diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rw-r--r-- | wqflask/base/data_set.py | 54 |
1 files changed, 43 insertions, 11 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index d766e284..ebf3f021 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 @@ -46,6 +47,8 @@ from utility import chunks from utility import gen_geno_ob from utility.tools import locate, locate_ignore_error, flat_files +from wqflask.api import gen_menu + from maintenance import get_group_samplelists from MySQLdb import escape_string as escape @@ -61,7 +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) @@ -75,7 +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. @@ -91,8 +94,10 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - if USE_GN_SERVER: - data = menu_main() + 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: @@ -190,7 +195,7 @@ class Markers(object): markers.append(marker) for marker in markers: - if (marker['chr'] != "X") and (marker['chr'] != "Y"): + if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"): marker['chr'] = int(marker['chr']) marker['Mb'] = float(marker['Mb']) @@ -302,9 +307,11 @@ class DatasetGroup(object): mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] if mapping_id == "1": - mapping_names = ["QTLReaper", "R/qtl"] + mapping_names = ["GEMMA", "QTLReaper", "R/qtl"] elif mapping_id == "2": mapping_names = ["GEMMA"] + elif mapping_id == "3": + mapping_names = ["R/qtl"] elif mapping_id == "4": mapping_names = ["GEMMA", "PLINK"] else: @@ -342,9 +349,18 @@ class DatasetGroup(object): if maternal and paternal: self.parlist = [maternal, paternal] + def get_genofiles(self): + jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) + try: + f = open(jsonfile) + except: + return None + jsondata = json.load(f) + return jsondata['genofile'] + def get_samplelist(self): result = None - key = "samplelist:v2:" + self.name + key = "samplelist:v3:" + self.name if USE_REDIS: result = Redis.get(key) @@ -378,7 +394,10 @@ class DatasetGroup(object): # reaper barfs on unicode filenames, so here we ensure it's a string if self.genofile: - full_filename = str(locate(self.genofile, 'genotype')) + if "RData" in self.genofile: #ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData + full_filename = str(locate(self.genofile.split(".")[0] + ".geno", 'genotype')) + else: + full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) @@ -416,7 +435,8 @@ def datasets(group_name, this_group = None): WHERE PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' and PublishFreeze.public > %s - and PublishFreeze.confidentiality < 1) + and PublishFreeze.confidentiality < 1 + ORDER BY PublishFreeze.Id ASC) UNION (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, InbredSet @@ -440,12 +460,21 @@ def datasets(group_name, this_group = None): sorted_results = sorted(the_results, key=lambda kv: kv[0]) + pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown + geno_inserted = False for dataset_item in sorted_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)])) + if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'): + dataset_menu.insert(0, dict(tissue=None, datasets=[(dataset, dataset_short)])) + pheno_inserted = True + elif pheno_inserted and tissue_name == '#GenoFreeze': + dataset_menu.insert(1, dict(tissue=None, datasets=[(dataset, dataset_short)])) + geno_inserted = True + else: + dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) else: tissue_already_exists = False for i, tissue_dict in enumerate(dataset_menu): @@ -681,6 +710,7 @@ class PhenotypeDataSet(DataSet): 'Phenotype.Pre_publication_description', 'Phenotype.Pre_publication_abbreviation', 'Phenotype.Post_publication_abbreviation', + 'PublishXRef.mean', 'Phenotype.Lab_code', 'Publication.PubMed_ID', 'Publication.Abstract', @@ -689,13 +719,14 @@ 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', 'original_description', 'pre_publication_abbreviation', 'post_publication_abbreviation', + 'mean', 'lab_code', 'submitter', 'owner', 'authorized_users', @@ -910,6 +941,7 @@ class MrnaAssayDataSet(DataSet): 'blatseq', 'targetseq', 'chipid', 'comments', 'strand_probe', 'strand_gene', + 'proteinid', 'uniprotid', 'probe_set_target_region', 'probe_set_specificity', 'probe_set_blat_score', |