diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/data_set.py | 55 | ||||
| -rw-r--r-- | wqflask/base/species.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 3 |
4 files changed, 39 insertions, 31 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index f301cc05..e4bdb5c3 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -46,17 +46,18 @@ 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)) @@ -228,16 +229,17 @@ class DataSets(object): def __init__(self): self.datasets = list() - type_dict = {'phenotype': 'PublishFreeze', - 'mrna_assay': 'ProbeSetFreeze', - 'genotype': 'GenoFreeze'} + 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 - create_dataset(result.Name) + print("type: {}\tname: {}".format(dataset_type, result.Name)) + create_dataset(result.Name, dataset_type) #query = """SELECT Name FROM ProbeSetFreeze @@ -265,6 +267,8 @@ 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() @@ -324,7 +328,7 @@ 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 @@ -332,17 +336,17 @@ 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' @@ -971,6 +975,5 @@ 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 diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index f76af374..504a67ce 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -162,8 +162,6 @@ class SearchResultPage(object): import redis Redis = redis.Redis() - - #def get_group_species_tree(self): # self.species_groups = collections.default_dict(list) # for key in self.results: diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index fcb34d31..e48506ab 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -54,7 +54,8 @@ def connect_db(): @app.route("/") def index_page(): print("Sending index_page") - ds = DataSets() + with Bench("Creating DataSets object"): + ds = DataSets() print("[orange] ds:", ds.datasets) return render_template("index_page.html") |