Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

7 files changed, 1924 insertions, 0 deletions

diff --git a/gn2/wqflask/api/__init__.py b/gn2/wqflask/api/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/wqflask/api/__init__.py
diff --git a/gn2/wqflask/api/correlation.py b/gn2/wqflask/api/correlation.py
new file mode 100644
index 00000000..090d13ac
--- /dev/null
+++ b/gn2/wqflask/api/correlation.py
@@ -0,0 +1,244 @@
+import collections
+import scipy
+import numpy
+
+from gn2.base import data_set
+from gn2.base.trait import create_trait, retrieve_sample_data
+from gn2.utility import corr_result_helpers
+from gn2.utility.tools import get_setting
+from gn2.wqflask.correlation import correlation_functions
+from gn2.wqflask.database import database_connection
+
+def do_correlation(start_vars):
+    if 'db' not in start_vars:
+        raise ValueError("'db' not found!")
+    if 'target_db' not in start_vars:
+        raise ValueError("'target_db' not found!")
+    if 'trait_id' not in start_vars:
+        raise ValueError("'trait_id' not found!")
+
+    this_dataset = data_set.create_dataset(dataset_name=start_vars['db'])
+    target_dataset = data_set.create_dataset(
+        dataset_name=start_vars['target_db'])
+    this_trait = create_trait(dataset=this_dataset,
+                              name=start_vars['trait_id'])
+    this_trait = retrieve_sample_data(this_trait, this_dataset)
+
+    corr_params = init_corr_params(start_vars)
+
+    corr_results = calculate_results(
+        this_trait, this_dataset, target_dataset, corr_params)
+
+    final_results = []
+    for _trait_counter, trait in enumerate(list(corr_results.keys())[:corr_params['return_count']]):
+        if corr_params['type'] == "tissue":
+            [sample_r, num_overlap, sample_p, symbol] = corr_results[trait]
+            result_dict = {
+                "trait": trait,
+                "sample_r": sample_r,
+                "#_strains": num_overlap,
+                "p_value": sample_p,
+                "symbol": symbol
+            }
+        elif corr_params['type'] == "literature" or corr_params['type'] == "lit":
+            [gene_id, sample_r] = corr_results[trait]
+            result_dict = {
+                "trait": trait,
+                "sample_r": sample_r,
+                "gene_id": gene_id
+            }
+        else:
+            [sample_r, sample_p, num_overlap] = corr_results[trait]
+            result_dict = {
+                "trait": trait,
+                "sample_r": sample_r,
+                "#_strains": num_overlap,
+                "p_value": sample_p
+            }
+        final_results.append(result_dict)
+    return final_results
+
+
+def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
+    corr_results = {}
+
+    target_dataset.get_trait_data()
+
+    if corr_params['type'] == "tissue":
+        trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
+        corr_results = do_tissue_correlation_for_all_traits(
+            this_trait, trait_symbol_dict, corr_params)
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
+                                                        key=lambda t: -abs(t[1][1])))
+    # ZS: Just so a user can use either "lit" or "literature"
+    elif corr_params['type'] == "literature" or corr_params['type'] == "lit":
+        trait_geneid_dict = this_dataset.retrieve_genes("GeneId")
+        corr_results = do_literature_correlation_for_all_traits(
+            this_trait, this_dataset, trait_geneid_dict, corr_params)
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
+                                                        key=lambda t: -abs(t[1][1])))
+    else:
+        for target_trait, target_vals in list(target_dataset.trait_data.items()):
+            result = get_sample_r_and_p_values(
+                this_trait, this_dataset, target_vals, target_dataset, corr_params['type'])
+            if result is not None:
+                corr_results[target_trait] = result
+
+        sorted_results = collections.OrderedDict(
+            sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0])))
+
+    return sorted_results
+
+
+def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
+    # Gets tissue expression values for the primary trait
+    primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+        symbol_list=[this_trait.symbol])
+
+    if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
+        primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower(
+        )]
+
+        corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+            symbol_list=list(trait_symbol_dict.values()))
+
+        tissue_corr_data = {}
+        for trait, symbol in list(trait_symbol_dict.items()):
+            if symbol and symbol.lower() in corr_result_tissue_vals_dict:
+                this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower(
+                )]
+
+                result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
+                                                                            this_trait_tissue_values,
+                                                                            corr_params['method'])
+
+                tissue_corr_data[trait] = [
+                    result[0], result[1], result[2], symbol]
+
+        return tissue_corr_data
+
+
+def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params):
+    input_trait_mouse_gene_id = convert_to_mouse_gene_id(
+        target_dataset.group.species.lower(), this_trait.geneid)
+
+    lit_corr_data = {}
+    for trait, gene_id in list(trait_geneid_dict.items()):
+        mouse_gene_id = convert_to_mouse_gene_id(
+            target_dataset.group.species.lower(), gene_id)
+
+        if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
+            result = ""
+            with database_connection(get_setting("SQL_URI")) as conn:
+                with conn.cursor() as cursor:
+                    cursor.execute(
+                        ("SELECT value FROM LCorrRamin3 "
+                         "WHERE GeneId1=%s AND GeneId2=%s"),
+                        (mouse_gene_id,
+                         input_trait_mouse_gene_id))
+                    result = cursor.fetchone()
+                    if not result:
+                        cursor.execute(
+                            ("SELECT value FROM LCorrRamin3 "
+                             "WHERE GeneId2=%s AND GeneId1=%s"),
+                            (mouse_gene_id,
+                             input_trait_mouse_gene_id))
+                        result = cursor.fetchone()
+            if result:
+                lit_corr = result[0]
+                lit_corr_data[trait] = [gene_id, lit_corr]
+            else:
+                lit_corr_data[trait] = [gene_id, 0]
+        else:
+            lit_corr_data[trait] = [gene_id, 0]
+
+    return lit_corr_data
+
+
+def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type):
+    """
+    Calculates the sample r (or rho) and p-value
+
+    Given a primary trait and a target trait's sample values,
+    calculates either the pearson r or spearman rho and the p-value
+    using the corresponding scipy functions.
+    """
+
+    this_trait_vals = []
+    shared_target_vals = []
+    for i, sample in enumerate(target_dataset.group.samplelist):
+        if sample in this_trait.data:
+            this_sample_value = this_trait.data[sample].value
+            target_sample_value = target_vals[i]
+            this_trait_vals.append(this_sample_value)
+            shared_target_vals.append(target_sample_value)
+
+    this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(
+        this_trait_vals, shared_target_vals)
+
+    if type == 'pearson':
+        sample_r, sample_p = scipy.stats.pearsonr(
+            this_trait_vals, shared_target_vals)
+    else:
+        sample_r, sample_p = scipy.stats.spearmanr(
+            this_trait_vals, shared_target_vals)
+
+    if num_overlap > 5:
+        if numpy.isnan(sample_r):
+            return None
+        else:
+            return [sample_r, sample_p, num_overlap]
+
+
+def convert_to_mouse_gene_id(species=None, gene_id=None):
+    """If the species is rat or human, translate the gene_id to the mouse geneid
+
+    If there is no input gene_id or there's no corresponding mouse gene_id, return None
+
+    """
+    if not gene_id:
+        return None
+
+    mouse_gene_id = None
+    with database_connection(get_setting("SQL_URI")) as conn:
+        with conn.cursor() as cursor:
+            if species == 'mouse':
+                mouse_gene_id = gene_id
+            elif species == 'rat':
+                cursor.execute(
+                    ("SELECT mouse FROM GeneIDXRef "
+                     "WHERE rat=%s"), gene_id)
+                result = cursor.fetchone()
+                if result:
+                    mouse_gene_id = result[0]
+            elif species == 'human':
+                cursor.execute(
+                    "SELECT mouse FROM GeneIDXRef "
+                    "WHERE human=%s", gene_id)
+                result = cursor.fetchone()
+                if result:
+                    mouse_gene_id = result[0]
+    return mouse_gene_id
+
+
+def init_corr_params(start_vars):
+    method = "pearson"
+    if 'method' in start_vars:
+        method = start_vars['method']
+
+    type = "sample"
+    if 'type' in start_vars:
+        type = start_vars['type']
+
+    return_count = 500
+    if 'return_count' in start_vars:
+        assert(start_vars['return_count'].isdigit())
+        return_count = int(start_vars['return_count'])
+
+    corr_params = {
+        'method': method,
+        'type': type,
+        'return_count': return_count
+    }
+
+    return corr_params
diff --git a/gn2/wqflask/api/gen_menu.py b/gn2/wqflask/api/gen_menu.py
new file mode 100644
index 00000000..45d5739e
--- /dev/null
+++ b/gn2/wqflask/api/gen_menu.py
@@ -0,0 +1,217 @@
+from gn3.db.species import get_all_species
+
+def gen_dropdown_json(conn):
+    """Generates and outputs (as json file) the data for the main dropdown menus on
+    the home page
+    """
+    species = get_all_species(conn)
+    groups = get_groups(species, conn)
+    types = get_types(groups, conn)
+    datasets = get_datasets(types, conn)
+    return dict(species=species,
+                groups=groups,
+                types=types,
+                datasets=datasets)
+
+
+def get_groups(species, conn):
+    """Build groups list"""
+    groups = {}
+    with conn.cursor() as cursor:
+        for species_name, _species_full_name in species:
+            groups[species_name] = []
+            query = ("SELECT InbredSet.Name, InbredSet.FullName, "
+                 "IFNULL(InbredSet.Family, 'None') "
+                 "FROM InbredSet, Species WHERE Species.Name = '{}' "
+                 "AND InbredSet.SpeciesId = Species.Id GROUP by "
+                 "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+                 "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+                 "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+                 "InbredSet.MenuOrderId ASC").format(species_name)
+            cursor.execute(query)
+            results = cursor.fetchall()
+            for result in results:
+                family_name = "Family:" + str(result[2])
+                groups[species_name].append(
+                    [str(result[0]), str(result[1]), family_name])
+    return groups
+
+
+def get_types(groups, conn):
+    """Build types list"""
+    types = {}
+
+    for species, group_dict in list(groups.items()):
+        types[species] = {}
+        for group_name, _group_full_name, _family_name in group_dict:
+            if phenotypes_exist(group_name, conn):
+                types[species][group_name] = [
+                    ("Phenotypes", "Traits and Cofactors", "Phenotypes")]
+            if genotypes_exist(group_name, conn):
+                if group_name in types[species]:
+                    types[species][group_name] += [
+                        ("Genotypes", "DNA Markers and SNPs", "Genotypes")]
+                else:
+                    types[species][group_name] = [
+                        ("Genotypes", "DNA Markers and SNPs", "Genotypes")]
+            if group_name in types[species]:
+                types_list = build_types(species, group_name, conn)
+                if len(types_list) > 0:
+                    types[species][group_name] += types_list
+            else:
+                types_list = build_types(species, group_name, conn)
+                if len(types_list) > 0:
+                    types[species][group_name] = types_list
+                else:
+                    types[species].pop(group_name, None)
+                    groups[species] = list(
+                        group for group in groups[species]
+                        if group[0] != group_name)
+    return types
+
+
+def phenotypes_exist(group_name, conn):
+    results = []
+    with conn.cursor() as cursor:
+        cursor.execute(
+            ("SELECT Name FROM PublishFreeze "
+             "WHERE PublishFreeze.Name = "
+             "'{}'").format(group_name + "Publish"))
+        results = cursor.fetchone()
+    return bool(results)
+
+
+def genotypes_exist(group_name, conn):
+    with conn.cursor() as cursor:
+        cursor.execute(
+            ("SELECT Name FROM GenoFreeze " +
+             "WHERE GenoFreeze.Name = '{}'").format(
+                 group_name + "Geno"))
+        results = cursor.fetchone()
+        return bool(results)
+
+
+def build_types(species, group, conn):
+    """Fetches tissues
+
+    Gets the tissues with data for this species/group
+    (all types except phenotype/genotype are tissues)
+
+    """
+
+    query = ("SELECT DISTINCT Tissue.Name "
+             "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+             "Tissue, Species WHERE Species.Name = '{0}' "
+             "AND Species.Id = InbredSet.SpeciesId AND "
+             "InbredSet.Name = '{1}' AND ProbeFreeze.TissueId = "
+             "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id "
+             "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+             "ORDER BY Tissue.Name").format(species, group)
+
+    results = []
+    with conn.cursor() as cursor:
+        cursor.execute(query)
+        for result in cursor.fetchall():
+            if bool(result):
+                these_datasets = build_datasets(species,
+                                                group, result[0], conn)
+                if len(these_datasets) > 0:
+                    results.append([str(result[0]), str(result[0]),
+                                    "Molecular Traits"])
+    return results
+
+
+def get_datasets(types, conn):
+    """Build datasets list"""
+    datasets = {}
+    for species, group_dict in list(types.items()):
+        datasets[species] = {}
+        for group, type_list in list(group_dict.items()):
+            datasets[species][group] = {}
+            for type_name in type_list:
+                these_datasets = build_datasets(species, group,
+                                                type_name[0], conn)
+                if bool(these_datasets):
+                    datasets[species][group][type_name[0]] = these_datasets
+
+    return datasets
+
+
+def build_datasets(species, group, type_name, conn):
+    """Gets dataset names from database"""
+    dataset_text = dataset_value = None
+    datasets = []
+    with conn.cursor() as cursor:
+        if type_name == "Phenotypes":
+            cursor.execute(
+                ("SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, "
+                 "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, "
+                 "InbredSet WHERE InbredSet.Name = '{}' AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id AND "
+                 "InfoFiles.InfoPageName = PublishFreeze.Name "
+                 "ORDER BY PublishFreeze.CreateTime ASC").format(group))
+            results = cursor.fetchall()
+            if bool(results):
+                for result in results:
+                    dataset_id = str(result[0])
+                    dataset_value = str(result[1])
+                    dataset_text = str(result[2])
+                    if group == 'MDP':
+                        dataset_text = "Mouse Phenome Database"
+
+                    datasets.append([dataset_id, dataset_value, dataset_text])
+            else:
+                cursor.execute(
+                    ("SELECT PublishFreeze.Name, PublishFreeze.FullName "
+                     "FROM PublishFreeze, InbredSet "
+                     "WHERE InbredSet.Name = '{}' AND "
+                     "PublishFreeze.InbredSetId = InbredSet.Id "
+                     "ORDER BY PublishFreeze.CreateTime ASC")
+                    .format(group))
+                result = cursor.fetchone()
+                dataset_id = "None"
+                dataset_value = str(result[0])
+                dataset_text = str(result[1])
+                datasets.append([dataset_id, dataset_value, dataset_text])
+
+        elif type_name == "Genotypes":
+            cursor.execute(
+                ("SELECT InfoFiles.GN_AccesionId "
+                 "FROM InfoFiles, GenoFreeze, InbredSet "
+                 "WHERE InbredSet.Name = '{}' AND "
+                 "GenoFreeze.InbredSetId = InbredSet.Id AND "
+                 "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+                 "ORDER BY GenoFreeze.CreateTime "
+                 "DESC").format(group))
+            results = cursor.fetchone()
+            dataset_id = "None"
+            if bool(results):
+                dataset_id = str(results[0])
+
+            dataset_value = "%sGeno" % group
+            dataset_text = "%s Genotypes" % group
+            datasets.append([dataset_id, dataset_value, dataset_text])
+
+        else:  # for mRNA expression/ProbeSet
+            cursor.execute(
+                ("SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+                 "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+                 "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+                 "Species.Name = '{0}' AND Species.Id = "
+                 "InbredSet.SpeciesId AND InbredSet.Name = '{1}' "
+                 "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                 "AND Tissue.Name = '{2}' AND ProbeFreeze.TissueId = "
+                 "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id "
+                 "AND ProbeSetFreeze.public > 0 "
+                 "ORDER BY -ProbeSetFreeze.OrderList DESC, "
+                 "ProbeSetFreeze.CreateTime "
+                 "DESC").format(species, group, type_name))
+            results = cursor.fetchall()
+            datasets = []
+            for dataset_info in results:
+                this_dataset_info = []
+                for info in dataset_info:
+                    this_dataset_info.append(str(info))
+                datasets.append(this_dataset_info)
+
+    return datasets
diff --git a/gn2/wqflask/api/jobs.py b/gn2/wqflask/api/jobs.py
new file mode 100644
index 00000000..7a948e1a
--- /dev/null
+++ b/gn2/wqflask/api/jobs.py
@@ -0,0 +1,54 @@
+import uuid
+from datetime import datetime
+
+from redis import Redis
+from pymonad.io import IO
+from flask import Blueprint, render_template
+
+from gn2.jobs.jobs import job
+
+jobs = Blueprint("jobs", __name__)
+
+@jobs.route("/debug/<uuid:job_id>")
+def debug_job(job_id: uuid.UUID):
+    """Display job data to assist in debugging."""
+    from gn2.utility.tools import REDIS_URL # Avoids circular import error
+
+    def __stream_to_lines__(stream):
+        removables = (
+            "Set global log level to", "runserver.py: ******",
+            "APPLICATION_ROOT:", "DB_", "DEBUG:", "ELASTICSEARCH_", "ENV:",
+            "EXPLAIN_TEMPLATE_LOADING:", "GEMMA_", "GENENETWORK_FILES",
+            "GITHUB_", "GN2_", "GN3_", "GN_", "HOME:", "JSONIFY_", "JS_",
+            "JSON_", "LOG_", "MAX_", "ORCID_", "PERMANENT_", "PLINK_",
+            "PREFERRED_URL_SCHEME", "PRESERVE_CONTEXT_ON_EXCEPTION",
+            "PROPAGATE_EXCEPTIONS", "REAPER_COMMAND", "REDIS_URL", "SECRET_",
+            "SECURITY_", "SEND_FILE_MAX_AGE_DEFAULT", "SERVER_", "SESSION_",
+            "SMTP_", "SQL_", "TEMPLATES_", "TESTING:", "TMPDIR", "TRAP_",
+            "USE_", "WEBSERVER_")
+        return tuple(filter(
+            lambda line: not any(line.startswith(item) for item in removables),
+            stream.split("\n")))
+
+    def __fmt_datetime(val):
+        return datetime.strptime(val, "%Y-%m-%dT%H:%M:%S.%f").strftime(
+            "%A, %d %B %Y at %H:%M:%S.%f")
+
+    def __render_debug_page__(job):
+        job_details = {key.replace("-", "_"): val for key,val in job.items()}
+        return render_template(
+            "jobs/debug.html",
+            **{
+                **job_details,
+                "request_received_time": __fmt_datetime(
+                    job_details["request_received_time"]),
+                "stderr": __stream_to_lines__(job_details["stderr"]),
+                "stdout": __stream_to_lines__(job_details["stdout"])
+            })
+
+    with Redis.from_url(REDIS_URL, decode_responses=True) as rconn:
+        the_job = job(rconn, job_id)
+
+    return the_job.maybe(
+        render_template("jobs/no-such-job.html", job_id=job_id),
+        lambda job: __render_debug_page__(job))
diff --git a/gn2/wqflask/api/mapping.py b/gn2/wqflask/api/mapping.py
new file mode 100644
index 00000000..1e330963
--- /dev/null
+++ b/gn2/wqflask/api/mapping.py
@@ -0,0 +1,186 @@
+from gn2.base import data_set
+from gn2.base.trait import create_trait, retrieve_sample_data
+
+from gn2.wqflask.marker_regression import gemma_mapping, rqtl_mapping
+from gn2.wqflask.show_trait.show_trait import normf
+
+def do_mapping_for_api(start_vars):
+    if ('db' not in start_vars) or ("trait_id" not in start_vars):
+        raise ValueError("Mapping: db and trait_id are not in start_vars")
+
+    dataset = data_set.create_dataset(dataset_name=start_vars['db'])
+    dataset.group.get_markers()
+    this_trait = create_trait(dataset=dataset, name=start_vars['trait_id'])
+    this_trait = retrieve_sample_data(this_trait, dataset)
+
+    samples = []
+    vals = []
+
+    mapping_params = initialize_parameters(start_vars, dataset, this_trait)
+
+    genofile_samplelist = []
+    if mapping_params.get('genofile'):
+        dataset.group.genofile = mapping_params['genofile']
+        genofile_samplelist = get_genofile_samplelist(dataset)
+
+    if (len(genofile_samplelist) > 0):
+        samplelist = genofile_samplelist
+        for sample in samplelist:
+            in_trait_data = False
+            for item in this_trait.data:
+                if this_trait.data[item].name == sample:
+                    value = str(this_trait.data[item].value)
+                    samples.append(item)
+                    vals.append(value)
+                    in_trait_data = True
+                    break
+            if not in_trait_data:
+                vals.append("x")
+    else:
+        samplelist = dataset.group.samplelist
+        for sample in samplelist:
+            in_trait_data = False
+            for item in this_trait.data:
+                if this_trait.data[item].name == sample:
+                    value = str(this_trait.data[item].value)
+                    samples.append(item)
+                    vals.append(value)
+                    in_trait_data = True
+                    break
+            if not in_trait_data:
+                vals.append("x")
+
+    if mapping_params.get('transform') == "qnorm":
+        vals_minus_x = [float(val) for val in vals if val != "x"]
+        qnorm_vals = normf(vals_minus_x)
+        qnorm_vals_with_x = []
+        counter = 0
+        for val in vals:
+            if val == "x":
+                qnorm_vals_with_x.append("x")
+            else:
+                qnorm_vals_with_x.append(qnorm_vals[counter])
+                counter += 1
+
+        vals = qnorm_vals_with_x
+
+    # It seems to take an empty string as default. This should probably be changed.
+    covariates = ""
+
+    if mapping_params.get('mapping_method') == "gemma":
+        header_row = ["name", "chr", "Mb", "lod_score", "p_value"]
+        # gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
+        if mapping_params.get('use_loco') == "True":
+            result_markers = gemma_mapping.run_gemma(
+                this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0]
+        else:
+            result_markers = gemma_mapping.run_gemma(
+                this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])
+    elif mapping_params.get('mapping_method') == "rqtl":
+        header_row = ["name", "chr", "cM", "lod_score"]
+        if mapping_params['num_perm'] > 0:
+            _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl(this_trait.name, vals, samples, dataset, None, "Mb", mapping_params['rqtl_model'],
+                                                                                             mapping_params['rqtl_method'], mapping_params['num_perm'], None,
+                                                                                             mapping_params['do_control'], mapping_params['control_marker'],
+                                                                                             mapping_params['manhattan_plot'], None)
+        else:
+            result_markers = rqtl_mapping.run_rqtl(this_trait.name, vals, samples, dataset, None, "Mb", mapping_params['rqtl_model'],
+                                                   mapping_params['rqtl_method'], mapping_params['num_perm'], None,
+                                                   mapping_params['do_control'], mapping_params['control_marker'],
+                                                   mapping_params['manhattan_plot'], None)
+
+    if mapping_params.get('limit_to'):
+        result_markers = result_markers[:mapping_params['limit_to']]
+
+    if mapping_params.get('format') == "csv":
+        output_rows = []
+        output_rows.append(header_row)
+        for marker in result_markers:
+            this_row = [marker[header] for header in header_row]
+            output_rows.append(this_row)
+
+        return output_rows, mapping_params['format']
+    elif mapping_params['format'] == "json":
+        return result_markers, mapping_params['format']
+    else:
+        return result_markers, None
+
+
+def initialize_parameters(start_vars, dataset, this_trait):
+    mapping_params = {}
+
+    mapping_params['format'] = "json"
+    if 'format' in start_vars:
+        mapping_params['format'] = start_vars['format']
+
+    mapping_params['limit_to'] = False
+    if 'limit_to' in start_vars:
+        if start_vars['limit_to'].isdigit():
+            mapping_params['limit_to'] = int(start_vars['limit_to'])
+
+    mapping_params['mapping_method'] = "gemma"
+    if 'method' in start_vars:
+        mapping_params['mapping_method'] = start_vars['method']
+
+    if mapping_params['mapping_method'] == "rqtl":
+        mapping_params['rqtl_method'] = "hk"
+        mapping_params['rqtl_model'] = "normal"
+        mapping_params['do_control'] = False
+        mapping_params['control_marker'] = ""
+        mapping_params['manhattan_plot'] = True
+        mapping_params['pair_scan'] = False
+        if 'rqtl_method' in start_vars:
+            mapping_params['rqtl_method'] = start_vars['rqtl_method']
+        if 'rqtl_model' in start_vars:
+            mapping_params['rqtl_model'] = start_vars['rqtl_model']
+        if 'control_marker' in start_vars:
+            mapping_params['control_marker'] = start_vars['control_marker']
+            mapping_params['do_control'] = True
+        if 'pair_scan' in start_vars:
+            if start_vars['pair_scan'].lower() == "true":
+                mapping_params['pair_scan'] = True
+
+        if 'interval_mapping' in start_vars:
+            if start_vars['interval_mapping'].lower() == "true":
+                mapping_params['manhattan_plot'] = False
+        elif 'manhattan_plot' in start_vars:
+            if start_vars['manhattan_plot'].lower() != "true":
+                mapping_params['manhattan_plot'] = False
+
+    mapping_params['maf'] = 0.01
+    if 'maf' in start_vars:
+        mapping_params['maf'] = start_vars['maf']  # Minor allele frequency
+
+    mapping_params['use_loco'] = True
+    if 'use_loco' in start_vars:
+        if (start_vars['use_loco'].lower() == "false") or (start_vars['use_loco'].lower() == "no"):
+            mapping_params['use_loco'] = False
+
+    mapping_params['num_perm'] = 0
+    mapping_params['perm_check'] = False
+    if 'num_perm' in start_vars:
+        try:
+            mapping_params['num_perm'] = int(start_vars['num_perm'])
+            mapping_params['perm_check'] = "ON"
+        except:
+            mapping_params['perm_check'] = False
+
+    mapping_params['transform'] = False
+    if 'transform' in start_vars:
+        mapping_params['transform'] = start_vars['transform']
+
+    mapping_params['genofile'] = False
+    if 'genofile' in start_vars:
+        mapping_params['genofile'] = start_vars['genofile']
+
+    return mapping_params
+
+def get_genofile_samplelist(dataset):
+    genofile_samplelist = []
+
+    genofile_json = dataset.group.get_genofiles()
+    for genofile in genofile_json:
+        if genofile['location'] == dataset.group.genofile and 'sample_list' in genofile:
+            genofile_samplelist = genofile['sample_list']
+
+    return genofile_samplelist
diff --git a/gn2/wqflask/api/markdown.py b/gn2/wqflask/api/markdown.py
new file mode 100644
index 00000000..580b9ac0
--- /dev/null
+++ b/gn2/wqflask/api/markdown.py
@@ -0,0 +1,186 @@
+"""Markdown routes
+
+Render pages from github, or if they are unavailable, look for it else where
+"""
+
+import requests
+import markdown
+import os
+import sys
+
+from bs4 import BeautifulSoup  # type: ignore
+
+from flask import send_from_directory
+from flask import Blueprint
+from flask import render_template
+
+from typing import Dict
+from typing import List
+
+glossary_blueprint = Blueprint('glossary_blueprint', __name__)
+references_blueprint = Blueprint("references_blueprint", __name__)
+environments_blueprint = Blueprint("environments_blueprint", __name__)
+links_blueprint = Blueprint("links_blueprint", __name__)
+policies_blueprint = Blueprint("policies_blueprint", __name__)
+facilities_blueprint = Blueprint("facilities_blueprint", __name__)
+news_blueprint = Blueprint("news_blueprint", __name__)
+
+blogs_blueprint = Blueprint("blogs_blueprint", __name__)
+
+
+def render_markdown(file_name, is_remote_file=True):
+    """Try to fetch the file name from Github and if that fails, try to
+look for it inside the file system """
+    github_url = ("https://raw.githubusercontent.com/"
+                  "genenetwork/gn-docs/master/")
+
+    if not is_remote_file:
+        text = ""
+        with open(file_name, "r", encoding="utf-8") as input_file:
+            text = input_file.read()
+        return markdown.markdown(text,
+                                 extensions=['tables'])
+
+    md_content = requests.get(f"{github_url}{file_name}")
+
+    if md_content.status_code == 200:
+        return markdown.markdown(md_content.content.decode("utf-8"),
+                                 extensions=['tables'])
+
+    return (f"\nContent for {file_name} not available. "
+            "Please check "
+            "(here to see where content exists)"
+            "[https://github.com/genenetwork/gn-docs]. "
+            "Please reach out to the gn2 team to have a look at this")
+
+
+def get_file_from_python_search_path(pathname_suffix):
+    cands = [os.path.join(d, pathname_suffix) for d in sys.path]
+    try:
+        return list(filter(os.path.exists, cands))[0]
+    except IndexError:
+        return None
+
+
+def get_blogs(user: str = "genenetwork",
+              repo_name: str = "gn-docs") -> dict:
+
+    blogs: Dict[int, List] = {}
+    github_url = f"https://api.github.com/repos/{user}/{repo_name}/git/trees/master?recursive=1"
+
+    repo_tree = requests.get(github_url).json()["tree"]
+
+    for data in repo_tree:
+        path_name = data["path"]
+        if path_name.startswith("blog") and path_name.endswith(".md"):
+            split_path = path_name.split("/")[1:]
+            try:
+                year, title, file_name = split_path
+            except Exception as e:
+                year, file_name = split_path
+                title = ""
+
+            subtitle = os.path.splitext(file_name)[0]
+
+            blog = {
+                "title": title,
+                "subtitle": subtitle,
+                "full_path": path_name
+            }
+
+            if year in blogs:
+                blogs[int(year)].append(blog)
+            else:
+                blogs[int(year)] = [blog]
+
+    return dict(sorted(blogs.items(), key=lambda x: x[0], reverse=True))
+
+
+@glossary_blueprint.route('/')
+def glossary():
+    return render_template(
+        "glossary.html",
+        rendered_markdown=render_markdown("general/glossary/glossary.md")), 200
+
+
+@references_blueprint.route('/')
+def references():
+    return render_template(
+        "references.html",
+        rendered_markdown=render_markdown("general/references/references.md")), 200
+
+
+@news_blueprint.route('/')
+def news():
+    return render_template(
+        "news.html",
+        rendered_markdown=render_markdown("general/news/news.md")), 200
+
+
+@environments_blueprint.route("/")
+def environments():
+
+    md_file = get_file_from_python_search_path("wqflask/DEPENDENCIES.md")
+    svg_file = get_file_from_python_search_path(
+        "wqflask/dependency-graph.html")
+    svg_data = None
+    if svg_file:
+        with open(svg_file, 'r') as f:
+            svg_data = "".join(
+                BeautifulSoup(f.read(),
+                              'lxml').body.script.contents)
+
+    if md_file is not None:
+        return (
+            render_template("environment.html",
+                            svg_data=svg_data,
+                            rendered_markdown=render_markdown(
+                                md_file,
+                                is_remote_file=False)),
+            200
+        )
+    # Fallback: Fetch file from server
+    return (render_template(
+        "environment.html",
+        svg_data=None,
+        rendered_markdown=render_markdown(
+            "general/environments/environments.md")),
+            200)
+
+
+@environments_blueprint.route('/svg-dependency-graph')
+def svg_graph():
+    directory, file_name, _ = get_file_from_python_search_path(
+        "wqflask/dependency-graph.svg").partition("dependency-graph.svg")
+    return send_from_directory(directory, file_name)
+
+
+@links_blueprint.route("/")
+def links():
+    return render_template(
+        "links.html",
+        rendered_markdown=render_markdown("general/links/links.md")), 200
+
+
+@policies_blueprint.route("/")
+def policies():
+    return render_template(
+        "policies.html",
+        rendered_markdown=render_markdown("general/policies/policies.md")), 200
+
+
+@facilities_blueprint.route("/")
+def facilities():
+    return render_template("facilities.html", rendered_markdown=render_markdown("general/help/facilities.md")), 200
+
+
+@blogs_blueprint.route("/<path:blog_path>")
+def display_blog(blog_path):
+    return render_template("blogs.html", rendered_markdown=render_markdown(blog_path))
+
+
+@blogs_blueprint.route("/")
+def blogs_list():
+    blogs = get_blogs()
+
+    return render_template("blogs_list.html", blogs=blogs)
diff --git a/gn2/wqflask/api/router.py b/gn2/wqflask/api/router.py
new file mode 100644
index 00000000..bcd08e8d
--- /dev/null
+++ b/gn2/wqflask/api/router.py
@@ -0,0 +1,1037 @@
+# GN2 API
+
+import os
+import io
+import csv
+import json
+import datetime
+import requests
+
+from zipfile import ZipFile, ZIP_DEFLATED
+
+
+import flask
+from flask import current_app
+from gn2.wqflask.database import database_connection
+from flask import request
+from flask import make_response
+from flask import send_file
+
+from gn2.wqflask import app
+
+from gn2.wqflask.api import correlation, mapping, gen_menu
+
+from gn2.utility.tools import flat_files, get_setting
+
+from gn2.wqflask.database import database_connection
+
+
+version = "pre1"
+
+
+@app.route("/api/v_{}/".format(version))
+def hello_world():
+    return flask.jsonify({"hello": "world"})
+
+
+@app.route("/api/v_{}/species".format(version))
+def get_species_list():
+    species_list = []
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species"
+        )
+        for species in cursor.fetchall():
+            species_dict = {
+            "Id": species[0],
+            "Name": species[1],
+            "FullName": species[2],
+            "TaxonomyId": species[3]
+            }
+            species_list.append(species_dict)
+    return flask.jsonify(species_list)
+
+
+@app.route("/api/v_{}/species/<path:species_name>".format(version))
+@app.route("/api/v_{}/species/<path:species_name>.<path:file_format>".format(version))
+def get_species_info(species_name, file_format="json"):
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT SpeciesId, Name, FullName, TaxonomyId "
+            "FROM Species WHERE (Name=%s OR FullName=%s "
+            "OR SpeciesName=%s)", ((species_name,)*3))
+        _species = cursor.fetchone()
+        species_dict = {
+            "Id": _species[0],
+            "Name": _species[1],
+            "FullName": _species[2],
+            "TaxonomyId": _species[3]
+        }
+
+        return flask.jsonify(species_dict)
+
+
+@app.route("/api/v_{}/groups".format(version))
+@app.route("/api/v_{}/groups/<path:species_name>".format(version))
+def get_groups_list(species_name=None):
+    _groups = ()
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        if species_name:
+            cursor.execute(
+                "SELECT InbredSet.InbredSetId, "
+                "InbredSet.SpeciesId, InbredSet.InbredSetName, "
+                "InbredSet.Name, InbredSet.FullName, "
+                "InbredSet.public, IFNULL(InbredSet.MappingMethodId, "
+                "'None'), IFNULL(InbredSet.GeneticType, 'None') "
+                "FROM InbredSet, Species WHERE "
+                "InbredSet.SpeciesId = Species.Id AND "
+                "(Species.Name = %s OR Species.FullName=%s "
+                "OR Species.SpeciesName=%s)", ((species_name,) * 3)
+            )
+        else:
+            cursor.execute(
+                "SELECT InbredSet.InbredSetId, "
+                "InbredSet.SpeciesId, InbredSet.InbredSetName, "
+                "InbredSet.Name, InbredSet.FullName, "
+                "InbredSet.public, IFNULL(InbredSet.MappingMethodId, "
+                "'None'), IFNULL(InbredSet.GeneticType, 'None') "
+                "FROM InbredSet"
+            )
+        _groups = cursor.fetchall()
+
+    if _groups:
+        groups_list = []
+        for group in _groups:
+            group_dict = {
+                "Id": group[0],
+                "SpeciesId": group[1],
+                "DisplayName": group[2],
+                "Name": group[3],
+                "FullName": group[4],
+                "public": group[5],
+                "MappingMethodId": group[6],
+                "GeneticType": group[7]
+            }
+            groups_list.append(group_dict)
+        return flask.jsonify(groups_list)
+    return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/group/<path:group_name>".format(version))
+@app.route("/api/v_{}/group/<path:group_name>.<path:file_format>".format(version))
+@app.route("/api/v_{}/group/<path:species_name>/<path:group_name>".format(version))
+@app.route("/api/v_{}/group/<path:species_name>/<path:group_name>.<path:file_format>".format(version))
+def get_group_info(group_name, species_name=None, file_format="json"):
+    group = tuple()
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        if species_name:
+            cursor.execute(
+                "SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, "
+                "InbredSet.InbredSetName, InbredSet.Name, "
+                "InbredSet.FullName, InbredSet.public, "
+                "IFNULL(InbredSet.MappingMethodId, 'None'), "
+                "IFNULL(InbredSet.GeneticType, 'None') "
+                "FROM InbredSet, Species WHERE "
+                "InbredSet.SpeciesId = Species.Id "
+                "AND (InbredSet.InbredSetName = %s OR "
+                "InbredSet.Name = %s OR InbredSet.FullName = %s) "
+                "AND (Species.Name = %s OR "
+                "Species.FullName = %s OR Species.SpeciesName = %s)",
+                (*(group_name,)*3, *(species_name,)*3)
+            )
+        else:
+            cursor.execute(
+                "SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, "
+                "InbredSet.InbredSetName, InbredSet.Name, "
+                "InbredSet.FullName, InbredSet.public, "
+                "IFNULL(InbredSet.MappingMethodId, 'None'), "
+                "IFNULL(InbredSet.GeneticType, 'None') "
+                "FROM InbredSet WHERE "
+                "(InbredSet.InbredSetName = %s OR "
+                "InbredSet.Name = %s OR "
+                "InbredSet.FullName = %s)",
+                ((group_name,)*3)
+            )
+        group = cursor.fetchone()
+
+    if group:
+        group_dict = {
+            "Id": group[0],
+            "SpeciesId": group[1],
+            "DisplayName": group[2],
+            "Name": group[3],
+            "FullName": group[4],
+            "public": group[5],
+            "MappingMethodId": group[6],
+            "GeneticType": group[7]
+        }
+
+        return flask.jsonify(group_dict)
+    else:
+        return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/datasets/<path:group_name>".format(version))
+@app.route("/api/v_{}/datasets/<path:species_name>/<path:group_name>".format(version))
+def get_datasets_for_group(group_name, species_name=None):
+    _datasets = ()
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        if species_name:
+            cursor.execute(
+                "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.ProbeFreezeId, "
+                "ProbeSetFreeze.AvgID, ProbeSetFreeze.Name, "
+                "ProbeSetFreeze.Name2, "
+                "ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, "
+                "ProbeSetFreeze.CreateTime, ProbeSetFreeze.public, "
+                "ProbeSetFreeze.confidentiality, ProbeSetFreeze.DataScale "
+                "FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Species "
+                "WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                "AND ProbeFreeze.InbredSetId = InbredSet.Id "
+                "AND (InbredSet.Name = %s OR "
+                "InbredSet.InbredSetName = %s OR "
+                "InbredSet.FullName = %s) AND "
+                "InbredSet.SpeciesId = Species.Id AND "
+                "(Species.SpeciesName = %s OR "
+                "Species.MenuName = %s OR Species.FullName = %s);",
+                (*(group_name,)*3, *(species_name)*3)
+            )
+        else:
+            cursor.execute(
+                "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.ProbeFreezeId, "
+                "ProbeSetFreeze.AvgID, ProbeSetFreeze.Name, "
+                "ProbeSetFreeze.Name2, ProbeSetFreeze.FullName, "
+                "ProbeSetFreeze.ShortName, ProbeSetFreeze.CreateTime, "
+                "ProbeSetFreeze.public, ProbeSetFreeze.confidentiality, "
+                "ProbeSetFreeze.DataScale FROM ProbeSetFreeze, "
+                "ProbeFreeze, InbredSet WHERE "
+                "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                "AND ProbeFreeze.InbredSetId = InbredSet.Id "
+                "AND (InbredSet.Name = %s OR "
+                "InbredSet.InbredSetName = %s OR "
+                "InbredSet.FullName = %s)",
+                ((group_name,) * 3)
+            )
+        _datasets = cursor.fetchall()
+
+    if _datasets:
+        datasets_list = []
+        for dataset in _datasets:
+            dataset_dict = {
+                "Id": dataset[0],
+                "ProbeFreezeId": dataset[1],
+                "AvgID": dataset[2],
+                "Short_Abbreviation": dataset[3],
+                "Long_Abbreviation": dataset[4],
+                "FullName": dataset[5],
+                "ShortName": dataset[6],
+                "CreateTime": dataset[7],
+                "public": dataset[8],
+                "confidentiality": dataset[9],
+                "DataScale": dataset[10]
+            }
+            datasets_list.append(dataset_dict)
+
+        return flask.jsonify(datasets_list)
+    else:
+        return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/dataset/<path:dataset_name>".format(version))
+@app.route("/api/v_{}/dataset/<path:dataset_name>.<path:file_format>".format(version))
+@app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version))
+@app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>.<path:file_format>".format(version))
+def get_dataset_info(dataset_name, group_name=None, file_format="json"):
+    # ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets
+
+    # ZS: I figure I might as well return a list if there are multiple
+    # matches, though I don"t know if this will actually happen in
+    # practice
+    datasets_list, dataset_dict = [], {}
+    probeset_query = """
+                SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName,
+                       ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, ProbeFreeze.TissueId,
+                       Tissue.Name, ProbeSetFreeze.public, ProbeSetFreeze.confidentiality
+                FROM ProbeSetFreeze, ProbeFreeze, Tissue
+            """
+
+    where_statement = """
+                         WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
+                               ProbeFreeze.TissueId = Tissue.Id AND
+                               ProbeSetFreeze.public > 0 AND
+                               ProbeSetFreeze.confidentiality < 1 AND
+                      """
+    if dataset_name.isdigit():
+        where_statement += """
+                              ProbeSetFreeze.Id = "{}"
+                           """.format(dataset_name)
+    else:
+        where_statement += """
+                              (ProbeSetFreeze.Name = "{0}" OR ProbeSetFreeze.Name2 = "{0}" OR
+                              ProbeSetFreeze.FullName = "{0}" OR ProbeSetFreeze.ShortName = "{0}")
+                           """.format(dataset_name)
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(f"{probeset_query}{where_statement}")
+
+        if dataset := cursor.fetchone():
+            dataset_dict = {
+                "dataset_type": "mRNA expression",
+                "id": dataset[0],
+                "name": dataset[1],
+                "full_name": dataset[2],
+                "short_name": dataset[3],
+                "data_scale": dataset[4],
+                "tissue_id": dataset[5],
+                "tissue": dataset[6],
+                "public": dataset[7],
+                "confidential": dataset[8]
+            }
+
+            datasets_list.append(dataset_dict)
+
+        if group_name:
+            cursor.execute(
+                "SELECT PublishXRef.Id, "
+                "Phenotype.Post_publication_abbreviation, "
+                "Phenotype.Post_publication_description, "
+                "Phenotype.Pre_publication_abbreviation, "
+                "Phenotype.Pre_publication_description, "
+                "Publication.PubMed_ID, Publication.Title, "
+                "Publication.Year FROM PublishXRef, Phenotype, "
+                "Publication, InbredSet, PublishFreeze WHERE "
+                "PublishXRef.InbredSetId = InbredSet.Id "
+                "AND PublishXRef.PhenotypeId = Phenotype.Id "
+                "AND PublishXRef.PublicationId = Publication.Id "
+                "AND PublishFreeze.InbredSetId = InbredSet.Id "
+                "AND PublishFreeze.public > 0 AND "
+                "PublishFreeze.confidentiality < 1 "
+                "AND InbredSet.Name = %s AND PublishXRef.Id = %s",
+                (group_name, dataset_name,)
+            )
+
+            if dataset := cursor.fetchone():
+                if dataset[5]:
+                    dataset_dict = {
+                        "dataset_type": "phenotype",
+                        "id": dataset[0],
+                        "name": dataset[1],
+                        "description": dataset[2],
+                        "pubmed_id": dataset[5],
+                        "title": dataset[6],
+                        "year": dataset[7]
+                    }
+                elif dataset[4]:
+                    dataset_dict = {
+                        "dataset_type": "phenotype",
+                        "id": dataset[0],
+                        "name": dataset[3],
+                        "description": dataset[4]
+                    }
+                else:
+                    dataset_dict = {
+                        "dataset_type": "phenotype",
+                        "id": dataset[0]
+                    }
+
+                datasets_list.append(dataset_dict)
+
+    if len(datasets_list) > 1:
+        return flask.jsonify(datasets_list)
+    elif len(datasets_list) == 1:
+        return flask.jsonify(dataset_dict)
+    else:
+        return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",))
+@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",))
+def fetch_traits(dataset_name, file_format="json"):
+    trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(
+        dataset_name, request.args)
+    if ("ids_only" in request.args) and (len(trait_ids) > 0):
+        if file_format == "json":
+            filename = dataset_name + "_trait_ids.json"
+            return flask.jsonify(trait_ids)
+        else:
+            filename = dataset_name + "_trait_ids.csv"
+
+            si = io.StringIO()
+            csv_writer = csv.writer(si)
+            csv_writer.writerows([[trait_id] for trait_id in trait_ids])
+            output = make_response(si.getvalue())
+            output.headers["Content-Disposition"] = "attachment; filename=" + filename
+            output.headers["Content-type"] = "text/csv"
+            return output
+    elif ("names_only" in request.args) and (len(trait_ids) > 0):
+        if file_format == "json":
+            filename = dataset_name + "_trait_names.json"
+            return flask.jsonify(trait_names)
+        else:
+            filename = dataset_name + "_trait_names.csv"
+
+            si = io.StringIO()
+            csv_writer = csv.writer(si)
+            csv_writer.writerows([[trait_name] for trait_name in trait_names])
+            output = make_response(si.getvalue())
+            output.headers["Content-Disposition"] = "attachment; filename=" + filename
+            output.headers["Content-type"] = "text/csv"
+            return output
+    else:
+        if len(trait_ids) > 0:
+            if data_type == "ProbeSet":
+                query = """
+                            SELECT
+                                ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias,
+                                ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.h2
+                            FROM
+                                ProbeSet, ProbeSetXRef, ProbeSetFreeze
+                            WHERE
+                                ProbeSetXRef.ProbeSetFreezeId = "{0}" AND
+                                ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+                                ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+                                ProbeSetFreeze.public > 0 AND
+                                ProbeSetFreeze.confidentiality < 1
+                            ORDER BY
+                                ProbeSet.Id
+                        """
+
+                field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb",
+                              "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"]
+            elif data_type == "Geno":
+                query = """
+                            SELECT
+                                Geno.Id, Geno.Name, Geno.Marker_Name, Geno.Chr, Geno.Mb, Geno.Sequence, Geno.Source
+                            FROM
+                                Geno, GenoXRef, GenoFreeze
+                            WHERE
+                                GenoXRef.GenoFreezeId = "{0}" AND
+                                GenoXRef.GenoId = Geno.Id AND
+                                GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+                                GenoFreeze.public > 0 AND
+                                GenoFreeze.confidentiality < 1
+                            ORDER BY
+                                Geno.Id
+                        """
+
+                field_list = ["Id", "Name", "Marker_Name",
+                              "Chr", "Mb", "Sequence", "Source"]
+            else:
+                query = """SELECT PublishXRef.Id,
+                        Phenotype.`Original_description`,
+                        Publication.`Authors`,
+                        Publication.`Year`,
+                        Publication.`PubMed_ID`,
+                        PublishXRef.`mean`,
+                        PublishXRef.`LRS`,
+                        PublishXRef.`additive`,
+                        PublishXRef.`Locus`,
+                        Geno.`Chr`, Geno.`Mb`
+                        FROM Species
+                            INNER JOIN InbredSet ON InbredSet.`SpeciesId` = Species.`Id`
+                            INNER JOIN PublishXRef ON PublishXRef.`InbredSetId` = InbredSet.`Id`
+                            INNER JOIN PublishFreeze ON PublishFreeze.`InbredSetId` = InbredSet.`Id`
+                            INNER JOIN Publication ON Publication.`Id` = PublishXRef.`PublicationId`
+                            INNER JOIN Phenotype ON Phenotype.`Id` = PublishXRef.`PhenotypeId`
+                            LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
+                        WHERE
+                            PublishXRef.InbredSetId = {0} AND
+                            PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND
+                            PublishFreeze.public > 0 AND
+                            PublishFreeze.confidentiality < 1
+                            ORDER BY
+                                PublishXRef.Id"""
+
+                field_list = ["Id", "Description", "Authors", "Year", "PubMedID", "Mean",
+                              "LRS", "Additive", "Locus", "Chr", "Mb"]
+
+            if 'limit_to' in request.args:
+                limit_number = request.args['limit_to']
+                query += "LIMIT " + str(limit_number)
+            with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+                if file_format == "json":
+                    filename = dataset_name + "_traits.json"
+                    cursor.execute(query.format(dataset_id))
+                    result_list = []
+                    for result in cursor.fetchall():
+                        trait_dict = {}
+                        for i, field in enumerate(field_list):
+                            if result[i]:
+                                trait_dict[field] = result[i]
+                        result_list.append(trait_dict)
+                    return flask.jsonify(result_list)
+                elif file_format == "csv":
+                    filename = dataset_name + "_traits.csv"
+
+                    results_list = []
+                    header_list = []
+                    header_list += field_list
+                    results_list.append(header_list)
+                    cursor.execute(query.format(dataset_id))
+                    for result in cursor.fetchall():
+                        results_list.append(result)
+
+                    si = io.StringIO()
+                    csv_writer = csv.writer(si)
+                    csv_writer.writerows(results_list)
+                    output = make_response(si.getvalue())
+                    output.headers["Content-Disposition"] = "attachment; filename=" + filename
+                    output.headers["Content-type"] = "text/csv"
+                    return output
+                else:
+                    return return_error(
+                        code=400,
+                        source=request.url_rule.rule,
+                        title="Invalid Output Format",
+                        details="Current formats available are JSON and CSV, with CSV as default"
+                    )
+        else:
+            return return_error(
+                code=204,
+                source=request.url_rule.rule,
+                title="No Results",
+                details="")
+
+
+@app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version))
+@app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version))
+def all_sample_data(dataset_name, file_format="csv"):
+    trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(
+        dataset_name, request.args)
+
+    if len(trait_ids) > 0:
+        sample_list = get_samplelist(dataset_name)
+
+        if data_type == "ProbeSet":
+            query = """
+                        SELECT
+                            Strain.Name, Strain.Name2, ProbeSetData.value, ProbeSetData.Id, ProbeSetSE.error
+                        FROM
+                            (ProbeSetData, Strain, ProbeSetXRef, ProbeSetFreeze)
+                        LEFT JOIN ProbeSetSE ON
+                            (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
+                        WHERE
+                            ProbeSetXRef.ProbeSetFreezeId = "{0}" AND
+                            ProbeSetXRef.ProbeSetId = "{1}" AND
+                            ProbeSetXRef.DataId = ProbeSetData.Id AND
+                            ProbeSetData.StrainId = Strain.Id AND
+                            ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+                            ProbeSetFreeze.public > 0 AND
+                            ProbeSetFreeze.confidentiality < 1
+                        ORDER BY
+                            Strain.Name
+                    """
+        elif data_type == "Geno":
+            query = """
+                        SELECT
+                            Strain.Name, Strain.Name2, GenoData.value, GenoData.Id, GenoSE.error
+                        FROM
+                            (GenoData, Strain, GenoXRef, GenoFreeze)
+                        LEFT JOIN GenoSE ON
+                            (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
+                        WHERE
+                            GenoXRef.GenoFreezeId = "{0}" AND
+                            GenoXRef.GenoId = "{1}" AND
+                            GenoXRef.DataId = GenoData.Id AND
+                            GenoData.StrainId = Strain.Id AND
+                            GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+                            GenoFreeze.public > 0 AND
+                            GenoFreeze.confidentiality < 1
+                        ORDER BY
+                            Strain.Name
+                    """
+        else:
+            query = """
+                        SELECT
+                            Strain.Name, Strain.Name2, PublishData.value, PublishData.Id, PublishSE.error, NStrain.count
+                        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 = "{0}" AND
+                            PublishXRef.PhenotypeId = "{1}" AND
+                            PublishData.Id = PublishXRef.DataId AND
+                            PublishData.StrainId = Strain.Id AND
+                            PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+                            PublishFreeze.public > 0 AND
+                            PublishFreeze.confidentiality < 1
+                        ORDER BY
+                            Strain.Name
+                    """
+
+        if file_format == "csv":
+            filename = dataset_name + "_sample_data.csv"
+
+            results_list = []
+            header_list = []
+            header_list.append("id")
+            header_list += sample_list
+            results_list.append(header_list)
+            with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+                for i, trait_id in enumerate(trait_ids):
+                    line_list = []
+                    line_list.append(str(trait_names[i]))
+                    cursor.execute(query.format(dataset_id, trait_id))
+                    results = cursor.fetchall()
+                    results_dict = {}
+                    for item in results:
+                        results_dict[item[0]] = item[2]
+                    for sample in sample_list:
+                        if sample in results_dict:
+                            line_list.append(results_dict[sample])
+                        else:
+                            line_list.append("x")
+                    results_list.append(line_list)
+
+            results_list = list(map(list, zip(*results_list)))
+
+            si = io.StringIO()
+            csv_writer = csv.writer(si)
+            csv_writer.writerows(results_list)
+            output = make_response(si.getvalue())
+            output.headers["Content-Disposition"] = "attachment; filename=" + filename
+            output.headers["Content-type"] = "text/csv"
+            return output
+        else:
+            return return_error(code=415, source=request.url_rule.rule, title="Unsupported file format", details="")
+    else:
+        return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>".format(version))
+@app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
+def trait_sample_data(dataset_name, trait_name, file_format="json"):
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT Strain.Name, Strain.Name2, "
+            "ProbeSetData.value, ProbeSetData.Id, "
+            "ProbeSetSE.error FROM (ProbeSetData, "
+            "ProbeSetFreeze, Strain, ProbeSet, "
+            "ProbeSetXRef) LEFT JOIN ProbeSetSE ON "
+            "(ProbeSetSE.DataId = ProbeSetData.Id AND "
+            "ProbeSetSE.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",
+            (trait_name, dataset_name,)
+        )
+
+        sample_data = cursor.fetchall()
+        if len(sample_data) > 0:
+            sample_list = []
+            for sample in sample_data:
+                sample_dict = {
+                    "sample_name": sample[0],
+                    "sample_name_2": sample[1],
+                    "value": sample[2],
+                    "data_id": sample[3],
+                }
+                if sample[4]:
+                    sample_dict["se"] = sample[4]
+                sample_list.append(sample_dict)
+
+            return flask.jsonify(sample_list)
+        else:
+            if not dataset_name.isdigit():
+                group_id = get_group_id(dataset_name)
+                if group_id:
+                    dataset_or_group = group_id
+                else:
+                    dataset_or_group = dataset_name
+            else:
+                dataset_or_group = dataset_name
+
+            cursor.execute(
+                "SELECT DISTINCT Strain.Name, Strain.Name2, "
+                "PublishData.value, PublishData.Id, PublishSE.error, "
+                "NStrain.count 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 "
+                "OR PublishFreeze.Name = %s OR "
+                "PublishFreeze.ShortName = %s OR "
+                "PublishXRef.InbredSetId = %s) AND "
+                "PublishData.StrainId = Strain.Id "
+                "ORDER BY Strain.Name",
+                (trait_name, *(dataset_or_group,)*4)
+            )
+            if len(sample_data := cursor.fetchall()) > 0:
+                sample_list = []
+                for sample in sample_data:
+                    sample_dict = {
+                        "sample_name": sample[0],
+                        "sample_name_2": sample[1],
+                        "value": sample[2],
+                        "data_id": sample[3]
+                    }
+                    if sample[4]:
+                        sample_dict["se"] = sample[4]
+                    if sample[5]:
+                        sample_dict["n_cases"] = sample[5]
+                    sample_list.append(sample_dict)
+
+                return flask.jsonify(sample_list)
+            else:
+                return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version))
+@app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
+@app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version))
+@app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
+def get_trait_info(dataset_name, trait_name, file_format="json"):
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, "
+            "ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, "
+            "ProbeSet.alias, ProbeSetXRef.mean, ProbeSetXRef.se, "
+            "ProbeSetXRef.Locus, ProbeSetXRef.LRS, "
+            "ProbeSetXRef.pValue, ProbeSetXRef.additive "
+            "FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze "
+            "WHERE ProbeSet.Name = %s AND "
+            "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
+            "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
+            "AND ProbeSetFreeze.Name = %s",
+            (trait_name, dataset_name,)
+        )
+        if trait_info := cursor.fetchone():
+            trait_dict = {
+                "id": trait_info[0],
+                "name": trait_info[1],
+                "symbol": trait_info[2],
+                "description": trait_info[3],
+                "chr": trait_info[4],
+                "mb": trait_info[5],
+                "alias": trait_info[6],
+                "mean": trait_info[7],
+                "se": trait_info[8],
+                "locus": trait_info[9],
+                "lrs": trait_info[10],
+                "p_value": trait_info[11],
+                "additive": trait_info[12]
+            }
+
+            return flask.jsonify(trait_dict)
+        else:
+            # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish"
+            if "Publish" in dataset_name:
+                dataset_name = dataset_name.replace("Publish", "")
+
+            group_id = get_group_id(dataset_name)
+            cursor.execute(
+                "SELECT PublishXRef.PhenotypeId, "
+                "PublishXRef.Locus, PublishXRef.LRS, "
+                "PublishXRef.additive FROM "
+                "PublishXRef WHERE "
+                "PublishXRef.Id = %s AND "
+                "PublishXRef.InbredSetId = %s",
+                (trait_name, group_id,)
+            )
+            if trait_info := cursor.fetchone():
+                trait_dict = {
+                    "id": trait_info[0],
+                    "locus": trait_info[1],
+                    "lrs": trait_info[2],
+                    "additive": trait_info[3]
+                }
+
+                return flask.jsonify(trait_dict)
+            else:
+                return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/correlation".format(version), methods=("GET",))
+def get_corr_results():
+    results = correlation.do_correlation(request.args)
+
+    if len(results) > 0:
+        # ZS: I think flask.jsonify expects a dict/list instead of JSON
+        return flask.jsonify(results)
+    else:
+        return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/mapping".format(version), methods=("GET",))
+def get_mapping_results():
+    results, format = mapping.do_mapping_for_api(request.args)
+
+    if len(results) > 0:
+        if format == "csv":
+            filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv"
+
+            si = io.StringIO()
+            csv_writer = csv.writer(si)
+            csv_writer.writerows(results)
+            output = make_response(si.getvalue())
+            output.headers["Content-Disposition"] = "attachment; filename=" + filename
+            output.headers["Content-type"] = "text/csv"
+
+            return output
+        elif format == "json":
+            return flask.jsonify(results)
+        else:
+            return return_error(code=415, source=request.url_rule.rule, title="Unsupported Format", details="")
+    else:
+        return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+
+@app.route("/api/v_{}/genotypes/view/<string:group_name>".format(version))
+def view_genotype_files(group_name):
+    if os.path.isfile("{0}/{1}.json".format(flat_files("genotype"), group_name)):
+        with open("{0}/{1}.json".format(flat_files("genotype"), group_name)) as geno_json:
+            return flask.jsonify(json.load(geno_json))
+
+
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version))
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version))
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version))
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>".format(version))
+@app.route("/api/v_{}/genotypes/<string:group_name>.<string:file_format>".format(version))
+def get_genotypes(group_name, file_format="csv", dataset_name=None):
+    limit_num = None
+    if 'limit_to' in request.args:
+        if request.args['limit_to'].isdigit():
+            limit_num = int(request.args['limit_to'])
+
+    si = io.StringIO()
+    if file_format == "csv" or file_format == "geno":
+        filename = group_name + ".geno"
+
+        if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)):
+            output_lines = []
+            with open("{0}/{1}.geno".format(flat_files("genotype"), group_name)) as genofile:
+                i = 0
+                for line in genofile:
+                    if line[0] == "#" or line[0] == "@":
+                        output_lines.append([line.strip()])
+                    else:
+                        if limit_num and i >= limit_num:
+                            break
+                        output_lines.append(line.split())
+                        i += 1
+
+            csv_writer = csv.writer(
+                si, delimiter="\t", escapechar="\\", quoting=csv.QUOTE_NONE)
+        else:
+            return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+    elif file_format == "rqtl2":
+        memory_file = io.BytesIO()
+        if dataset_name:
+            filename = dataset_name
+        else:
+            filename = group_name
+
+        if os.path.isfile("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name)):
+            yaml_file = json.load(
+                open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name)))
+            yaml_file["geno"] = filename + "_geno.csv"
+            yaml_file["gmap"] = filename + "_gmap.csv"
+            yaml_file["pheno"] = filename + "_pheno.csv"
+            config_file = [filename + ".json", json.dumps(yaml_file)]
+            #config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))]
+            geno_file = [filename + "_geno.csv",
+                         open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))]
+            gmap_file = [filename + "_gmap.csv",
+                         open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))]
+            if dataset_name:
+                phenotypes = requests.get(
+                    "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name)
+            else:
+                phenotypes = requests.get(
+                    "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish")
+
+            with ZipFile(memory_file, 'w', compression=ZIP_DEFLATED) as zf:
+                zf.writestr(config_file[0], config_file[1])
+                for this_file in [geno_file, gmap_file]:
+                    zf.writestr(this_file[0], this_file[1].read())
+                zf.writestr(filename + "_pheno.csv", phenotypes.content)
+
+            memory_file.seek(0)
+
+            return send_file(memory_file, attachment_filename=filename + ".zip", as_attachment=True)
+        else:
+            return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+    else:
+        filename = group_name + ".bimbam"
+
+        if os.path.isfile("{0}/{1}.geno".format(flat_files("genotype"), group_name)):
+            output_lines = []
+            with open("{0}/{1}_geno.txt".format(flat_files("genotype/bimbam"), group_name)) as genofile:
+                i = 0
+                for line in genofile:
+                    if limit_num and i >= limit_num:
+                        break
+                    output_lines.append([line.strip()
+                                         for line in line.split(",")])
+                    i += 1
+
+            csv_writer = csv.writer(si, delimiter=",")
+        else:
+            return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
+    csv_writer.writerows(output_lines)
+    output = make_response(si.getvalue())
+    output.headers["Content-Disposition"] = "attachment; filename=" + filename
+    output.headers["Content-type"] = "text/csv"
+
+    return output
+
+
+@app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",))
+def gen_dropdown_menu():
+    with database_connection(get_setting("SQL_URI")) as conn:
+        results = gen_menu.gen_dropdown_json(conn)
+
+    if len(results) > 0:
+        return flask.jsonify(results)
+    else:
+        return return_error(code=500, source=request.url_rule.rule, title="Some error occurred", details="")
+
+
+def return_error(code, source, title, details):
+    json_ob = {"errors": [
+        {
+            "status": code,
+            "source": {"pointer": source},
+            "title": title,
+            "detail": details
+        }
+    ]}
+
+    return flask.jsonify(json_ob)
+
+
+def get_dataset_trait_ids(dataset_name, start_vars):
+
+    if 'limit_to' in start_vars:
+        limit_string = "LIMIT " + str(start_vars['limit_to'])
+    else:
+        limit_string = ""
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        if "Geno" in dataset_name:
+            data_type = "Geno"  # ZS: Need to pass back the dataset type
+            cursor.execute(
+                "SELECT GenoXRef.GenoId, Geno.Name, "
+                "GenoXRef.GenoFreezeId FROM Geno, "
+                "GenoXRef, GenoFreeze WHERE "
+                "Geno.Id = GenoXRef.GenoId AND "
+                "GenoXRef.GenoFreezeId = GenoFreeze.Id "
+                f"AND GenoFreeze.Name = %s {limit_string}",
+            (dataset_name,))
+
+            results = cursor.fetchall()
+
+            trait_ids = [result[0] for result in results]
+            trait_names = [result[1] for result in results]
+            dataset_id = results[0][2]
+            return trait_ids, trait_names, data_type, dataset_id
+
+        elif "Publish" in dataset_name or get_group_id(dataset_name):
+            data_type = "Publish"
+            dataset_name = dataset_name.replace("Publish", "")
+            dataset_id = get_group_id(dataset_name)
+            cursor.execute(
+                "SELECT PublishXRef.PhenotypeId, "
+                "PublishXRef.Id, InbredSet.InbredSetCode "
+                "FROM PublishXRef, InbredSet WHERE "
+                "PublishXRef.InbredSetId = %s AND "
+                "InbredSet.Id = PublishXRef.InbredSetId "
+                f"{limit_string}",
+                (dataset_id,)
+            )
+            results = cursor.fetchall()
+
+            trait_ids = [result[0] for result in results]
+            trait_names = [str(result[2]) + "_" + str(result[1])
+                           for result in results]
+
+            return trait_ids, trait_names, data_type, dataset_id
+
+        else:
+            data_type = "ProbeSet"
+            cursor.execute(
+                "SELECT ProbeSetXRef.ProbeSetId, "
+                "ProbeSet.Name, ProbeSetXRef.ProbeSetFreezeId "
+                "FROM ProbeSet, ProbeSetXRef, "
+                "ProbeSetFreeze WHERE "
+                "ProbeSet.Id = ProbeSetXRef.ProbeSetId AND "
+                "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
+                f"AND ProbeSetFreeze.Name = %s {limit_string}",
+                (dataset_name,)
+            )
+            results = cursor.fetchall()
+            trait_ids = [result[0] for result in results]
+            trait_names = [result[1] for result in results]
+            dataset_id = results[0][2]
+            return trait_ids, trait_names, data_type, dataset_id
+
+
+def get_samplelist(dataset_name):
+    group_id = get_group_id_from_dataset(dataset_name)
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT Strain.Name FROM Strain, StrainXRef "
+            "WHERE StrainXRef.StrainId = Strain.Id AND "
+            "StrainXRef.InbredSetId = %s",
+            (group_id,)
+        )
+        # sample list
+        return [result[0] for result in cursor.fetchall()]
+
+
+def get_group_id_from_dataset(dataset_name):
+    result = ()
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        if "Publish" in dataset_name:
+            cursor.execute(
+                "SELECT InbredSet.Id FROM "
+                "InbredSet, PublishFreeze "
+                "WHERE PublishFreeze.InbredSetId = InbredSet.Id "
+                "AND PublishFreeze.Name = %s",
+                (dataset_name,)
+            )
+        elif "Geno" in dataset_name:
+            cursor.execute(
+                "SELECT InbredSet.Id FROM "
+                "InbredSet, GenoFreeze WHERE "
+                "GenoFreeze.InbredSetId = InbredSet.Id "
+                "AND GenoFreeze.Name = %s",
+                (dataset_name,)
+            )
+        else:
+            cursor.execute(
+                "SELECT InbredSet.Id FROM "
+                "InbredSet, ProbeSetFreeze, "
+                "ProbeFreeze WHERE "
+                "ProbeFreeze.InbredSetId = InbredSet.Id "
+                "AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId "
+                "AND ProbeSetFreeze.Name = %s",
+                (dataset_name,)
+            )
+        if result := cursor.fetchone():
+            return result[0]
+        return None
+
+
+def get_group_id(group_name):
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT InbredSet.Id FROM InbredSet "
+            "WHERE InbredSet.Name = %s",
+            (group_name,)
+        )
+        if group_id := cursor.fetchone():
+            return group_id[0]
+        return None