diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 113 | ||||
| -rw-r--r-- | wqflask/base/webqtlCaseData.py | 41 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 2 |
3 files changed, 68 insertions, 88 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 5d562871..cfba9104 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -93,7 +93,7 @@ Publish or ProbeSet. E.g. """ self.redis_instance = redis_instance self.datasets = {} - data = redis_instance.get("dataset_structure") + data = self.redis_instance.get("dataset_structure") if data: self.datasets = json.loads(data) else: # ZS: I don't think this should ever run unless Redis is emptied @@ -115,73 +115,58 @@ Publish or ProbeSet. E.g. except: pass - redis_instance.set("dataset_structure", json.dumps(self.datasets)) + self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) - # Set LOG_LEVEL_DEBUG=5 to see the following: - logger.debugf(5, "datasets", self.datasets) + def set_dataset_key(self, t, name): + """If name is not in the object's dataset dictionary, set it, and update + dataset_structure in Redis + + args: + t: Type of dataset structure which can be: 'mrna_expr', 'pheno', + 'other_pheno', 'geno' + name: The name of the key to inserted in the datasets dictionary + + """ + sql_query_mapping = { + 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ + + """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """), + 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ + + """FROM InfoFiles, PublishFreeze, InbredSet """ + + """WHERE InbredSet.Name = '{}' AND """ + + """PublishFreeze.InbredSetId = InbredSet.Id AND """ + + """InfoFiles.InfoPageName = PublishFreeze.Name"""), + 'other_pheno': ("""SELECT PublishFreeze.Name """ + + """FROM PublishFreeze, InbredSet """ + + """WHERE InbredSet.Name = '{}' AND """ + + """PublishFreeze.InbredSetId = InbredSet.Id"""), + 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ + + """GenoFreeze.Name = "{}" """) + } + + dataset_name_mapping = { + "mrna_expr": "ProbeSet", + "pheno": "Publish", + "other_pheno": "Publish", + "geno": "Geno", + } + + if t in ['pheno', 'other_pheno']: + name = name.replace("Publish", "") + if bool(len(g.db.execute(sql_query_mapping[t].format(name)))): + self.datasets[name] = dataset_name_mapping[t] + self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) + return True + + return None def __call__(self, name): + if name not in self.datasets: - mrna_expr_query = """ - SELECT - ProbeSetFreeze.Id - FROM - ProbeSetFreeze - WHERE - ProbeSetFreeze.Name = "{0}" - """.format(name) - - results = g.db.execute(mrna_expr_query).fetchall() - if len(results): - self.datasets[name] = "ProbeSet" - redis_instance.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] - - group_name = name.replace("Publish", "") - - pheno_query = """SELECT InfoFiles.GN_AccesionId - FROM InfoFiles, PublishFreeze, InbredSet - WHERE InbredSet.Name = '{0}' AND - PublishFreeze.InbredSetId = InbredSet.Id AND - InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name) - - results = g.db.execute(pheno_query).fetchall() - if len(results): - self.datasets[name] = "Publish" - redis_instance.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] - - # ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary - other_pheno_query = """SELECT PublishFreeze.Name - FROM PublishFreeze, InbredSet - WHERE InbredSet.Name = '{}' AND - PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name) - - results = g.db.execute(other_pheno_query).fetchall() - if len(results): - self.datasets[name] = "Publish" - redis_instance.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] - - geno_query = """ - SELECT - GenoFreeze.Id - FROM - GenoFreeze - WHERE - GenoFreeze.Name = "{0}" - """.format(name) - - results = g.db.execute(geno_query).fetchall() - if len(results): - self.datasets[name] = "Geno" - self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] - - # ZS: It shouldn't ever reach this - return None - else: - return self.datasets[name] + for t in ["mrna_expr", "pheno", "other_pheno", "geno"]: + # 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 # Do the intensive work at startup one time only diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index d8487f01..2844cedd 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -19,8 +19,7 @@ # This module is used by GeneNetwork project (www.genenetwork.org) # # Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 + from utility.logger import getLogger logger = getLogger(__name__) @@ -29,7 +28,7 @@ import utility.tools utility.tools.show_settings() -class webqtlCaseData(object): +class webqtlCaseData: """one case data in one trait""" def __init__(self, name, value=None, variance=None, num_cases=None, name2=None): @@ -43,44 +42,40 @@ class webqtlCaseData(object): self.outlier = None # Not set to True/False until later def __repr__(self): - str = "<webqtlCaseData> " - if self.value != None: - str += "value=%2.3f" % self.value - if self.variance != None: - str += " variance=%2.3f" % self.variance + case_data_string = "<webqtlCaseData> " + if self.value is not None: + case_data_string += "value=%2.3f" % self.value + if self.variance is not None: + case_data_string += " variance=%2.3f" % self.variance if self.num_cases: - str += " ndata=%s" % self.num_cases + case_data_string += " ndata=%s" % self.num_cases if self.name: - str += " name=%s" % self.name + case_data_string += " name=%s" % self.name if self.name2: - str += " name2=%s" % self.name2 - return str + case_data_string += " name2=%s" % self.name2 + return case_data_string @property def class_outlier(self): """Template helper""" if self.outlier: return "outlier" - else: - return "" + return "" @property def display_value(self): - if self.value != None: + if self.value is not None: return "%2.3f" % self.value - else: - return "x" + return "x" @property def display_variance(self): - if self.variance != None: + if self.variance is not None: return "%2.3f" % self.variance - else: - return "x" + return "x" @property def display_num_cases(self): - if self.num_cases != None: + if self.num_cases is not None: return "%s" % self.num_cases - else: - return "x" + return "x" diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 3d86bc22..862ac881 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -85,7 +85,7 @@ assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories GENODIR = flat_files('genotype')+'/' assert_dir(GENODIR) -assert_dir(GENODIR+'bimbam') # for gemma +# assert_dir(GENODIR+'bimbam') # for gemma # JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' |