diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rw-r--r-- | wqflask/base/data_set.py | 228 |
1 files changed, 158 insertions, 70 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4a422ee4..1f99df49 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 @@ -43,8 +44,11 @@ from db import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench 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 @@ -52,7 +56,7 @@ from pprint import pformat as pf from db.gn_server import menu_main from db.call import fetchall,fetchone,fetch1 -from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL from utility.logger import getLogger logger = getLogger(__name__ ) @@ -63,7 +67,6 @@ DS_NAME_MAP = {} 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] @@ -90,12 +93,9 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - if USE_GN_SERVER: - data = menu_main() - else: - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" - with open(file_name, 'r') as fh: - data = json.load(fh) + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) + #data = gen_menu.gen_dropdown_json() + for species in data['datasets']: for group in data['datasets'][species]: @@ -109,11 +109,70 @@ Publish or ProbeSet. E.g. else: new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type + # Set LOG_LEVEL_DEBUG=5 to see the following: logger.debugf(5, "datasets",self.datasets) def __call__(self, name): - return self.datasets[name] + if name not in self.datasets: + mrna_expr_query = """ + SELECT + ProbeSetFreeze.Id + FROM + ProbeSetFreeze + WHERE + ProbeSetFreeze.Name = "{0}" + """.format(name) + + results = g.db.execute(geno_query).fetchall() + if len(results): + self.datasets[name] = "ProbeSet" + return self.datasets[name] + + group_name = name.replace("Publish", "") + + pheno_query = """SELECT InfoFiles.GN_AccesionId + FROM InfoFiles, PublishFreeze, InbredSet + WHERE InbredSet.Name = '{0}' AND + PublishFreeze.InbredSetId = InbredSet.Id AND + InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name) + + results = g.db.execute(pheno_query).fetchall() + if len(results): + self.datasets[name] = "Publish" + return self.datasets[name] + + #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary + other_pheno_query = """SELECT PublishFreeze.Name + FROM PublishFreeze, InbredSet + WHERE InbredSet.Name = '{}' AND + PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name) + + results = g.db.execute(other_pheno_query).fetchall() + if len(results): + self.datasets[name] = "Publish" + return self.datasets[name] + + geno_query = """ + SELECT + GenoFreezeId + FROM + GenoFreeze + WHERE + GenoFreeze.Name = "{0}" + {1} + """.format(name) + + results = g.db.execute(geno_query).fetchall() + if len(results): + self.datasets[name] = "Geno" + return self.datasets[name] + + #ZS: It shouldn't ever reach this + return None + + else: + return self.datasets[name] # Do the intensive work at startup one time only Dataset_Getter = Dataset_Types() @@ -170,31 +229,25 @@ class Markers(object): def __init__(self, name): json_data_fh = open(locate(name + ".json",'genotype/json')) - try: - markers = [] - with open(locate(name + "_snps.txt", 'r')) as bimbam_fh: + markers = [] + with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh: + if len(bimbam_fh.readline().split(", ")) > 2: + delimiter = ", " + elif len(bimbam_fh.readline().split(",")) > 2: + delimiter = "," + elif len(bimbam_fh.readline().split("\t")) > 2: + delimiter = "\t" + else: + delimiter = " " + for line in bimbam_fh: marker = {} - if len(bimbam_fh[0].split(", ")) > 2: - delimiter = ", " - elif len(bimbam_fh[0].split(",")) > 2: - delimiter = "," - elif len(bimbam_fh[0].split("\t")) > 2: - delimiter = "\t" - else: - delimiter = " " - for line in bimbam_fh: - marker['name'] = line.split(delimiter)[0] - marker['Mb'] - marker['chr'] = line.split(delimiter)[2] - marker['cM'] - markers.append(marker) - #try: - # markers = json.load(json_data_fh) - except: - markers = [] + marker['name'] = line.split(delimiter)[0].rstrip() + marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000 + marker['chr'] = line.split(delimiter)[2].rstrip() + 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']) @@ -282,7 +335,6 @@ class DatasetGroup(object): """ def __init__(self, dataset, name=None): """This sets self.group and self.group_id""" - #logger.debug("DATASET NAME2:", dataset.name) if name == None: self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) else: @@ -294,7 +346,6 @@ class DatasetGroup(object): self.parlist = None self.get_f1_parent_strains() - self.accession_id = self.get_accession_id() self.mapping_id, self.mapping_names = self.get_mapping_methods() self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -304,27 +355,15 @@ class DatasetGroup(object): self._datasets = None self.genofile = None - def get_accession_id(self): - results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where - InbredSet.Name = %s and - PublishFreeze.InbredSetId = InbredSet.Id and - InfoFiles.InfoPageName = PublishFreeze.Name and - PublishFreeze.public > 0 and - PublishFreeze.confidentiality < 1 order by - PublishFreeze.CreateTime desc""", (self.name)).fetchone() - - if results != None: - return str(results[0]) - else: - return "None" - def get_mapping_methods(self): mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] if mapping_id == "1": - mapping_names = ["QTLReaper", "PYLMM", "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: @@ -333,8 +372,6 @@ class DatasetGroup(object): return mapping_id, mapping_names def get_markers(self): - logger.debug("self.species is:", self.species) - def check_plink_gemma(): if flat_file_exists("mapping"): MAPPING_PATH = flat_files("mapping")+"/" @@ -364,30 +401,32 @@ 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) if result is not None: - #logger.debug("Sample List Cache hit!!!") - #logger.debug("Before unjsonifying {}: {}".format(type(result), result)) self.samplelist = json.loads(result) - #logger.debug(" type: ", type(self.samplelist)) - #logger.debug(" self.samplelist: ", self.samplelist) else: logger.debug("Cache not hit") genotype_fn = locate_ignore_error(self.name+".geno",'genotype') - mapping_fn = locate_ignore_error(self.name+".fam",'mapping') - if mapping_fn: - self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn) - elif genotype_fn: + if genotype_fn: self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn) else: self.samplelist = None - logger.debug("Sample list: ",self.samplelist) + if USE_REDIS: Redis.set(key, json.dumps(self.samplelist)) Redis.expire(key, 60*5) @@ -398,19 +437,27 @@ class DatasetGroup(object): [result.extend(l) for l in lists if l] return result - def read_genotype_file(self): + def read_genotype_file(self, use_reaper=False): '''Read genotype from .geno file instead of database''' #genotype_1 is Dataset Object without parents and f1 #genotype_2 is Dataset Object with parents and f1 (not for intercross) - genotype_1 = reaper.Dataset() + #genotype_1 = reaper.Dataset() # 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')) - genotype_1.read(full_filename) + + if use_reaper: + genotype_1 = reaper.Dataset() + genotype_1.read(full_filename) + else: + genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) @@ -440,7 +487,8 @@ 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 @@ -457,17 +505,28 @@ def datasets(group_name, this_group = None): and InbredSet.Name like %s and ProbeSetFreeze.public > %s and ProbeSetFreeze.confidentiality < 1 - ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId) + ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) ''' % (group_name, webqtlConfig.PUBLICTHRESH, group_name, webqtlConfig.PUBLICTHRESH, "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) - for dataset_item in the_results: + 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): @@ -512,11 +571,12 @@ class DataSet(object): self.setup() 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 + self.group = DatasetGroup(self, name=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 + self.accession_id = self.get_accession_id() if get_samplelist == True: self.group.get_samplelist() self.species = species.TheSpecies(self) @@ -531,6 +591,31 @@ class DataSet(object): def riset(): Weve_Renamed_This_As_Group + def get_accession_id(self): + if self.type == "Publish": + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where + InbredSet.Name = %s and + PublishFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = PublishFreeze.Name and + PublishFreeze.public > 0 and + PublishFreeze.confidentiality < 1 order by + PublishFreeze.CreateTime desc""", (self.group.name)).fetchone() + elif self.type == "Geno": + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where + InbredSet.Name = %s and + GenoFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = GenoFreeze.ShortName and + GenoFreeze.public > 0 and + GenoFreeze.confidentiality < 1 order by + GenoFreeze.CreateTime desc""", (self.group.name)).fetchone() + else: + results = None + + if results != None: + return str(results[0]) + else: + return "None" + def retrieve_other_names(self): """This method fetches the the dataset names in search_result. @@ -677,6 +762,7 @@ 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', @@ -685,13 +771,14 @@ 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', @@ -906,6 +993,7 @@ class MrnaAssayDataSet(DataSet): 'blatseq', 'targetseq', 'chipid', 'comments', 'strand_probe', 'strand_gene', + 'proteinid', 'uniprotid', 'probe_set_target_region', 'probe_set_specificity', 'probe_set_blat_score', |