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-rw-r--r--gn3/base/trait.py366
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 10:30:42 +0000