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authorAlexander Kabui2021-03-16 11:38:13 +0300
committerGitHub2021-03-16 11:38:13 +0300
commit56ce88ad31dec3cece63e9370ca4e4c02139753b (patch)
tree766504dfaca75a14cc91fc3d88c41d1e775d415f /gn3/base
parent43d1bb7f6cd2b5890d5b3eb7c357caafda25a35c (diff)
downloadgenenetwork3-56ce88ad31dec3cece63e9370ca4e4c02139753b.tar.gz
delete unwanted correlation stuff (#5)
* delete unwanted correlation stuff * Refactor/clean up correlations (#4) * initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com> * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
Diffstat (limited to 'gn3/base')
-rw-r--r--gn3/base/__init__.py0
-rw-r--r--gn3/base/data_set.py882
-rw-r--r--gn3/base/mrna_assay_tissue_data.py94
-rw-r--r--gn3/base/species.py64
-rw-r--r--gn3/base/trait.py366
-rw-r--r--gn3/base/webqtlCaseData.py84
6 files changed, 0 insertions, 1490 deletions
diff --git a/gn3/base/__init__.py b/gn3/base/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/gn3/base/__init__.py
+++ /dev/null
diff --git a/gn3/base/data_set.py b/gn3/base/data_set.py
deleted file mode 100644
index 01913f2..0000000
--- a/gn3/base/data_set.py
+++ /dev/null
@@ -1,882 +0,0 @@
-
-import json
-import math
-import collections
-import requests
-from redis import Redis
-from flask import g
-from gn3.utility.db_tools import escape
-from gn3.utility.db_tools import mescape
-from gn3.utility.db_tools import create_in_clause
-from gn3.utility.tools import locate_ignore_error
-from gn3.db.calls import fetch1
-from gn3.db.calls import fetchone
-from gn3.db.webqtlDatabaseFunction import retrieve_species
-from gn3.utility import chunks
-
-from gn3.utility import get_group_samplelists
-from gn3.base.species import TheSpecies
-r = Redis()
-
-# should probably move this to its own configuration files
-
-USE_REDIS = True
-
-# todo move to config file
-GN2_BASE_URL = "https://genenetwork.org/"
-
-DS_NAME_MAP = {}
-
-# pylint: disable-all
-#todo file not linted
-# pylint: disable=C0103
-
-
-
-def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None):
-
- if dataset_name == "Temp":
- dataset_type = "Temp"
-
- if dataset_type is None:
- dataset_type = Dataset_Getter(dataset_name)
- dataset_ob = DS_NAME_MAP[dataset_type]
- dataset_class = globals()[dataset_ob]
-
- if dataset_type == "Temp":
- results = dataset_class(dataset_name, get_samplelist, group_name)
-
- else:
- results = dataset_class(dataset_name, get_samplelist)
-
- return results
-
-
-class DatasetType:
- def __init__(self, redis_instance):
- self.redis_instance = redis_instance
- self.datasets = {}
-
- data = self.redis_instance.get("dataset_structure")
- if data:
- self.datasets = json.loads(data)
-
- else:
-
- try:
-
- data = json.loads(requests.get(
- GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content)
-
- # todo:Refactor code below n^4 loop
-
- for species in data["datasets"]:
- for group in data["datasets"][species]:
- for dataset_type in data['datasets'][species][group]:
- for dataset in data['datasets'][species][group][dataset_type]:
-
- short_dataset_name = dataset[1]
- if dataset_type == "Phenotypes":
- new_type = "Publish"
-
- elif dataset_type == "Genotypes":
- new_type = "Geno"
- else:
- new_type = "ProbeSet"
-
- self.datasets[short_dataset_name] = new_type
-
- except Exception as e:
- raise e
-
- self.redis_instance.set(
- "dataset_structure", json.dumps(self.datasets))
-
- def set_dataset_key(self, t, name):
- """If name is not in the object's dataset dictionary, set it, and update
- dataset_structure in Redis
-
- args:
- t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
- 'other_pheno', 'geno'
- name: The name of the key to inserted in the datasets dictionary
-
- """
-
- sql_query_mapping = {
- 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
- """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
- 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
- """FROM InfoFiles, PublishFreeze, InbredSet """ +
- """WHERE InbredSet.Name = '{}' AND """ +
- """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
- """InfoFiles.InfoPageName = PublishFreeze.Name"""),
- 'other_pheno': ("""SELECT PublishFreeze.Name """ +
- """FROM PublishFreeze, InbredSet """ +
- """WHERE InbredSet.Name = '{}' AND """ +
- """PublishFreeze.InbredSetId = InbredSet.Id"""),
- 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
- """GenoFreeze.Name = "{}" """)
- }
-
- dataset_name_mapping = {
- "mrna_expr": "ProbeSet",
- "pheno": "Publish",
- "other_pheno": "Publish",
- "geno": "Geno",
- }
-
- group_name = name
- if t in ['pheno', 'other_pheno']:
- group_name = name.replace("Publish", "")
-
- results = g.db.execute(
- sql_query_mapping[t].format(group_name)).fetchone()
- if results:
- self.datasets[name] = dataset_name_mapping[t]
- self.redis_instance.set(
- "dataset_structure", json.dumps(self.datasets))
-
- return True
-
- return None
-
- def __call__(self, name):
- if name not in self.datasets:
- for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
-
- if(self.set_dataset_key(t, name)):
- # This has side-effects, with the end result being a truth-y value
- break
-
- return self.datasets.get(name, None)
-
-
-# Do the intensive work at startup one time only
-# could replace the code below
-Dataset_Getter = DatasetType(r)
-
-
-class DatasetGroup:
- """
- Each group has multiple datasets; each species has multiple groups.
-
- For example, Mouse has multiple groups (BXD, BXA, etc), and each group
- has multiple datasets associated with it.
-
- """
-
- def __init__(self, dataset, name=None):
- """This sets self.group and self.group_id"""
- if name == None:
- self.name, self.id, self.genetic_type = fetchone(
- dataset.query_for_group)
-
- else:
- self.name, self.id, self.genetic_type = fetchone(
- "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
-
- if self.name == 'BXD300':
- self.name = "BXD"
-
- self.f1list = None
-
- self.parlist = None
-
- self.get_f1_parent_strains()
-
- # remove below not used in correlation
-
- self.mapping_id, self.mapping_names = self.get_mapping_methods()
-
- self.species = retrieve_species(self.name)
-
- def get_f1_parent_strains(self):
- try:
- # should import ParInfo
- raise e
- # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
- f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
- except Exception as e:
- f1 = f12 = maternal = paternal = None
-
- if f1 and f12:
- self.f1list = [f1, f12]
-
- if maternal and paternal:
- self.parlist = [maternal, paternal]
-
- 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 = ["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:
- mapping_names = []
-
- return mapping_id, mapping_names
-
- def get_samplelist(self):
- result = None
- key = "samplelist:v3:" + self.name
- if USE_REDIS:
- result = r.get(key)
-
- if result is not None:
-
- self.samplelist = json.loads(result)
-
- else:
- # logger.debug("Cache not hit")
- # should enable logger
- genotype_fn = locate_ignore_error(self.name+".geno", 'genotype')
- if genotype_fn:
- self.samplelist = get_group_samplelists.get_samplelist(
- "geno", genotype_fn)
-
- else:
- self.samplelist = None
-
- if USE_REDIS:
- r.set(key, json.dumps(self.samplelist))
- r.expire(key, 60*5)
-
-
-class DataSet:
- """
- DataSet class defines a dataset in webqtl, can be either Microarray,
- Published phenotype, genotype, or user input dataset(temp)
-
- """
-
- def __init__(self, name, get_samplelist=True, group_name=None):
-
- assert name, "Need a name"
- self.name = name
- self.id = None
- self.shortname = None
- self.fullname = None
- self.type = None
- self.data_scale = None # ZS: For example log2
-
- self.setup()
-
- if self.type == "Temp": # Need to supply group name as input if temp trait
- # sets self.group and self.group_id and gets genotype
- self.group = DatasetGroup(self, name=group_name)
- else:
- self.check_confidentiality()
- self.retrieve_other_names()
- # sets self.group and self.group_id and gets genotype
- self.group = DatasetGroup(self)
- self.accession_id = self.get_accession_id()
- if get_samplelist == True:
- self.group.get_samplelist()
- self.species = TheSpecies(self)
-
- def get_desc(self):
- """Gets overridden later, at least for Temp...used by trait's get_given_name"""
- return None
-
-
- 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.
-
- If the data set name parameter is not found in the 'Name' field of
- the data set table, check if it is actually the FullName or
- ShortName instead.
-
- This is not meant to retrieve the data set info if no name at
- all is passed.
-
- """
-
- try:
- if self.type == "ProbeSet":
- query_args = tuple(escape(x) for x in (
- self.name,
- self.name,
- self.name))
-
- self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
- SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
- FROM ProbeSetFreeze, ProbeFreeze, Tissue
- WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
- AND ProbeFreeze.TissueId = Tissue.Id
- AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
- """ % (query_args), "/dataset/"+self.name+".json",
- lambda r: (r["id"], r["name"], r["full_name"],
- r["short_name"], r["data_scale"], r["tissue"])
- )
- else:
- query_args = tuple(escape(x) for x in (
- (self.type + "Freeze"),
- self.name,
- self.name,
- self.name))
-
- self.tissue = "N/A"
- self.id, self.name, self.fullname, self.shortname = fetchone("""
- SELECT Id, Name, FullName, ShortName
- FROM %s
- WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
- """ % (query_args))
-
- except TypeError as e:
- logger.debug(
- "Dataset {} is not yet available in GeneNetwork.".format(self.name))
- pass
-
- def get_trait_data(self, sample_list=None):
- if sample_list:
- self.samplelist = sample_list
- else:
- self.samplelist = self.group.samplelist
-
- if self.group.parlist != None and self.group.f1list != None:
- if (self.group.parlist + self.group.f1list) in self.samplelist:
- self.samplelist += self.group.parlist + self.group.f1list
-
- query = """
- SELECT Strain.Name, Strain.Id FROM Strain, Species
- WHERE Strain.Name IN {}
- and Strain.SpeciesId=Species.Id
- and Species.name = '{}'
- """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
- # logger.sql(query)
- results = dict(g.db.execute(query).fetchall())
- sample_ids = [results[item] for item in self.samplelist]
-
- # MySQL limits the number of tables that can be used in a join to 61,
- # so we break the sample ids into smaller chunks
- # Postgres doesn't have that limit, so we can get rid of this after we transition
- chunk_size = 50
- number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
- trait_sample_data = []
- for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
- if self.type == "Publish":
- dataset_type = "Phenotype"
- else:
- dataset_type = self.type
- temp = ['T%s.value' % item for item in sample_ids_step]
- if self.type == "Publish":
- query = "SELECT {}XRef.Id,".format(escape(self.type))
- else:
- query = "SELECT {}.Name,".format(escape(dataset_type))
- data_start_pos = 1
- query += ', '.join(temp)
- query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
- self.type,
- self.type))
-
- for item in sample_ids_step:
- query += """
- left join {}Data as T{} on T{}.Id = {}XRef.DataId
- and T{}.StrainId={}\n
- """.format(*mescape(self.type, item, item, self.type, item, item))
-
- if self.type == "Publish":
- query += """
- WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId
- and {}Freeze.Name = '{}'
- and {}.Id = {}XRef.{}Id
- order by {}.Id
- """.format(*mescape(self.type, self.type, self.type, self.name,
- dataset_type, self.type, dataset_type, dataset_type))
- else:
- query += """
- WHERE {}XRef.{}FreezeId = {}Freeze.Id
- and {}Freeze.Name = '{}'
- and {}.Id = {}XRef.{}Id
- order by {}.Id
- """.format(*mescape(self.type, self.type, self.type, self.type,
- self.name, dataset_type, self.type, self.type, dataset_type))
-
- results = g.db.execute(query).fetchall()
- trait_sample_data.append(results)
-
- trait_count = len(trait_sample_data[0])
- self.trait_data = collections.defaultdict(list)
-
- # put all of the separate data together into a dictionary where the keys are
- # trait names and values are lists of sample values
- for trait_counter in range(trait_count):
- trait_name = trait_sample_data[0][trait_counter][0]
- for chunk_counter in range(int(number_chunks)):
- self.trait_data[trait_name] += (
- trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
-
-
-class MrnaAssayDataSet(DataSet):
- '''
- An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait
-
- This used to be called ProbeSet, but that term only refers specifically to the Affymetrix
- platform and is far too specific.
-
- '''
- DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
-
- def setup(self):
- # Fields in the database table
- self.search_fields = ['Name',
- 'Description',
- 'Probe_Target_Description',
- 'Symbol',
- 'Alias',
- 'GenbankId',
- 'UniGeneId',
- 'RefSeq_TranscriptId']
-
- # Find out what display_fields is
- self.display_fields = ['name', 'symbol',
- 'description', 'probe_target_description',
- 'chr', 'mb',
- 'alias', 'geneid',
- 'genbankid', 'unigeneid',
- 'omim', 'refseq_transcriptid',
- 'blatseq', 'targetseq',
- 'chipid', 'comments',
- 'strand_probe', 'strand_gene',
- 'proteinid', 'uniprotid',
- 'probe_set_target_region',
- 'probe_set_specificity',
- 'probe_set_blat_score',
- 'probe_set_blat_mb_start',
- 'probe_set_blat_mb_end',
- 'probe_set_strand',
- 'probe_set_note_by_rw',
- 'flag']
-
- # Fields displayed in the search results table header
- self.header_fields = ['Index',
- 'Record',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
-
- # Todo: Obsolete or rename this field
- self.type = 'ProbeSet'
-
- self.query_for_group = '''
- SELECT
- InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
- FROM
- InbredSet, ProbeSetFreeze, ProbeFreeze
- WHERE
- ProbeFreeze.InbredSetId = InbredSet.Id AND
- ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
- ProbeSetFreeze.Name = "%s"
- ''' % escape(self.name)
-
- def check_confidentiality(self):
- return geno_mrna_confidentiality(self)
-
- def get_trait_info(self, trait_list=None, species=''):
-
- # Note: setting trait_list to [] is probably not a great idea.
- if not trait_list:
- trait_list = []
-
- for this_trait in trait_list:
-
- if not this_trait.haveinfo:
- this_trait.retrieveInfo(QTL=1)
-
- if not this_trait.symbol:
- this_trait.symbol = "N/A"
-
- # XZ, 12/08/2008: description
- # XZ, 06/05/2009: Rob asked to add probe target description
- description_string = str(
- str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string = str(
- str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
-
- if len(description_string) > 1 and description_string != 'None':
- description_display = description_string
- else:
- description_display = this_trait.symbol
-
- if (len(description_display) > 1 and description_display != 'N/A' and
- len(target_string) > 1 and target_string != 'None'):
- description_display = description_display + '; ' + target_string.strip()
-
- # Save it for the jinja2 template
- this_trait.description_display = description_display
-
- if this_trait.chr and this_trait.mb:
- this_trait.location_repr = 'Chr%s: %.6f' % (
- this_trait.chr, float(this_trait.mb))
-
- # Get mean expression value
- query = (
- """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
- where ProbeSetXRef.ProbeSetFreezeId = %s and
- ProbeSet.Id = ProbeSetXRef.ProbeSetId and
- ProbeSet.Name = '%s'
- """ % (escape(str(this_trait.dataset.id)),
- escape(this_trait.name)))
-
- #logger.debug("query is:", pf(query))
- logger.sql(query)
- result = g.db.execute(query).fetchone()
-
- mean = result[0] if result else 0
-
- if mean:
- this_trait.mean = "%2.3f" % mean
-
- # LRS and its location
- this_trait.LRS_score_repr = 'N/A'
- this_trait.LRS_location_repr = 'N/A'
-
- # Max LRS and its Locus location
- if this_trait.lrs and this_trait.locus:
- query = """
- select Geno.Chr, Geno.Mb from Geno, Species
- where Species.Name = '{}' and
- Geno.Name = '{}' and
- Geno.SpeciesId = Species.Id
- """.format(species, this_trait.locus)
- logger.sql(query)
- result = g.db.execute(query).fetchone()
-
- if result:
- lrs_chr, lrs_mb = result
- this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
- lrs_chr, float(lrs_mb))
-
- return trait_list
-
- def retrieve_sample_data(self, trait):
- query = """
- SELECT
- Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
- FROM
- (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
- left join ProbeSetSE on
- (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
- left join NStrain on
- (NStrain.DataId = ProbeSetData.Id AND
- NStrain.StrainId = ProbeSetData.StrainId)
- WHERE
- ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetFreeze.Name = '%s' AND
- ProbeSetXRef.DataId = ProbeSetData.Id AND
- ProbeSetData.StrainId = Strain.Id
- Order BY
- Strain.Name
- """ % (escape(trait), escape(self.name))
- # logger.sql(query)
- results = g.db.execute(query).fetchall()
- #logger.debug("RETRIEVED RESULTS HERE:", results)
- return results
-
- def retrieve_genes(self, column_name):
- query = """
- select ProbeSet.Name, ProbeSet.%s
- from ProbeSet,ProbeSetXRef
- where ProbeSetXRef.ProbeSetFreezeId = %s and
- ProbeSetXRef.ProbeSetId=ProbeSet.Id;
- """ % (column_name, escape(str(self.id)))
- # logger.sql(query)
- results = g.db.execute(query).fetchall()
-
- return dict(results)
-
-
-class TempDataSet(DataSet):
- '''Temporary user-generated data set'''
-
- DS_NAME_MAP['Temp'] = 'TempDataSet'
-
- def setup(self):
- self.search_fields = ['name',
- 'description']
-
- self.display_fields = ['name',
- 'description']
-
- self.header_fields = ['Name',
- 'Description']
-
- self.type = 'Temp'
-
- # Need to double check later how these are used
- self.id = 1
- self.fullname = 'Temporary Storage'
- self.shortname = 'Temp'
-
-
-class PhenotypeDataSet(DataSet):
- DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
-
- def setup(self):
-
- #logger.debug("IS A PHENOTYPEDATASET")
-
- # Fields in the database table
- self.search_fields = ['Phenotype.Post_publication_description',
- 'Phenotype.Pre_publication_description',
- 'Phenotype.Pre_publication_abbreviation',
- 'Phenotype.Post_publication_abbreviation',
- 'PublishXRef.mean',
- 'Phenotype.Lab_code',
- 'Publication.PubMed_ID',
- 'Publication.Abstract',
- 'Publication.Title',
- 'Publication.Authors',
- 'PublishXRef.Id']
-
- # Figure out what display_fields is
- 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',
- 'authors', 'title',
- 'abstract', 'journal',
- 'volume', 'pages',
- 'month', 'year',
- 'sequence', 'units', 'comments']
-
- # Fields displayed in the search results table header
- self.header_fields = ['Index',
- 'Record',
- 'Description',
- 'Authors',
- 'Year',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
-
- self.type = 'Publish'
-
- self.query_for_group = '''
- SELECT
- InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
- FROM
- InbredSet, PublishFreeze
- WHERE
- PublishFreeze.InbredSetId = InbredSet.Id AND
- PublishFreeze.Name = "%s"
- ''' % escape(self.name)
-
- def check_confidentiality(self):
- # (Urgently?) Need to write this
- pass
-
- def get_trait_info(self, trait_list, species=''):
- for this_trait in trait_list:
-
- if not this_trait.haveinfo:
- this_trait.retrieve_info(get_qtl_info=True)
-
- description = this_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
- if this_trait.confidential:
- this_trait.description_display = ""
- continue # todo for now, because no authorization features
-
- if not webqtlUtil.has_access_to_confidentail_phenotype_trait(
- privilege=self.privilege,
- userName=self.userName,
- authorized_users=this_trait.authorized_users):
-
- description = this_trait.pre_publication_description
-
- if len(description) > 0:
- this_trait.description_display = description.strip()
- else:
- this_trait.description_display = ""
-
- if not this_trait.year.isdigit():
- this_trait.pubmed_text = "N/A"
- else:
- this_trait.pubmed_text = this_trait.year
-
- if this_trait.pubmed_id:
- this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
-
- # LRS and its location
- this_trait.LRS_score_repr = "N/A"
- this_trait.LRS_location_repr = "N/A"
-
- if this_trait.lrs:
- query = """
- select Geno.Chr, Geno.Mb from Geno, Species
- where Species.Name = '%s' and
- Geno.Name = '%s' and
- Geno.SpeciesId = Species.Id
- """ % (species, this_trait.locus)
-
- result = g.db.execute(query).fetchone()
-
- if result:
- if result[0] and result[1]:
- LRS_Chr = result[0]
- LRS_Mb = result[1]
-
- this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
- LRS_Chr, float(LRS_Mb))
-
- def retrieve_sample_data(self, trait):
- query = """
- SELECT
- Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
- FROM
- (PublishData, Strain, PublishXRef, PublishFreeze)
- left join PublishSE on
- (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
- left join NStrain on
- (NStrain.DataId = PublishData.Id AND
- NStrain.StrainId = PublishData.StrainId)
- WHERE
- PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
- PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
- PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id
- Order BY
- Strain.Name
- """
-
- results = g.db.execute(query, (trait, self.id)).fetchall()
- return results
-
-
-class GenotypeDataSet(DataSet):
- DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
-
- def setup(self):
- # Fields in the database table
- self.search_fields = ['Name',
- 'Chr']
-
- # Find out what display_fields is
- self.display_fields = ['name',
- 'chr',
- 'mb',
- 'source2',
- 'sequence']
-
- # Fields displayed in the search results table header
- self.header_fields = ['Index',
- 'ID',
- 'Location']
-
- # Todo: Obsolete or rename this field
- self.type = 'Geno'
-
- self.query_for_group = '''
- SELECT
- InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
- FROM
- InbredSet, GenoFreeze
- WHERE
- GenoFreeze.InbredSetId = InbredSet.Id AND
- GenoFreeze.Name = "%s"
- ''' % escape(self.name)
-
- def check_confidentiality(self):
- return geno_mrna_confidentiality(self)
-
- def get_trait_info(self, trait_list, species=None):
- for this_trait in trait_list:
- if not this_trait.haveinfo:
- this_trait.retrieveInfo()
-
- if this_trait.chr and this_trait.mb:
- this_trait.location_repr = 'Chr%s: %.6f' % (
- this_trait.chr, float(this_trait.mb))
-
- def retrieve_sample_data(self, trait):
- query = """
- SELECT
- Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
- FROM
- (GenoData, GenoFreeze, Strain, Geno, GenoXRef)
- left join GenoSE on
- (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
- WHERE
- Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND
- GenoXRef.GenoFreezeId = GenoFreeze.Id AND
- GenoFreeze.Name = %s AND
- GenoXRef.DataId = GenoData.Id AND
- GenoData.StrainId = Strain.Id
- Order BY
- Strain.Name
- """
- results = g.db.execute(query,
- (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
- trait, self.name)).fetchall()
- return results
-
-
-def geno_mrna_confidentiality(ob):
- dataset_table = ob.type + "Freeze"
- #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
-
- query = '''SELECT Id, Name, FullName, confidentiality,
- AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
- #
- result = g.db.execute(query)
-
- (_dataset_id,
- _name,
- _full_name,
- confidential,
- _authorized_users) = result.fetchall()[0]
-
- if confidential:
- return True
diff --git a/gn3/base/mrna_assay_tissue_data.py b/gn3/base/mrna_assay_tissue_data.py
deleted file mode 100644
index 0f51ade..0000000
--- a/gn3/base/mrna_assay_tissue_data.py
+++ /dev/null
@@ -1,94 +0,0 @@
-
-# pylint: disable-all
-import collections
-
-from flask import g
-
-from gn3.utility.db_tools import create_in_clause
-from gn3.utility.db_tools import escape
-from gn3.utility.bunch import Bunch
-
-
-# from utility.logger import getLogger
-# logger = getLogger(__name__ )
-
-class MrnaAssayTissueData(object):
-
- def __init__(self, gene_symbols=None):
- self.gene_symbols = gene_symbols
- if self.gene_symbols == None:
- self.gene_symbols = []
-
- self.data = collections.defaultdict(Bunch)
-
- query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
- from (
- select Symbol, max(Mean) as maxmean
- from TissueProbeSetXRef
- where TissueProbeSetFreezeId=1 and '''
-
- # Note that inner join is necessary in this query to get distinct record in one symbol group
- # with highest mean value
- # Due to the limit size of TissueProbeSetFreezeId table in DB,
- # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
- if len(gene_symbols) == 0:
- query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
- as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
- and t.Mean = x.maxmean;
- '''
- else:
- in_clause = create_in_clause(gene_symbols)
-
- # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
- query += ''' Symbol in {} group by Symbol)
- as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
- and t.Mean = x.maxmean;
- '''.format(in_clause)
-
- results = g.db.execute(query).fetchall()
-
- lower_symbols = []
- for gene_symbol in gene_symbols:
- if gene_symbol != None:
- lower_symbols.append(gene_symbol.lower())
-
- for result in results:
- symbol = result[0]
- if symbol.lower() in lower_symbols:
- symbol = symbol.lower()
-
- self.data[symbol].gene_id = result.GeneId
- self.data[symbol].data_id = result.DataId
- self.data[symbol].chr = result.Chr
- self.data[symbol].mb = result.Mb
- self.data[symbol].description = result.description
- self.data[symbol].probe_target_description = result.Probe_Target_Description
-
- ###########################################################################
- # Input: cursor, symbolList (list), dataIdDict(Dict)
- # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
- # key is symbol, value is one list of expression values of one probeSet;
- # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
- # Attention! All keys are lower case!
- ###########################################################################
-
- def get_symbol_values_pairs(self):
- id_list = [self.data[symbol].data_id for symbol in self.data]
-
- symbol_values_dict = {}
-
- if len(id_list) > 0:
- query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
- FROM TissueProbeSetXRef, TissueProbeSetData
- WHERE TissueProbeSetData.Id IN {} and
- TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(create_in_clause(id_list))
-
- results = g.db.execute(query).fetchall()
- for result in results:
- if result.Symbol.lower() not in symbol_values_dict:
- symbol_values_dict[result.Symbol.lower()] = [result.value]
- else:
- symbol_values_dict[result.Symbol.lower()].append(
- result.value)
-
- return symbol_values_dict
diff --git a/gn3/base/species.py b/gn3/base/species.py
deleted file mode 100644
index 9fb08fb..0000000
--- a/gn3/base/species.py
+++ /dev/null
@@ -1,64 +0,0 @@
-
-# pylint: disable-all
-import collections
-from flask import g
-from dataclasses import dataclass
-
-class TheSpecies:
- def __init__(self, dataset=None, species_name=None):
- if species_name is not None:
- self.name = species_name
-
- self.chromosomes = Chromosomes(species=self.name)
-
- else:
- self.dataset = dataset
- self.chromosomes = Chromosomes(dataset=self.dataset)
-
-
-class Chromosomes:
- def __init__(self, dataset=None, species=None):
- self.chromosomes = collections.OrderedDict()
-
- if species is not None:
- query = """
- Select
- Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
- where
- Chr_Length.SpeciesId = Species.SpeciesId AND
- Species.Name = '%s'
- Order by OrderId
- """ % species.capitalize()
-
- else:
- self.dataset = dataset
-
- query = """
- Select
- Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
- where
- Chr_Length.SpeciesId = InbredSet.SpeciesId AND
- InbredSet.Name = '%s'
- Order by OrderId
- """ % self.dataset.group.name
-
- # logger.sql(query)
-
- results = g.db.execute(query).fetchall()
-
- for item in results:
- self.chromosomes[item.OrderId] = IndChromosome(
- item.Name, item.Length)
-
-
-# @dataclass
-class IndChromosome:
- def __init__(self,name,length):
- self.name= name
- self.length = length
-
- @property
- def mb_length(self):
- """Chromosome length in megabases"""
- return self.length/ 1000000
-
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
diff --git a/gn3/base/webqtlCaseData.py b/gn3/base/webqtlCaseData.py
deleted file mode 100644
index 8395af8..0000000
--- a/gn3/base/webqtlCaseData.py
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-
-
-# uncomment below
-
-# from utility.logger import getLogger
-# logger = getLogger(__name__)
-
-# import utility.tools
-
-# utility.tools.show_settings()
-# pylint: disable-all
-
-class webqtlCaseData:
- """one case data in one trait"""
-
- def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
- self.name = name
- self.name2 = name2 # Other name (for traits like BXD65a)
- self.value = value # Trait Value
- self.variance = variance # Trait Variance
- self.num_cases = num_cases # Number of individuals/cases
- self.extra_attributes = None
- self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word)
- self.outlier = None # Not set to True/False until later
-
- def __repr__(self):
- case_data_string = "<webqtlCaseData> "
- if self.value is not None:
- case_data_string += "value=%2.3f" % self.value
- if self.variance is not None:
- case_data_string += " variance=%2.3f" % self.variance
- if self.num_cases:
- case_data_string += " ndata=%s" % self.num_cases
- if self.name:
- case_data_string += " name=%s" % self.name
- if self.name2:
- case_data_string += " name2=%s" % self.name2
- return case_data_string
-
- @property
- def class_outlier(self):
- """Template helper"""
- if self.outlier:
- return "outlier"
- return ""
-
- @property
- def display_value(self):
- if self.value is not None:
- return "%2.3f" % self.value
- return "x"
-
- @property
- def display_variance(self):
- if self.variance is not None:
- return "%2.3f" % self.variance
- return "x"
-
- @property
- def display_num_cases(self):
- if self.num_cases is not None:
- return "%s" % self.num_cases
- return "x" \ No newline at end of file