diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 120 |
1 files changed, 90 insertions, 30 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 3daf9ea9..e454c593 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -3,14 +3,18 @@ from __future__ import absolute_import, division, print_function import string import resource import codecs +import requests -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 from db import webqtlDatabaseFunction from utility import webqtlUtil +from utility import hmac +from utility.tools import GN2_BASE_URL from wqflask import app @@ -23,8 +27,6 @@ from flask import Flask, g, request, url_for from utility.logger import getLogger logger = getLogger(__name__ ) -from wqflask import user_manager - class GeneralTrait(object): """ Trait class defines a trait in webqtl, can be either Microarray, @@ -35,13 +37,15 @@ 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) @@ -57,6 +61,7 @@ class GeneralTrait(object): self.num_overlap = None self.strand_probe = None self.symbol = None + self.display_name = self.name self.LRS_score_repr = "N/A" self.LRS_location_repr = "N/A" @@ -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): """ @@ -117,11 +122,36 @@ class GeneralTrait(object): @property def alias_fmt(self): '''Return a text formatted alias''' + + alias = 'Not available' if self.alias: alias = string.replace(self.alias, ";", " ") alias = string.join(string.split(alias), ", ") - else: - alias = 'Not available' + + return alias + + @property + def wikidata_alias_fmt(self): + '''Return a text formatted alias''' + + alias = 'Not available' + if self.symbol: + human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) + + if human_response and mouse_response and other_response: + alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) + + filtered_aliases = [] + seen = set() + for item in alias_list: + if item in seen: + continue + else: + filtered_aliases.append(item) + seen.add(item) + alias = "; ".join(filtered_aliases) return alias @@ -154,18 +184,27 @@ 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") @@ -189,7 +228,8 @@ def get_sample_data(): trait_dict['symbol'] = trait_ob.symbol trait_dict['location'] = trait_ob.location_repr elif trait_ob.dataset.type == "Publish": - trait_dict['pubmed_link'] = trait_ob.pubmed_link + if trait_ob.pubmed_id: + trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) @@ -205,6 +245,7 @@ def jsonable(trait): return dict(name=trait.name, symbol=trait.symbol, dataset=dataset.name, + dataset_name = dataset.shortname, description=trait.description_display, mean=trait.mean, location=trait.location_repr, @@ -216,7 +257,9 @@ def jsonable(trait): if trait.pubmed_id: return dict(name=trait.name, dataset=dataset.name, + dataset_name = dataset.shortname, description=trait.description_display, + abbreviation=trait.abbreviation, authors=trait.authors, pubmed_text=trait.pubmed_text, pubmed_link=trait.pubmed_link, @@ -227,7 +270,9 @@ def jsonable(trait): else: return dict(name=trait.name, dataset=dataset.name, + dataset_name = dataset.shortname, description=trait.description_display, + abbreviation=trait.abbreviation, authors=trait.authors, pubmed_text=trait.pubmed_text, lrs_score=trait.LRS_score_repr, @@ -237,6 +282,7 @@ def jsonable(trait): elif dataset.type == "Geno": return dict(name=trait.name, dataset=dataset.name, + dataset_name = dataset.shortname, location=trait.location_repr ) else: @@ -258,7 +304,7 @@ def jsonable_table_row(trait, dataset_name, index): additive = "N/A" else: additive = "%.3f" % round(float(trait.additive), 2) - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.symbol, @@ -274,7 +320,7 @@ def jsonable_table_row(trait, dataset_name, index): else: additive = "%.2f" % round(float(trait.additive), 2) if trait.pubmed_id: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.description_display, @@ -284,7 +330,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] else: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.description_display, @@ -294,7 +340,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] elif dataset.type == "Geno": - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.location_repr] @@ -307,21 +353,22 @@ 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.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, Publication.Authors, Publication.Title, Publication.Abstract, Publication.Journal, Publication.Volume, Publication.Pages, 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) @@ -371,17 +418,25 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait_info = g.db.execute(query, (string.join(dataset.display_fields,','), dataset.type, trait.name)).fetchone() + if trait_info: trait.haveinfo = True #XZ: assign SQL query result to trait attributes. for i, field in enumerate(dataset.display_fields): holder = trait_info[i] + # if isinstance(trait_info[i], basestring): + # logger.debug("HOLDER:", holder) + # logger.debug("HOLDER2:", holder.decode(encoding='latin1')) + # holder = unicode(trait_info[i], "utf-8", "ignore") if isinstance(trait_info[i], basestring): - holder = unicode(trait_info[i], "utf-8", "ignore") + holder = holder.encode('latin1') setattr(trait, field, holder) if dataset.type == 'Publish': + if trait.group_code: + trait.display_name = trait.group_code + "_" + str(trait.name) + trait.confidential = 0 if trait.pre_publication_description and not trait.pubmed_id: trait.confidential = 1 @@ -392,6 +447,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #phenotype traits, then display the pre-publication description instead #of the post-publication description if trait.confidential: + trait.abbreviation = trait.pre_publication_abbreviation trait.description_display = trait.pre_publication_description #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( @@ -401,11 +457,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): # # description = self.pre_publication_description else: + trait.abbreviation = trait.post_publication_abbreviation if description: trait.description_display = description.strip() else: trait.description_display = "" + trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + if not trait.year.isdigit(): trait.pubmed_text = "N/A" else: @@ -443,7 +504,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #LRS and its location trait.LRS_score_repr = "N/A" trait.LRS_location_repr = "N/A" + trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = "" if dataset.type == 'ProbeSet' and not trait.cellid: + trait.mean = "" query = """ SELECT ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive @@ -474,9 +537,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" else: trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" - else: - trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = "" - if dataset.type == 'Publish': query = """ |