diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 90 |
1 files changed, 69 insertions, 21 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 03b24230..30221503 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -48,32 +48,67 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf # Used by create_database to instantiate objects +# Each subclass will add to this DS_NAME_MAP = {} def create_dataset(dataset_name, dataset_type = None): - #print("dataset_name:", dataset_name) - + + print("dataset_type:", dataset_type) 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 = Dataset_Getter(dataset_name) + #dataset_type = get_dataset_type_from_json(dataset_name) - #dataset_type = cursor.fetchone()[0] - #print("[blubber] dataset_type:", pf(dataset_type)) + print("dataset_type is:", dataset_type) + #query = """ + # SELECT DBType.Name + # FROM DBList, DBType + # WHERE DBList.Name = '{}' and + # DBType.Id = DBList.DBTypeId + # """.format(escape(dataset_name)) + #dataset_type = g.db.execute(query).fetchone().Name - dataset_ob = DS_NAME_MAP[dataset_type] - #dataset_class = getattr(data_set, dataset_ob) - #print("dataset_ob:", dataset_ob) - #print("DS_NAME_MAP:", pf(DS_NAME_MAP)) + dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] return dataset_class(dataset_name) + +#def get_dataset_type_from_json(dataset_name): + +class Dataset_Types(object): + + def __init__(self): + self.datasets = {} + file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" + with open(file_name, 'r') as fh: + data = json.load(fh) + + print("*" * 70) + for species in data['datasets']: + for group in data['datasets'][species]: + for dataset_type in data['datasets'][species][group]: + for dataset in data['datasets'][species][group][dataset_type]: + print("dataset is:", dataset) + + short_dataset_name = dataset[0] + if dataset_type == "Phenotypes": + new_type = "Publish" + elif dataset_type == "Genotypes": + new_type = "Geno" + else: + new_type = "ProbeSet" + self.datasets[short_dataset_name] = new_type + + def __call__(self, name): + return self.datasets[name] + +# Do the intensive work at startup one time only +Dataset_Getter = Dataset_Types() + +# +#print("Running at startup:", get_dataset_type_from_json("HBTRC-MLPFC_0611")) + + def create_datasets_list(): key = "all_datasets" result = Redis.get(key) @@ -212,7 +247,7 @@ class DatasetGroup(object): marker_class = Markers self.markers = marker_class(self.name) - + def get_f1_parent_strains(self): try: @@ -225,7 +260,7 @@ class DatasetGroup(object): self.f1list = [f1, f12] if maternal and paternal: self.parlist = [maternal, paternal] - + def read_genotype_file(self): '''Read genotype from .geno file instead of database''' #if self.group == 'BXD300': @@ -375,6 +410,9 @@ class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' def setup(self): + + print("IS A PHENOTYPEDATASET") + # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', @@ -445,14 +483,24 @@ class PhenotypeDataSet(DataSet): def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: if not this_trait.haveinfo: - this_trait.retrieveInfo(QTL=1) + this_trait.retrieve_info(get_qtl_info=True) description = this_trait.post_publication_description + + #If the dataset is confidential and the user has access to confidential + #phenotype traits, then display the pre-publication description instead + #of the post-publication description if this_trait.confidential: continue # for now - if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): + + if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( + privilege=self.privilege, + userName=self.userName, + authorized_users=this_trait.authorized_users): + description = this_trait.pre_publication_description - this_trait.description_display = unicode(description, "utf8") + + this_trait.description_display = description if not this_trait.year.isdigit(): this_trait.pubmed_text = "N/A" |