diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 4 | ||||
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 14 |
2 files changed, 13 insertions, 5 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index e20f2f98..75ddf278 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -124,6 +124,7 @@ class DatasetType: self.datasets[short_dataset_name] = new_type except Exception: # Do nothing pass + self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) self.data = data @@ -165,6 +166,7 @@ class DatasetType: if t in ['pheno', 'other_pheno']: group_name = name.replace("Publish", "") + results = g.db.execute(sql_query_mapping[t] % group_name).fetchone() if results: self.datasets[name] = dataset_name_mapping[t] @@ -646,6 +648,8 @@ class DataSet: "Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass + + def get_trait_data(self, sample_list=None): if sample_list: self.samplelist = sample_list diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 882ae911..8f8e2b0a 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -6,6 +6,7 @@ from utility import db_tools from utility import Bunch from utility.db_tools import escape +from gn3.db_utils import database_connector from utility.logger import getLogger @@ -45,16 +46,18 @@ class MrnaAssayTissueData: and t.Mean = x.maxmean; '''.format(in_clause) - results = g.db.execute(query).fetchall() - lower_symbols = [] + # lower_symbols = [] + lower_symbols = {} for gene_symbol in gene_symbols: + # lower_symbols[gene_symbol.lower()] = True if gene_symbol != None: - lower_symbols.append(gene_symbol.lower()) - + lower_symbols[gene_symbol.lower()] = True + results = list(g.db.execute(query).fetchall()) for result in results: symbol = result[0] - if symbol.lower() in lower_symbols: + if symbol is not None and lower_symbols.get(symbol.lower()): + symbol = symbol.lower() self.data[symbol].gene_id = result.GeneId @@ -83,6 +86,7 @@ class MrnaAssayTissueData: WHERE TissueProbeSetData.Id IN {} and TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) + results = g.db.execute(query).fetchall() for result in results: if result.Symbol.lower() not in symbol_values_dict: |