diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 105 | ||||
| -rw-r--r-- | wqflask/base/species.py | 10 |
2 files changed, 89 insertions, 26 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1668940c..03b24230 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -27,8 +27,12 @@ import string import collections import json +import cPickle as pickle import itertools +from redis import Redis +Redis = Redis() + from flask import Flask, g import reaper @@ -46,17 +50,18 @@ from pprint import pformat as pf # Used by create_database to instantiate objects DS_NAME_MAP = {} -def create_dataset(dataset_name): +def create_dataset(dataset_name, dataset_type = None): #print("dataset_name:", dataset_name) - query = """ - SELECT DBType.Name - FROM DBList, DBType - WHERE DBList.Name = '{}' and - DBType.Id = DBList.DBTypeId - """.format(escape(dataset_name)) - #print("query is: ", pf(query)) - dataset_type = g.db.execute(query).fetchone().Name + if not dataset_type: + query = """ + SELECT DBType.Name + FROM DBList, DBType + WHERE DBList.Name = '{}' and + DBType.Id = DBList.DBTypeId + """.format(escape(dataset_name)) + #print("query is: ", pf(query)) + dataset_type = g.db.execute(query).fetchone().Name #dataset_type = cursor.fetchone()[0] #print("[blubber] dataset_type:", pf(dataset_type)) @@ -69,6 +74,36 @@ def create_dataset(dataset_name): dataset_class = globals()[dataset_ob] return dataset_class(dataset_name) +def create_datasets_list(): + key = "all_datasets" + result = Redis.get(key) + + if result: + print("Cache hit!!!") + datasets = pickle.loads(result) + + else: + datasets = list() + with Bench("Creating DataSets object"): + type_dict = {'Publish': 'PublishFreeze', + 'ProbeSet': 'ProbeSetFreeze', + 'Geno': 'GenoFreeze'} + + for dataset_type in type_dict: + query = "SELECT Name FROM {}".format(type_dict[dataset_type]) + for result in g.db.execute(query).fetchall(): + #The query at the beginning of this function isn't necessary here, but still would + #rather just reuse it + print("type: {}\tname: {}".format(dataset_type, result.Name)) + dataset = create_dataset(result.Name, dataset_type) + datasets.append(dataset) + + Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*60) + + return datasets + + def create_in_clause(items): """Create an in clause for mysql""" in_clause = ', '.join("'{}'".format(x) for x in mescape(*items)) @@ -167,8 +202,8 @@ class DatasetGroup(object): self.incparentsf1 = False self.allsamples = None - - + + def get_markers(self): #print("self.species is:", self.species) if self.species == "human": @@ -222,6 +257,27 @@ class DatasetGroup(object): self.samplelist = list(genotype.prgy) +#class DataSets(object): +# """Builds a list of DataSets""" +# +# def __init__(self): +# self.datasets = list() +# + + + #query = """SELECT Name FROM ProbeSetFreeze + # UNION + # SELECT Name From PublishFreeze + # UNION + # SELECT Name From GenoFreeze""" + # + #for result in g.db.execute(query).fetchall(): + # dataset = DataSet(result.Name) + # self.datasets.append(dataset) + +#ds = DataSets() +#print("[orange] ds:", ds.datasets) + class DataSet(object): """ DataSet class defines a dataset in webqtl, can be either Microarray, @@ -234,6 +290,8 @@ class DataSet(object): assert name, "Need a name" self.name = name self.id = None + self.shortname = None + self.fullname = None self.type = None self.setup() @@ -293,7 +351,7 @@ class DataSet(object): self.name, self.name, self.name)) - #print("query_args are:", query_args) + print("query_args are:", query_args) #print(""" # SELECT Id, Name, FullName, ShortName @@ -301,17 +359,17 @@ class DataSet(object): # WHERE public > %s AND # (Name = '%s' OR FullName = '%s' OR ShortName = '%s') # """ % (query_args)) - - self.id, self.name, self.fullname, self.shortname = g.db.execute(""" - SELECT Id, Name, FullName, ShortName - FROM %s - WHERE public > %s AND - (Name = '%s' OR FullName = '%s' OR ShortName = '%s') - """ % (query_args)).fetchone() - - #self.cursor.execute(query) - #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone() + try: + self.id, self.name, self.fullname, self.shortname = g.db.execute(""" + SELECT Id, Name, FullName, ShortName + FROM %s + WHERE public > %s AND + (Name = '%s' OR FullName = '%s' OR ShortName = '%s') + """ % (query_args)).fetchone() + except TypeError: + print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) + pass class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' @@ -940,6 +998,5 @@ def geno_mrna_confidentiality(ob): authorized_users) = result.fetchall()[0] if confidential: - # Allow confidential data later - NoConfindetialDataForYouTodaySorry + return True diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 191f4535..ebc2bfed 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -56,6 +56,7 @@ class Chromosomes(object): InbredSet.Name = %s Order by OrderId """, self.dataset.group.name).fetchall() + print("group: ", self.dataset.group.name) print("bike:", results) for item in results: @@ -68,9 +69,14 @@ class Chromosomes(object): def set_mb_graph_interval(self): """Empirical megabase interval""" + if self.chromosomes: + self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) + else: + self.mb_graph_interval = 1 + #if self.chromosomes: - assert self.chromosomes, "Have to add some code back in apparently to set it to 1" - self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) + #assert self.chromosomes, "Have to add some code back in apparently to set it to 1" + #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) #else: #self.mb_graph_interval = 1 |