Merge pull request #167 from kbase/develop

Merge Develop -> Main for release 0.0.22

Author: MrCreosote

.bandit.yaml

@@ -0,0 +1,2 @@
+assert_used:
+  skips: ['*_test.py', '*test_*.py']

CHANGELOG.md

@@ -5,6 +5,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.0.22] 2022-08-15
+### Changed
+- The NCBI taxa scientfic name lookup queries below were updated to make use of the new
+  NCBI taxa loader `species_or_below` flag and note that the `strain` flag is deprecated.
+  See https://github.com/kbase/relation_engine_importers/blob/d8f87fb74e984cae1c94985b82349b13bc7f277e/docs/NCBI_taxa_sciname_lookup_issues_22_07.md
+  - taxonomy_search_species_strain
+  - taxonomy_search_species_strain_no_sort
+- The NCBI and GTDB taxon collections were updated to include the new flag.
+
 ## [0.0.21] 2022-06-13
 ### Added
 - Dependabot

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.7-alpine
+FROM python:3.10-alpine
 
 ARG DEVELOPMENT
 ARG BUILD_DATE

README.md

@@ -49,3 +49,10 @@ The CI service is available in the `relationapi` service
 * Merge from Develop to Main
 * Draft a release using semantic versioning (e.g 1.2.3) by creating a tag with the target of Main
 * Ensure release notes are updated manually and/or by AutoGenerate Release Notes
+
+## Testing
+
+To run tests:
+```
+make test
+```

VERSION

@@ -1 +1 @@
-0.0.21
+0.0.22

dev-requirements.txt

@@ -1,10 +1,11 @@
-mypy>=0.630
-bandit==1.5.1
+mypy>=0.971
+bandit==1.7.4
+# mccabe 0.7.0 is not compatible with flake8 4.0.1
 mccabe==0.6.1
-flake8==3.5.0
-grequests==0.3.0
-coverage==5.2.1
-typed-ast>=1.4.0
-black==22.3.0
-pytest==6.2.5
-jinja2==3.0.3
+flake8==4.0.1
+grequests==0.6.0
+coverage==6.4.2
+black==22.6.0
+pytest==7.1.2
+python-arango==7.4.1
+frozendict==2.3.4

relation_engine_server/test/test_api_v1.py

@@ -15,9 +15,9 @@
 _CONF = get_config()
 
 # Use the mock auth tokens
-NON_ADMIN_TOKEN = "non_admin_token"
-ADMIN_TOKEN = "admin_token"
-INVALID_TOKEN = "invalid_token"
+NON_ADMIN_TOKEN = "non_admin_token"  # nosec
+ADMIN_TOKEN = "admin_token"  # nosec
+INVALID_TOKEN = "invalid_token"  # nosec
 
 # Use the docker-compose url of the running flask server
 URL = os.environ.get("TEST_URL", "http://localhost:5000")

relation_engine_server/test/test_json_validation.py

@@ -160,8 +160,8 @@ def test_non_validation_validator_errors(self):
         with self.assertRaisesRegex(TypeError, err_msg):
             run_validator(schema_file=test_file, data={})
 
-        # invalid jsonpointer string - note the grammar error is from jsonpointer
-        err_str = "location must starts with /"
+        # invalid jsonpointer string
+        err_str = "Location must start with /"
         json_loc = "start validating here"
         with self.assertRaisesRegex(JsonPointerException, err_str):
             run_validator(schema=test_schema, data={}, validate_at=json_loc)
@@ -271,7 +271,7 @@ def test_pattern_validation(self, schema_arg=None, schema_file_arg=None):
                     "distance": 3,
                 },
                 "file": "invalid_pattern",
-                "err_str": '"what\'s-the-problem with-this-string\?" does not match .*?',
+                "err_str": r'"what\'s-the-problem with-this-string\?" does not match .*?',
             },
             {
                 "input": {"name": "No_problem_with_this_string", "distance": 3},
@@ -309,7 +309,7 @@ def test_uri_validation(self, schema_arg=None, schema_file_arg=None):
             {
                 "input": {"name": "invalid_uri", "home_page": "where is it?"},
                 "file": "invalid_uri",
-                "err_str": "'where is it\?' is not a 'uri'",
+                "err_str": r"'where is it\?' is not a 'uri'",
             },
         ]
 
@@ -350,7 +350,7 @@ def test_date_format_validation(self, schema_arg=None, schema_file_arg=None):
 
         # pyyaml-specific issue: dates get automatically parsed into datetime objects (doh!)
         file_path = os_path.join(json_validation_dir, "unquoted_date.yaml")
-        err_str = "datetime.date\(2020, 6, 6\) is not of type 'string'"
+        err_str = r"datetime.date\(2020, 6, 6\) is not of type 'string'"
         with self.assertRaisesRegex(ValidationError, err_str):
             run_validator(
                 schema=schema_arg,

relation_engine_server/test/test_spec_loader.py

@@ -202,7 +202,7 @@ def test_get_schema_for_doc(self):
 
         fake_name = "fake_name/12345"
         # a nonexistent file raises the appropriate error
-        err_msg = f"Collection 'fake_name' does not exist."
+        err_msg = "Collection 'fake_name' does not exist."
         with self.assertRaisesRegex(SchemaNonexistent, err_msg):
             spec_loader.get_schema_for_doc(fake_name, path_only=True)
 

relation_engine_server/utils/ensure_specs.py

@@ -229,22 +229,25 @@ def excise_namespace(analyzer_name: str) -> str:
 
 
 def is_obj_subset_rec(
-    l: Union[dict, list, float, str, int],
-    r: Union[dict, list, float, str, int],
+    left: Union[dict, list, float, str, int],
+    right: Union[dict, list, float, str, int],
 ):
     """
-    Compare two JSON objects, to see if, essentially, l <= r
+    Compare two JSON objects, to see if, essentially, left <= right
     If comparing dicts, recursively compare
     If comparing lists, shallowly compare. For now, YAGN more
     """
-    if isinstance(l, dict) and isinstance(r, dict):
+    if isinstance(left, dict) and isinstance(right, dict):
         return all(
-            [k in r.keys() and is_obj_subset_rec(l[k], r[k]) for k in l.keys()]
+            [
+                k in right.keys() and is_obj_subset_rec(left[k], right[k])
+                for k in left.keys()
+            ]
         )  # ignore: typing
-    elif isinstance(l, list) and isinstance(r, list):
-        return all([le in r for le in l])
+    elif isinstance(left, list) and isinstance(right, list):
+        return all([le in right for le in left])
     else:
-        return l == r  # noqa: E741
+        return left == right
 
 
 def mod_obj_literal(