Add Endpoint to get menu items for use in UI

3 files changed, 245 insertions, 0 deletions

diff --git a/gn3/api/menu.py b/gn3/api/menu.py
new file mode 100644
index 0000000..cc77ab8
--- /dev/null
+++ b/gn3/api/menu.py
@@ -0,0 +1,14 @@
+"""API for data used to generate menus"""
+
+from flask import jsonify, Blueprint
+
+from gn3.db.menu import gen_dropdown_json
+from gn3.db_utils import database_connector
+
+menu = Blueprint("menu", __name__)
+
+@menu.route("/generate/json")
+def generate_json():
+    """Get the menu in the JSON format"""
+    with database_connector() as conn:
+        return jsonify(gen_dropdown_json(conn))
diff --git a/gn3/app.py b/gn3/app.py
index 790e87c..8a44983 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -16,6 +16,7 @@ from gn3.api.data_entry import data_entry
 from gn3.api.wgcna import wgcna
 from gn3.api.ctl import ctl
 from gn3.api.async_commands import async_commands
+from gn3.api.menu import menu
 
 def create_app(config: Union[Dict, str, None] = None) -> Flask:
     """Create a new flask object"""
@@ -49,4 +50,5 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     app.register_blueprint(wgcna, url_prefix="/api/wgcna")
     app.register_blueprint(ctl, url_prefix="/api/ctl")
     app.register_blueprint(async_commands, url_prefix="/api/async_commands")
+    app.register_blueprint(menu, url_prefix="/api/menu")
     return app
diff --git a/gn3/db/menu.py b/gn3/db/menu.py
new file mode 100644
index 0000000..8dccabf
--- /dev/null
+++ b/gn3/db/menu.py
@@ -0,0 +1,229 @@
+"""Menu generation code for the data in the dropdowns in the index page."""
+
+from typing import Tuple
+from functools import reduce
+
+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(conn, tuple(row[0] for row in species))
+    types = get_types(conn, groups)
+    datasets = get_datasets(conn, types)
+    return dict(species=species,
+                groups=groups,
+                types=types,
+                datasets=datasets)
+
+def get_groups(conn, species_names: Tuple[str, ...]):
+    """Build groups list"""
+    with conn.cursor() as cursor:
+        query = (
+            "SELECT InbredSet.Name, InbredSet.FullName, "
+            "IFNULL(InbredSet.Family, 'None'), "
+            "Species.Name AS species_name "
+            "FROM Species "
+            "INNER JOIN InbredSet ON InbredSet.SpeciesId = Species.Id "
+            "WHERE Species.Name IN "
+            f"({', '.join(['%s']*len(species_names))}) "
+            "GROUP BY InbredSet.Name "
+            "ORDER BY IFNULL(InbredSet.FamilyOrder, InbredSet.FullName) ASC, "
+            "IFNULL(InbredSet.Family, InbredSet.FullName) ASC, "
+            "InbredSet.FullName ASC, "
+            "InbredSet.MenuOrderId ASC")
+        cursor.execute(query, tuple(species_names))
+        results = cursor.fetchall()
+
+    def __organise_by_species(acc, row):
+        family_name = f"Family:{str(row[2])}"
+        species_name = row[3]
+        key_exists = bool(acc.get(species_name, False))
+        if not key_exists:
+            return {
+                **acc,
+                species_name: [[str(row[0]), str(row[1]), family_name],]
+            }
+
+        return {
+            **acc,
+            species_name: acc[species_name] + [
+                [str(row[0]), str(row[1]), family_name],]
+        }
+
+    return reduce(__organise_by_species, results, {})
+
+def get_types(conn, groups):
+    """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(conn, group_name):
+                types[species][group_name] = [
+                    ("Phenotypes", "Traits and Cofactors", "Phenotypes")]
+            if genotypes_exist(conn, group_name):
+                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(conn, species, group_name)
+                if len(types_list) > 0:
+                    types[species][group_name] += types_list
+            else:
+                types_list = build_types(conn, species, group_name)
+                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(conn, group_name):
+    "Check whether phenotypes exist for the given group"
+    with conn.cursor() as cursor:
+        cursor.execute(
+            ("SELECT Name FROM PublishFreeze "
+             "WHERE PublishFreeze.Name = %s"),
+            (group_name + "Publish",))
+        results = cursor.fetchone()
+        return bool(results)
+
+def genotypes_exist(conn, group_name):
+    "Check whether genotypes exist for the given group"
+    with conn.cursor() as cursor:
+        cursor.execute(
+            ("SELECT Name FROM GenoFreeze " +
+             "WHERE GenoFreeze.Name = %s"),
+            (group_name + "Geno",))
+        results = cursor.fetchone()
+        return bool(results)
+
+def build_types(conn, species, group):
+    """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 = %s "
+        "AND Species.Id = InbredSet.SpeciesId AND "
+        "InbredSet.Name = %s AND ProbeFreeze.TissueId = "
+        "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id "
+        "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+        "ORDER BY Tissue.Name")
+    results = []
+    with conn.cursor() as cursor:
+        cursor.execute(query, (species, group))
+        for result in cursor.fetchall():
+            if bool(result):
+                these_datasets = build_datasets(conn, species, group, result[0])
+                if len(these_datasets) > 0:
+                    results.append([
+                        str(result[0]), str(result[0]), "Molecular Traits"])
+
+    return results
+
+def get_datasets(conn, types):
+    """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(
+                    conn, species, group, type_name[0])
+                if bool(these_datasets):
+                    datasets[species][group][type_name[0]] = these_datasets
+
+    return datasets
+
+def build_datasets(conn, species, group, type_name):
+    """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 = %s AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id AND "
+                 "InfoFiles.InfoPageName = PublishFreeze.Name "
+                 "ORDER BY PublishFreeze.CreateTime ASC"), (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 = %s AND "
+                     "PublishFreeze.InbredSetId = InbredSet.Id "
+                     "ORDER BY PublishFreeze.CreateTime ASC"), (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 = %s AND "
+                 "GenoFreeze.InbredSetId = InbredSet.Id AND "
+                 "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+                 "ORDER BY GenoFreeze.CreateTime "
+                 "DESC"), (group,))
+            results = cursor.fetchone()
+            dataset_id = "None"
+            if bool(results):
+                dataset_id = str(results[0])
+
+            dataset_value = f"{group}Geno"
+            dataset_text = f"{group} Genotypes"
+            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 = %s AND Species.Id = "
+                 "InbredSet.SpeciesId AND InbredSet.Name = %s "
+                 "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                 "AND Tissue.Name = %s AND ProbeFreeze.TissueId = "
+                 "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id "
+                 "AND ProbeSetFreeze.public > 0 "
+                 "ORDER BY -ProbeSetFreeze.OrderList DESC, "
+                 "ProbeSetFreeze.CreateTime "
+                 "DESC"), (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