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authorzsloan2020-04-21 16:54:41 -0500
committerGitHub2020-04-21 16:54:41 -0500
commit821465df32bfcbab73a654d1e2386f2a07f4695f (patch)
tree871c8502774cb7a8fce950f46285f62ba3d0b113 /wqflask/base/data_set.py
parentd249d8fa90eabd47020926fdadbfe22ac2bba900 (diff)
parentcf8b4c21d81efaa01d347478dc126e6d9b53f7a9 (diff)
downloadgenenetwork2-821465df32bfcbab73a654d1e2386f2a07f4695f.tar.gz
Merge pull request #2 from genenetwork/testing
Pulling changes from main branch
Diffstat (limited to 'wqflask/base/data_set.py')
-rw-r--r--wqflask/base/data_set.py54
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',