diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 143 |
1 files changed, 80 insertions, 63 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 41c5d8ba..02b5e07c 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -273,6 +273,7 @@ class DatasetGroup(object): self.get_f1_parent_strains() self.accession_id = self.get_accession_id() + self.mapping_id, self.mapping_names = self.get_mapping_methods() self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -295,6 +296,20 @@ class DatasetGroup(object): else: return "None" + def get_mapping_methods(self): + + mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] + if mapping_id == "1": + mapping_names = ["QTLReaper", "PYLMM", "R/qtl"] + elif mapping_id == "2": + mapping_names = ["GEMMA"] + elif mapping_id == "4": + mapping_names = ["PLINK"] + else: + mapping_names = [] + + return mapping_id, mapping_names + def get_specified_markers(self, markers = []): self.markers = HumanMarkers(self.name, markers) @@ -317,69 +332,6 @@ class DatasetGroup(object): self.markers = marker_class(self.name) - def datasets(self): - key = "group_dataset_menu:v2:" + self.name - logger.debug("key is2:", key) - dataset_menu = [] - logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) - logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) - the_results = fetchall(''' - (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name - FROM PublishFreeze,InbredSet - WHERE PublishFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name = '%s' - and PublishFreeze.public > %s) - UNION - (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name - FROM GenoFreeze, InbredSet - WHERE GenoFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name = '%s' - and GenoFreeze.public > %s) - UNION - (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name - FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue - WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id - and ProbeFreeze.TissueId = Tissue.Id - and ProbeFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name like %s - and ProbeSetFreeze.public > %s - ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId) - ''' % (self.name, webqtlConfig.PUBLICTHRESH, - self.name, webqtlConfig.PUBLICTHRESH, - "'" + self.name + "'", webqtlConfig.PUBLICTHRESH)) - - #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)): - for dataset_item in the_results: - tissue_name = dataset_item[0] - dataset = dataset_item[1] - dataset_short = dataset_item[2] - if tissue_name in ['#PublishFreeze', '#GenoFreeze']: - dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) - else: - dataset_sub_menu = [item[1:] for item in dataset] - - tissue_already_exists = False - tissue_position = None - for i, tissue_dict in enumerate(dataset_menu): - if tissue_dict['tissue'] == tissue_name: - tissue_already_exists = True - tissue_position = i - break - - if tissue_already_exists: - #logger.debug("dataset_menu:", dataset_menu[i]['datasets']) - dataset_menu[i]['datasets'].append((dataset, dataset_short)) - else: - dataset_menu.append(dict(tissue=tissue_name, - datasets=[(dataset, dataset_short)])) - - if USE_REDIS: - Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) - Redis.expire(key, 60*5) - self._datasets = dataset_menu - - return self._datasets - def get_f1_parent_strains(self): try: # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; @@ -456,6 +408,71 @@ class DatasetGroup(object): return genotype +def datasets(group_name, this_group = None): + key = "group_dataset_menu:v2:" + group_name + logger.debug("key is2:", key) + dataset_menu = [] + logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) + logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) + the_results = fetchall(''' + (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name + FROM PublishFreeze,InbredSet + WHERE PublishFreeze.InbredSetId = InbredSet.Id + and InbredSet.Name = '%s' + and PublishFreeze.public > %s) + UNION + (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name + FROM GenoFreeze, InbredSet + WHERE GenoFreeze.InbredSetId = InbredSet.Id + and InbredSet.Name = '%s' + and GenoFreeze.public > %s) + UNION + (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name + FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue + WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id + and ProbeFreeze.TissueId = Tissue.Id + and ProbeFreeze.InbredSetId = InbredSet.Id + and InbredSet.Name like %s + and ProbeSetFreeze.public > %s + ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId) + ''' % (group_name, webqtlConfig.PUBLICTHRESH, + group_name, webqtlConfig.PUBLICTHRESH, + "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) + + #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)): + for dataset_item in the_results: + tissue_name = dataset_item[0] + dataset = dataset_item[1] + dataset_short = dataset_item[2] + if tissue_name in ['#PublishFreeze', '#GenoFreeze']: + dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) + else: + dataset_sub_menu = [item[1:] for item in dataset] + + tissue_already_exists = False + tissue_position = None + for i, tissue_dict in enumerate(dataset_menu): + if tissue_dict['tissue'] == tissue_name: + tissue_already_exists = True + tissue_position = i + break + + if tissue_already_exists: + #logger.debug("dataset_menu:", dataset_menu[i]['datasets']) + dataset_menu[i]['datasets'].append((dataset, dataset_short)) + else: + dataset_menu.append(dict(tissue=tissue_name, + datasets=[(dataset, dataset_short)])) + + if USE_REDIS: + Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*5) + + if this_group != None: + this_group._datasets = dataset_menu + return this_group._datasets + else: + return dataset_menu class DataSet(object): """ |