diff options
| -rw-r--r-- | wqflask/base/data_set.py | 51 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 3 |
3 files changed, 51 insertions, 5 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 178234fe..468c4da0 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -115,7 +115,8 @@ Publish or ProbeSet. E.g. except: pass - self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) + self.redis_instance.set( + "dataset_structure", json.dumps(self.datasets)) def set_dataset_key(self, t, name): """If name is not in the object's dataset dictionary, set it, and update @@ -154,10 +155,12 @@ Publish or ProbeSet. E.g. if t in ['pheno', 'other_pheno']: group_name = name.replace("Publish", "") - results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone() + results = g.db.execute( + sql_query_mapping[t].format(group_name)).fetchone() if results: self.datasets[name] = dataset_name_mapping[t] - self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) + self.redis_instance.set( + "dataset_structure", json.dumps(self.datasets)) return True return None @@ -169,7 +172,8 @@ Publish or ProbeSet. E.g. # This has side-effects, with the end result being a truth-y value if(self.set_dataset_key(t, name)): break - return self.datasets.get(name, None) # Return None if name has not been set + # Return None if name has not been set + return self.datasets.get(name, None) # Do the intensive work at startup one time only @@ -651,6 +655,43 @@ class DataSet(object): "Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass + def fetch_probe_trait_data(self, sample_list=None): + if sample_list: + self.samplelist = sample_list + else: + self.samplelist = self.group.samplelist + + if self.group.parlist != None and self.group.f1list != None: + if (self.group.parlist + self.group.f1list) in self.samplelist: + self.samplelist += self.group.parlist + self.group.f1list + + query = """ + SELECT Strain.Name, Strain.Id FROM Strain, Species + WHERE Strain.Name IN {} + and Strain.SpeciesId=Species.Id + and Species.name = '{}' + """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) + logger.sql(query) + results = dict(g.db.execute(query).fetchall()) + sample_ids = [results[item] for item in self.samplelist] + + query = """SELECT * from ProbeSetData WHERE Id in ( SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = 'HC_M2_0606_P' and ProbeSet.Id = ProbeSetXRef.ProbeSetId order by ProbeSet.Id ) and StrainId in ({})""".format( + ",".join(str(sample_id) for sample_id in sample_ids)) + + results = g.db.execute(query).fetchall() + + # with conn: + # cursor = conn.cursor() + # cursor.execute(query) + # results = cursor.fetchall() + trait_data = {} + for trait_id, StrainId, value in results: + if trait_id in trait_data: + trait_data[trait_id].append(value) + else: + trait_data[trait_id] = [value] + self.trait_data = trait_data + def get_trait_data(self, sample_list=None): if sample_list: self.samplelist = sample_list @@ -670,6 +711,7 @@ class DataSet(object): logger.sql(query) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] + print("the number of sample ids are", len(sample_ids)) # MySQL limits the number of tables that can be used in a join to 61, # so we break the sample ids into smaller chunks @@ -720,6 +762,7 @@ class DataSet(object): trait_sample_data.append(results) trait_count = len(trait_sample_data[0]) + print("the trait count is >>>", trait_count) self.trait_data = collections.defaultdict(list) # put all of the separate data together into a dictionary where the keys are diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index e7394647..51bf5fb5 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -78,7 +78,7 @@ def compute_correlation(start_vars, method="pearson"): # } sample_data = process_samples( start_vars, this_dataset.group.samplelist) - target_dataset.get_trait_data(list(sample_data.keys())) + target_dataset.fetch_probe_trait_data(list(sample_data.keys())) this_trait = retrieve_sample_data(this_trait, this_dataset) print("Creating dataset and trait took", time.time()-initial_time) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 072db466..2c239425 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -881,7 +881,10 @@ def network_graph_page(): def corr_compute_page(): logger.info("In corr_compute, request.form is:", pf(request.form)) logger.info(request.url) + import time + initial_time = time.time() correlation_results = compute_correlation(request.form) + print(">>>>Time taken by this endpoint",time.time()-initial_time) return render_template("demo_correlation_page.html",correlation_results=correlation_results[1:20]) @app.route("/corr_matrix", methods=('POST',)) |