UIP-49 - Fix appinfo tests

lib/NarrativeService/NarrativeServiceImpl.py

@@ -1,4 +1,6 @@
 #BEGIN_HEADER
+from installed_clients.CatalogClient import Catalog
+from installed_clients.NarrativeMethodStoreClient import NarrativeMethodStore
 from installed_clients.WorkspaceClient import Workspace
 from NarrativeService.apps.appinfo import get_all_app_info, get_ignore_categories
 from NarrativeService.data.fetcher import DataFetcher
@@ -658,8 +660,9 @@ def get_all_app_info(self, ctx, input):
         # ctx is the context object
         # return variables are: output
         #BEGIN get_all_app_info
-        output = get_all_app_info(input["tag"], input["user"],
-                                  self.narrativeMethodStoreURL, self.catalogURL)
+        catalog = Catalog(self.catalogURL)
+        nms = NarrativeMethodStore(self.narrativeMethodStoreURL)
+        output = get_all_app_info(input["tag"], input["user"], nms, catalog)
         #END get_all_app_info
 
         # At some point might do deeper type checking...

lib/NarrativeService/apps/appinfo.py

@@ -1,32 +1,31 @@
+import contextlib
+
 from installed_clients.CatalogClient import Catalog
 from installed_clients.NarrativeMethodStoreClient import NarrativeMethodStore
 
-IGNORE_CATEGORIES = {"inactive", "importers", "viewers"}
+IGNORE_CATEGORIES: set = {"inactive", "importers", "viewers"}
+APP_TAGS: set = {"release", "beta", "dev"}
 
 
-def get_ignore_categories():
-    return {x: 1 for x in IGNORE_CATEGORIES}
+def get_ignore_categories() -> dict[str, int]:
+    return dict.fromkeys(IGNORE_CATEGORIES, 1)
 
 
-def _shorten_types(type_list):
+def _shorten_types(type_list: list[str]) -> list[str]:
     """
     convert ['KBaseMatrices.AmpliconMatrix'] to ['AmpliconMatrix']
     """
-    shorten_types = list()
+    shorten_types = []
     for t in type_list:
-        try:
+        with contextlib.suppress(IndexError):
             shorten_types.append(t.split(".")[1])
-        except IndexError:
-            pass
 
     return shorten_types
 
 
-def get_all_app_info(tag, user, nms_url, catalog_url):
-    if tag not in ["release", "beta", "dev"]:
+def get_all_app_info(tag: str, user: str, nms: NarrativeMethodStore, catalog: Catalog):
+    if not isinstance(tag, str) or tag not in APP_TAGS:
         raise ValueError("tag must be one of 'release', 'beta', or 'dev'")
-    nms = NarrativeMethodStore(nms_url)
-    catalog = Catalog(catalog_url)
     apps = nms.list_methods({"tag": tag})
     app_infos = {}
     module_versions = {}

test/conftest.py

@@ -1,6 +1,8 @@
+import json
 import os
 from collections.abc import Generator
 from configparser import ConfigParser
+from pathlib import Path
 from time import time
 
 import pytest
@@ -11,7 +13,6 @@
 from lib.installed_clients.FakeObjectsForTestsClient import FakeObjectsForTests
 from lib.installed_clients.WorkspaceClient import Workspace
 
-
 @pytest.fixture(scope="session")
 def config() -> Generator[dict[str, str | int], None, None]:
     """Load and return the test config as a dictionary."""
@@ -106,3 +107,17 @@ def mock_token():
 @pytest.fixture
 def mock_user():
     return MOCK_USER_ID
+
+@pytest.fixture
+def json_data():
+    """
+    Loads test data relative to the test/data directory.
+    I.e. for loading the "test/data/test_app_data.json" file, use the fixture like this:
+    def test_stuff(json_data):
+        app_data = test_data("test_app_data.json")
+    """
+    data_root = Path(__file__).parent / "data"
+    def load_json_data(file_path: str | Path):
+        with open(data_root / file_path) as infile:
+            return json.load(infile)
+    return load_json_data

test/data/test_app_data.json

@@ -0,0 +1,98 @@
+[
+    {
+        "id": "CompoundSetUtils/compound_set_from_file",
+        "module_name": "CompoundSetUtils",
+        "git_commit_hash": "092bc8d86874fd83ee7d8b67a40b6a4339fe4289",
+        "name": "Import CompoundSet from File",
+        "ver": "2.1.3",
+        "subtitle": "This method imports a file from the staging area as a CompoundSet",
+        "tooltip": "This method imports a file from the staging area as a CompoundSet",
+        "icon": {
+            "url": "img?method_id=CompoundSetUtils/compound_set_from_file&image_name=data-blue.png&tag=release"
+        },
+        "categories": [
+            "active",
+            "upload"
+        ],
+        "authors": [
+            "jjeffryes"
+        ],
+        "input_types": [],
+        "output_types": [
+            "KBaseBiochem.CompoundSet"
+        ],
+        "app_type": "app",
+        "namespace": "CompoundSetUtils"
+    },
+    {
+        "id": "CompoundSetUtils/compound_set_from_model",
+        "module_name": "CompoundSetUtils",
+        "git_commit_hash": "092bc8d86874fd83ee7d8b67a40b6a4339fe4289",
+        "name": "Make CompoundSet from Metabolic Model",
+        "ver": "2.1.3",
+        "subtitle": "This method genrerate a CompoundSet from compounds in a Metabolic Model",
+        "tooltip": "This method genrerate a CompoundSet from compounds in a Metabolic Model",
+        "icon": {
+            "url": "img?method_id=CompoundSetUtils/compound_set_from_model&image_name=data-blue.png&tag=release"
+        },
+        "categories": [
+            "active",
+            "util"
+        ],
+        "authors": [
+            "jjeffryes"
+        ],
+        "input_types": [
+            "KBaseFBA.FBAModel"
+        ],
+        "output_types": [
+            "KBaseBiochem.CompoundSet"
+        ],
+        "app_type": "app",
+        "namespace": "CompoundSetUtils"
+    },
+    {
+        "id": "CompoundSetUtils/fetch_mol2_files_from_zinc",
+        "module_name": "CompoundSetUtils",
+        "git_commit_hash": "092bc8d86874fd83ee7d8b67a40b6a4339fe4289",
+        "name": "Fetch And Import Mol2 from ZINC Database To CompoundSet",
+        "ver": "2.1.3",
+        "subtitle": "This method fetches Mol2 file from ZINC by searching inchikey associated with compound and then save the Mol2 file to the compound object",
+        "tooltip": "This method fetches Mol2 file from ZINC by searching inchikey associated with compound and then save the Mol2 file to the compound object",
+        "icon": {
+            "url": "img?method_id=CompoundSetUtils/fetch_mol2_files_from_zinc&image_name=zinc15_72pt-aqua.png&tag=release"
+        },
+        "categories": [
+            "active",
+            "upload"
+        ],
+        "authors": [
+            "tgu2"
+        ],
+        "input_types": [
+            "KBaseBiochem.CompoundSet"
+        ],
+        "output_types": [],
+        "app_type": "app",
+        "namespace": "CompoundSetUtils"
+    },
+    {
+        "id": "KBaseRNASeq/view_rnaseq_analysis",
+        "module_name": "KBaseRNASeq",
+        "git_commit_hash": "07a2978aea7cabf4decec09c2dc51be81e26f02d",
+        "name": "View RNASeqAnalysis",
+        "ver": "1.0.5",
+        "subtitle": "View RNASeqAnalysis",
+        "tooltip": "View RNASeqAnalysis",
+        "categories": [
+            "viewers"
+        ],
+        "authors": [],
+        "input_types": [
+            "KBaseRNASeq.RNASeqAnalysis"
+        ],
+        "output_types": [],
+        "app_type": "app",
+        "namespace": "KBaseRNASeq"
+    }
+]

test/data/test_app_favorites.json

@@ -0,0 +1,7 @@
+[
+    {
+        "module_name_lc": "compoundsetutils",
+        "id": "compound_set_from_model",
+        "timestamp": 1585695012878
+    }
+]