Correlation api (#2)

* add file for correlation api

* register initial correlation api

* add correlation package

* add function  for getting page data

* delete loading page api

* modify code for correlation

* add tests folder for correlations

* fix error in correlation api

* add tests for correlation

* add tests for  correlation loading data

* add module for correlation computations

* modify api to return json when computing correlation

* add tests for computing correlation

* modify code for loading correlation data

* modify tests for correlation computation

* test loading correlation data using api endpoint

* add tests for asserting error in creating Correlation object

* add do correlation method

* add dummy tests for do_correlation method

* delete unused modules

* add tests for creating trait and dataset

* add intergration test for correlation api

* add tests for correlation api

* edit docorrelation method

* modify integration tests for correlation api

* modify tests for show_corr_results

* add create dataset function

* pep8 formatting and fix return value for api

* add more test data for doing correlation

* modify tests for correlation

* pep8 formatting

* add getting formatted corr type method

* import json library

add process samples method for correlation

* fix issue with sample_vals key_error

* create utility module for correlation

* refactor endpoint for /corr_compute

* add test and mocks for compute_correlation function

* add compute correlation function  and pep8 formatting

* move get genofile samplelist to utility module

* refactor code for CorrelationResults object

* pep8 formatting for module

* remove CorrelationResults from Api

* add base package

initialize data_set module with create_dataset,redis and Dataset_Getter

* set dataset_structure if redis is empty

* add callable for DatsetType

* add set_dataset_key method If name is not in the object's dataset dictionary

* add Dataset object and MrnaAssayDataSet

* add db_tools

* add mysql client

* add DatasetGroup object

* add species module

* get mapping method

* import helper functions and new dataset

* add connection to db before request

* add helper functions

* add logger module

* add get_group_samplelists module

* add logger for debug

* add code for adding sample_data

* pep8 formatting

* Add chunks module

* add correlation helper module

* add  get_sample_r_and_p_values method

add get_header_fields function

* add generate corr json method

* add function to retrieve_trait_info

* remove comments and clean up code in show_corr_results

* remove comments and clean up code for data_set module

* pep8 formatting for helper_functions module

* pep8 formatting for trait module

* add module for species

* add Temp Dataset Object

* add Phenotype Dataset

* add Genotype Dataset

* add rettrieve sample_sample_data method

* add webqtlUtil module

* add do lit correlation for all traits

* add webqtlCaseData:Settings not ported

* return the_trait for create trait method

* add correlation_test json data

* add tests fore show corr results

* add dictfier package

* add tests for show_corr_results

* add assertion for trait_id

* refactor code for show_corr_results

* add test file for compute_corr intergration tests

* add scipy dependency

* refactor show_corr_results object

add do lit correlation for trait_list

* add hmac module

* add bunch module:Dictionary using object notation

* add correlation functions

* add rpy2 dependency

* add hmac module

* add MrnaAssayTissueData object and get_symbol_values_pairs function

* add config module

* add get json_results method

* pep8 formatting remove comments

* add config file

* add db package

* refactor correlatio compuatation module

* add do tissue correlation for trait list

* add  do lit correlation for all traits

* add do tissue correlation for all traits

* add do_bicor for bicor method

* raise error for when initital start vars is None

* add support for both form and json data when for correlation input

* remove print statement and pep8 formatting

* add default settings file

* add tools module for locate_ignore_error

* refactor code remove comments for trait module

* Add new test data for  computing correlation

* pep8 formatting and use pickle

* refactor function for filtering form/json data

* remove unused imports

* remove mock functions in correlation_utility module

* refactor tests for compute correlation and pep8 formatting

* add tests for show_correlation results

* modify tests for show_corr_results

* add json files for tests

* pep8 formatting for show_corr_results

* Todo:Lint base files

* pylint for intergration tests

* add test module for test_corr_helpers

* Add test chunk module

* lint utility package

* refactoring and pep8 formatting

* implement simple metric for correlation

* add  hmac utility file

* add correlation prefix

* fix merge conflict

* minor fixes for endpoints

* import:python-scipy,python-sqlalchemy from guix

* add python mysqlclient

* remove pkg-resources from requirements

* add python-rpy3 from guix

* refactor code for species module

* pep8 formatting and refactor code

* add tests for genereating correlation results

* lint correlation functions

* fix failing tests for show_corr_results

* add new correlation test data fix errors

* fix issues related to getting group samplelists

* refactor intergration tests for correlation

* add todo  for refactoring_wanted_inputs

* replace custom Attribute setter with SimpleNamespace

* comparison of sample r correlation results btwn genenenetwork2 and genenetwork3

* delete AttributeSetter

* test request for /api/correlation/compute_correlation took 18.55710196495056 Seconds

* refactor tests and show_correlation results

* remove  unneccessary comments and print statements

* edit requirement txt file

* api/correlation took 114.29814600944519 Seconds for correlation resullts:20000

 - corr-type:lit

- corr-method:pearson

corr-dataset:corr_dataset:HC_M2_0606_P

* capture SQL_URI and GENENETWORK FILES path

* pep8 formatting edit && remove print statements

* delete filter_input function

update test and data for correlation

* add docstring for required correlation_input

* /api/correlation took 12.905632972717285 Seconds

 *  pearson

 * lit

 *dataset:HX_M2_0606_P

trait_id :1444666

p_range:(lower->-0.60,uppper->0.74)

corr_return_results: 100

* update integration and unittest for correlation

* add simple markdown docs for correlation

* update docs

* add tests and catch for invalid correlation_input

* minor fix for api

* Remove jupyter from deps

* guix.scm: Remove duplicate entry

* guix.scm: Add extra action items as comments

* Trim requirements.txt file

Co-authored-by: BonfaceKilz <me@bonfacemunyoki.com>

1 files changed, 886 insertions, 0 deletions

diff --git a/gn3/base/data_set.py b/gn3/base/data_set.py
new file mode 100644
index 0000000..e61e4eb
--- /dev/null
+++ b/gn3/base/data_set.py
@@ -0,0 +1,886 @@
+
+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
+
+    # Delete this eventually
+    @property
+    def riset():
+        Weve_Renamed_This_As_Group
+
+    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