diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 40 |
1 files changed, 27 insertions, 13 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 79aa196f..0689e950 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -6,6 +6,9 @@ import codecs from htmlgen import HTMLgen2 as HT +import redis +Redis = redis.StrictRedis() + from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset @@ -35,13 +38,15 @@ class GeneralTrait(object): def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): # xor assertion assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; + self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. if kw.get('dataset_name'): - self.dataset = create_dataset(kw.get('dataset_name')) - #print(" in GeneralTrait created dataset:", self.dataset) + if kw.get('dataset_name') == "Temp": + temp_group = self.name.split("_")[2] + self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + else: + self.dataset = create_dataset(kw.get('dataset_name')) else: self.dataset = kw.get('dataset') - self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. - #print("THE NAME IS:", self.name) self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') self.haveinfo = kw.get('haveinfo', False) @@ -73,8 +78,8 @@ class GeneralTrait(object): # So we could add a simple if statement to short-circuit this if necessary 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) + if get_sample_info != False: + self = retrieve_sample_data(self, self.dataset) def export_informative(self, include_variance=0): """ @@ -154,18 +159,27 @@ def retrieve_sample_data(trait, dataset, samplelist=None): if samplelist == None: samplelist = [] - results = dataset.retrieve_sample_data(trait.name) + if dataset.type == "Temp": + results = Redis.get(trait.name).split() + else: + results = dataset.retrieve_sample_data(trait.name) # Todo: is this necessary? If not remove trait.data.clear() - all_samples_ordered = dataset.group.all_samples_ordered() - if results: - for item in results: - name, value, variance, num_cases, name2 = item - if not samplelist or (samplelist and name in samplelist): - trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) + if dataset.type == "Temp": + all_samples_ordered = dataset.group.all_samples_ordered() + for i, item in enumerate(results): + try: + trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item)) + except: + pass + else: + for item in results: + name, value, variance, num_cases, name2 = item + if not samplelist or (samplelist and name in samplelist): + trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) return trait @app.route("/trait/get_sample_data") |