diff options
Diffstat (limited to 'gn3/base/trait.py')
| -rw-r--r-- | gn3/base/trait.py | 366 |
1 files changed, 0 insertions, 366 deletions
diff --git a/gn3/base/trait.py b/gn3/base/trait.py deleted file mode 100644 index f4be61c..0000000 --- a/gn3/base/trait.py +++ /dev/null @@ -1,366 +0,0 @@ - -# 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 |