_all_traits() - for trait in tissue_corr_data.keys()[:self.return_number]: - self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) - + if tissue_corr_data != None: + for trait in tissue_corr_data.keys()[:self.return_number]: + self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) + else: + for trait, values in self.target_dataset.trait_data.iteritems(): + self.get_sample_r_and_p_values(trait, values) + elif self.corr_type == "lit": self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId") lit_corr_data = self.do_lit_correlation_for_all_traits() @@ -244,7 +248,7 @@ class CorrelationResults(object): trait_object.tissue_corr = 0 trait_object.tissue_pvalue = 0 trait_object.lit_corr = 0 - if self.corr_type == "tissue": + if self.corr_type == "tissue" and tissue_corr_data != None: trait_object.tissue_corr = tissue_corr_data[trait][1] trait_object.tissue_pvalue = tissue_corr_data[trait][2] elif self.corr_type == "lit": diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 123aec33..a924c7c9 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -102,8 +102,6 @@ views.py). this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) - self.dataset.get_trait_info(self.trait_list, species) - #def get_group_species_tree(self): # self.species_groups = collections.default_dict(list) # for key in self.results: |