diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 37 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 16 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 2 |
3 files changed, 34 insertions, 21 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 54dd3c4b..4959457a 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -61,14 +61,17 @@ logger = getLogger(__name__ ) # Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): +def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) logger.debug("dataset_type", dataset_type) dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] - return dataset_class(dataset_name, get_samplelist) + if dataset_type == "Temp": + return dataset_class(dataset_name, get_samplelist, group_name) + else: + return dataset_class(dataset_name, get_samplelist) class Dataset_Types(object): @@ -261,10 +264,13 @@ class DatasetGroup(object): has multiple datasets associated with it. """ - def __init__(self, dataset): + def __init__(self, dataset, name=None): """This sets self.group and self.group_id""" #logger.debug("DATASET NAME2:", dataset.name) - self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) + if name == None: + self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) + else: + self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name) if self.name == 'BXD300': self.name = "BXD" @@ -304,7 +310,7 @@ class DatasetGroup(object): elif mapping_id == "2": mapping_names = ["GEMMA"] elif mapping_id == "4": - mapping_names = ["PLINK"] + mapping_names = ["GEMMA", "PLINK"] else: mapping_names = [] @@ -319,9 +325,7 @@ class DatasetGroup(object): def check_plink_gemma(): if flat_file_exists("mapping"): MAPPING_PATH = flat_files("mapping")+"/" - if (os.path.isfile(MAPPING_PATH+self.name+".bed") and - (os.path.isfile(MAPPING_PATH+self.name+".map") or - os.path.isfile(MAPPING_PATH+self.name+".bim"))): + if os.path.isfile(MAPPING_PATH+self.name+".bed"): return True return False @@ -481,7 +485,7 @@ class DataSet(object): """ - def __init__(self, name, get_samplelist = True): + def __init__(self, name, get_samplelist = True, group_name = None): assert name, "Need a name" self.name = name @@ -493,11 +497,12 @@ class DataSet(object): self.setup() - self.check_confidentiality() - - self.retrieve_other_names() - - self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + if self.type == "Temp": #Need to supply group name as input if temp trait + self.group = DatasetGroup(self, group_name) # sets self.group and self.group_id and gets genotype + else: + self.check_confidentiality() + self.retrieve_other_names() + self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype if get_samplelist == True: self.group.get_samplelist() self.species = species.TheSpecies(self) @@ -888,7 +893,7 @@ class GenotypeDataSet(DataSet): def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Sample.Name2 + Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2 FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) left join GenoSE on @@ -1156,6 +1161,8 @@ class MrnaAssayDataSet(DataSet): class TempDataSet(DataSet): '''Temporary user-generated data set''' + DS_NAME_MAP['Temp'] = 'TempDataSet' + def setup(self): self.search_fields = ['name', 'description'] diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index bf87e879..e22a51e4 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -62,6 +62,11 @@ class GeneralTrait(object): self.strand_probe = None self.symbol = None + self.LRS_score_repr = "N/A" + self.LRS_score_value = 0 + self.LRS_location_repr = "N/A" + self.LRS_location_value = 1000000 + if kw.get('fullname'): name2 = value.split("::") if len(name2) == 2: @@ -72,9 +77,10 @@ class GeneralTrait(object): # Todo: These two lines are necessary most of the time, but perhaps not all of the time # So we could add a simple if statement to short-circuit this if necessary - self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info) - if get_sample_info != False: - self = retrieve_sample_data(self, self.dataset) + if self.dataset.type != "Temp": + self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info) + if get_sample_info != False: + self = retrieve_sample_data(self, self.dataset) def get_name(self): @@ -315,12 +321,12 @@ def get_sample_data(): # #return jsonable_sample_data -def jsonable(trait, dataset_name): +def jsonable(trait): """Return a dict suitable for using as json Actual turning into json doesn't happen here though""" - dataset = create_dataset(dataset_name) + dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name) if dataset.type == "ProbeSet": return dict(name=trait.name, diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index e5f10edf..1e47e183 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -65,7 +65,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp # want to reach this base dir assert_writable_dir(TEMPDIR) -TMPDIR = mk_dir(TEMPDIR+'/gn2/') +TMPDIR = mk_dir(TEMPDIR+'gn2') assert_writable_dir(TMPDIR) CACHEDIR = mk_dir(TMPDIR+'/cache/') |