diff options
Diffstat (limited to 'gn3/base/trait.py')
| -rw-r--r-- | gn3/base/trait.py | 366 |
1 files changed, 366 insertions, 0 deletions
diff --git a/gn3/base/trait.py b/gn3/base/trait.py new file mode 100644 index 0000000..f4be61c --- /dev/null +++ b/gn3/base/trait.py @@ -0,0 +1,366 @@ + +# pylint: disable-all +from flask import g +from redis import Redis +from gn3.utility.db_tools import escape +from gn3.base.webqtlCaseData import webqtlCaseData + + +def check_resource_availability(dataset, name=None): + + # todo add code for this + # should probably work on this has to do with authentication + return {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']} + + +def create_trait(**kw): + # work on check resource availability deals with authentication + assert bool(kw.get("dataset")) != bool( + kw.get('dataset_name')), "Needs dataset ob. or name" + + assert bool(kw.get("name")), "Need trait name" + + if kw.get('dataset_name'): + if kw.get('dataset_name') != "Temp": + dataset = create_dataset(kw.get('dataset_name')) + else: + dataset = kw.get('dataset') + + if dataset.type == 'Publish': + permissions = check_resource_availability( + dataset, kw.get('name')) + else: + permissions = check_resource_availability(dataset) + + if "view" in permissions['data']: + the_trait = GeneralTrait(**kw) + if the_trait.dataset.type != "Temp": + the_trait = retrieve_trait_info( + the_trait, + the_trait.dataset, + get_qtl_info=kw.get('get_qtl_info')) + + + return the_trait + + return None + + +class GeneralTrait: + def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): + assert bool(kw.get('dataset')) != bool( + kw.get('dataset_name')), "Needs dataset ob. or name" + # Trait ID, ProbeSet ID, Published ID, etc. + self.name = kw.get('name') + if kw.get('dataset_name'): + 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.cellid = kw.get('cellid') + self.identification = kw.get('identification', 'un-named trait') + self.haveinfo = kw.get('haveinfo', False) + self.sequence = kw.get('sequence') + self.data = kw.get('data', {}) + self.view = True + + # Sets defaults + self.locus = None + self.lrs = None + self.pvalue = None + self.mean = None + self.additive = None + 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" + + if kw.get('fullname'): + name2 = value.split("::") + if len(name2) == 2: + self.dataset, self.name = name2 + + elif len(name2) == 3: + self.dataset, self.name, self.cellid = name2 + + # Todo: These two lines are necessary most of the time, but + # perhaps not all of the time So we could add a simple if + # statement to short-circuit this if necessary + if get_sample_info is not False: + self = retrieve_sample_data(self, self.dataset) + + +def retrieve_sample_data(trait, dataset, samplelist=None): + if samplelist is None: + samplelist = [] + + 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() + + if results: + 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 Exception as e: + 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) + + return trait + +def retrieve_trait_info(trait, dataset, get_qtl_info=False): + assert dataset, "Dataset doesn't exist" + + the_url = None + # some code should be added added here + + try: + response = requests.get(the_url).content + trait_info = json.loads(response) + except: # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait + if dataset.type == 'Publish': + query = """ + SELECT + PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID, + CAST(Phenotype.Pre_publication_description AS BINARY), + CAST(Phenotype.Post_publication_description AS BINARY), + CAST(Phenotype.Original_description AS BINARY), + CAST(Phenotype.Pre_publication_abbreviation AS BINARY), + CAST(Phenotype.Post_publication_abbreviation AS BINARY), PublishXRef.mean, + Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, + CAST(Publication.Authors AS BINARY), CAST(Publication.Title AS BINARY), CAST(Publication.Abstract AS BINARY), + CAST(Publication.Journal AS BINARY), Publication.Volume, Publication.Pages, + Publication.Month, Publication.Year, PublishXRef.Sequence, + Phenotype.Units, PublishXRef.comments + FROM + 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) + + trait_info = g.db.execute(query).fetchone() + + # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name + # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. + elif dataset.type == 'ProbeSet': + display_fields_string = ', ProbeSet.'.join(dataset.display_fields) + display_fields_string = 'ProbeSet.' + display_fields_string + query = """ + SELECT %s + FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSet.Name = '%s' + """ % (escape(display_fields_string), + escape(dataset.name), + escape(str(trait.name))) + + trait_info = g.db.execute(query).fetchone() + # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name + # to avoid the problem of same marker name from different species. + elif dataset.type == 'Geno': + display_fields_string = ',Geno.'.join(dataset.display_fields) + display_fields_string = 'Geno.' + display_fields_string + query = """ + SELECT %s + FROM Geno, GenoFreeze, GenoXRef + WHERE + GenoXRef.GenoFreezeId = GenoFreeze.Id AND + GenoXRef.GenoId = Geno.Id AND + GenoFreeze.Name = '%s' AND + Geno.Name = '%s' + """ % (escape(display_fields_string), + escape(dataset.name), + escape(trait.name)) + + trait_info = g.db.execute(query).fetchone() + else: # Temp type + query = """SELECT %s FROM %s WHERE Name = %s""" + + trait_info = g.db.execute(query, + ','.join(dataset.display_fields), + dataset.type, trait.name).fetchone() + + if trait_info: + trait.haveinfo = True + for i, field in enumerate(dataset.display_fields): + holder = trait_info[i] + if isinstance(holder, bytes): + holder = holder.decode("utf-8", errors="ignore") + 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 + + description = trait.post_publication_description + + # If the dataset is confidential and the user has access to confidential + # phenotype traits, then display the pre-publication description instead + # of the post-publication description + trait.description_display = "" + if not trait.pubmed_id: + trait.abbreviation = trait.pre_publication_abbreviation + trait.description_display = trait.pre_publication_description + else: + trait.abbreviation = trait.post_publication_abbreviation + if description: + trait.description_display = description.strip() + + if not trait.year.isdigit(): + trait.pubmed_text = "N/A" + else: + trait.pubmed_text = trait.year + + # moved to config + + PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" + + if trait.pubmed_id: + trait.pubmed_link = PUBMEDLINK_URL % trait.pubmed_id + + if dataset.type == 'ProbeSet' and dataset.group: + description_string = trait.description + target_string = trait.probe_target_description + + if str(description_string or "") != "" and description_string != 'None': + description_display = description_string + else: + description_display = trait.symbol + + if (str(description_display or "") != "" and + description_display != 'N/A' and + str(target_string or "") != "" and target_string != 'None'): + description_display = description_display + '; ' + target_string.strip() + + # Save it for the jinja2 template + trait.description_display = description_display + + trait.location_repr = 'N/A' + if trait.chr and trait.mb: + trait.location_repr = 'Chr%s: %.6f' % ( + trait.chr, float(trait.mb)) + + elif dataset.type == "Geno": + trait.location_repr = 'N/A' + if trait.chr and trait.mb: + trait.location_repr = 'Chr%s: %.6f' % ( + trait.chr, float(trait.mb)) + + if get_qtl_info: + # 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 + FROM + ProbeSetXRef, ProbeSet + WHERE + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSet.Name = "{}" AND + ProbeSetXRef.ProbeSetFreezeId ={} + """.format(trait.name, dataset.id) + + trait_qtl = g.db.execute(query).fetchone() + if trait_qtl: + trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl + if trait.locus: + query = """ + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = '{}' and + Geno.Name = '{}' and + Geno.SpeciesId = Species.Id + """.format(dataset.group.species, trait.locus) + + result = g.db.execute(query).fetchone() + if result: + trait.locus_chr = result[0] + trait.locus_mb = result[1] + else: + trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" + else: + trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" + + if dataset.type == 'Publish': + query = """ + SELECT + PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive + FROM + PublishXRef, PublishFreeze + WHERE + PublishXRef.Id = %s AND + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishFreeze.Id =%s + """ % (trait.name, dataset.id) + + trait_qtl = g.db.execute(query).fetchone() + if trait_qtl: + trait.locus, trait.lrs, trait.additive = trait_qtl + if trait.locus: + query = """ + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = '{}' and + Geno.Name = '{}' and + Geno.SpeciesId = Species.Id + """.format(dataset.group.species, trait.locus) + + result = g.db.execute(query).fetchone() + if result: + trait.locus_chr = result[0] + trait.locus_mb = result[1] + else: + 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.lrs = trait.additive = "" + if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "": + trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( + trait.locus_chr, float(trait.locus_mb)) + if str(trait.lrs or "") != "": + trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs + else: + raise KeyError(repr(trait.name) + + ' information is not found in the database.') + return trait |