diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 19 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 9 |
2 files changed, 16 insertions, 12 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index f58367ca..6e07e383 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -26,6 +26,7 @@ import collections import codecs import json +import requests import gzip import cPickle as pickle import itertools @@ -63,7 +64,7 @@ logger = getLogger(__name__ ) # Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None): +def create_dataset(dataset_name, rebuild=True, 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) @@ -77,7 +78,7 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, gro class Dataset_Types(object): - def __init__(self): + def __init__(self, rebuild=False): """Create a dictionary of samples where the value is set to Geno, Publish or ProbeSet. E.g. @@ -93,8 +94,10 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - if USE_GN_SERVER: - data = gen_menu.gen_dropdown_json() + if rebuild: #ZS: May make this the only option + data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content) + logger.debug("THE DATA:", data) + #data = gen_menu.gen_dropdown_json() else: file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: @@ -119,12 +122,8 @@ Publish or ProbeSet. E.g. def __call__(self, name): return self.datasets[name] -def rebuild_dataset_ob(): - Dataset_Getter = Dataset_Types() - return Dataset_Getter - # Do the intensive work at startup one time only -Dataset_Getter = rebuild_dataset_ob() +Dataset_Getter = Dataset_Types() def create_datasets_list(): if USE_REDIS: @@ -705,7 +704,7 @@ class PhenotypeDataSet(DataSet): 'PublishXRef.Id'] # Figure out what display_fields is - self.display_fields = ['name', + self.display_fields = ['name', 'group_code', 'pubmed_id', 'pre_publication_description', 'post_publication_description', diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 322fb252..5fae34cf 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -352,7 +352,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if dataset.type == 'Publish': query = """ SELECT - PublishXRef.Id, Publication.PubMed_ID, + PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID, Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, @@ -361,12 +361,13 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): Publication.Month, Publication.Year, PublishXRef.Sequence, Phenotype.Units, PublishXRef.comments FROM - PublishXRef, Publication, Phenotype, PublishFreeze + PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet WHERE PublishXRef.Id = %s AND Phenotype.Id = PublishXRef.PhenotypeId AND Publication.Id = PublishXRef.PublicationId AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishXRef.InbredSetId = InbredSet.Id AND PublishFreeze.Id = %s """ % (trait.name, dataset.id) @@ -428,6 +429,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): # holder = unicode(trait_info[i], "utf-8", "ignore") setattr(trait, field, holder) + trait.display_name = trait.name if dataset.type == 'Publish': trait.confidential = 0 if trait.pre_publication_description and not trait.pubmed_id: @@ -462,6 +464,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.pubmed_id: trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id + else: + if trait.group_code: + trait.display_name = trait.group_code + "_" + str(trait.name) if dataset.type == 'ProbeSet' and dataset.group: description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') |