Progress toward exercising less of the tool shed upload API.

So we can kill it.

.ci/flake8_ignorelist.txt

@@ -11,6 +11,7 @@ database
 doc/build
 eggs
 lib/galaxy/web/proxy/js/node_modules
+lib/tool_shed/test/test_data/repos
 static/maps
 static/scripts
 test/functional/tools/cwl_tools/v1.?/

.flake8

@@ -7,3 +7,4 @@
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
 ignore = B008,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+exclude = lib/tool_shed/test/test_data/repos

.isort.cfg

@@ -10,5 +10,5 @@ profile=black
 reverse_relative=true
 skip_gitignore=true
 # Make isort run faster by skipping database
-skip_glob=database/*
+skip_glob=database/*,lib/tool_shed/test/test_data/repos/*
 src_paths=lib

lib/tool_shed/test/base/api.py

@@ -35,7 +35,7 @@ class ShedBaseTestCase(DrivenFunctionalTestCase):
     @property
     def populator(self) -> ToolShedPopulator:
         if self._populator is None:
-            self._populator = ToolShedPopulator(self.admin_api_interactor, self.api_interactor)
+            self._populator = self._get_populator(self.api_interactor)
         return self._populator
 
     @property
@@ -50,7 +50,18 @@ def api_interactor(self) -> ShedApiInteractor:
             password = "testpassword"
             ensure_user_with_email(self.admin_api_interactor, email, password)
             user_api_key = self._api_key(email, password)
-        return ShedApiInteractor(self.url, user_api_key)
+        return self._api_interactor(user_api_key)
+
+    def _api_interactor_by_credentials(self, email: str, password: str) -> ShedApiInteractor:
+        ensure_user_with_email(self.admin_api_interactor, email, password)
+        user_api_key = self._api_key(email, password)
+        return self._api_interactor(user_api_key)
+
+    def _api_interactor(self, api_key: str) -> ShedApiInteractor:
+        return ShedApiInteractor(self.url, api_key)
+
+    def _get_populator(self, user_api_interactor) -> ToolShedPopulator:
+        return ToolShedPopulator(self.admin_api_interactor, user_api_interactor)
 
     def _api_key(self, email: str, password: str) -> str:
         headers = baseauth_headers(email, password)

lib/tool_shed/test/base/populators.py

@@ -81,21 +81,52 @@ def __init__(self, admin_api_interactor: ShedApiInteractor, api_interactor: Shed
         self._admin_api_interactor = admin_api_interactor
         self._api_interactor = api_interactor
 
-    def setup_test_data_repo(self, test_data_path: str) -> Repository:
-        prefix = test_data_path.replace("_", "")
-        category_id = self.new_category(prefix=prefix).id
-        repository = self.new_repository(category_id, prefix=prefix)
-        repository_id = repository.id
+    def setup_bismark_repo(self, repository_id: HasRepositoryId, end: Optional[int] = None):
+        self.setup_test_data_repo_by_id("bismark", repository_id, assert_ok=False, end=end)
+
+    def setup_test_data_repo_by_id(
+        self,
+        test_data_path: str,
+        repository_id: Optional[HasRepositoryId] = None,
+        assert_ok=True,
+        start: int = 0,
+        end: Optional[int] = None,
+    ) -> HasRepositoryId:
+        if repository_id is None:
+            prefix = test_data_path.replace("_", "")
+            category_id = self.new_category(prefix=prefix).id
+            repository = self.new_repository(category_id, prefix=prefix)
+            repository_id = repository.id
+
         assert repository_id
 
         for index, repo_tar in enumerate(repo_tars(test_data_path)):
+            if index < start:
+                continue
+
+            if end and index >= end:
+                break
+
             commit_message = f"Updating {test_data_path} with index {index} with tar {repo_tar}"
-            response = self.upload_revision(
-                repository_id,
-                repo_tar,
-                commit_message=commit_message,
-            )
-            assert response.is_ok
+            response = self.upload_revision_raw(repository_id, repo_tar, commit_message)
+            if assert_ok:
+                api_asserts.assert_status_code_is_ok(response)
+                assert RepositoryUpdate(__root__=response.json()).is_ok
+        return repository_id
+
+    def setup_test_data_repo(
+        self,
+        test_data_path: str,
+        repository: Optional[Repository] = None,
+        assert_ok=True,
+        start: int = 0,
+        end: Optional[int] = None,
+    ) -> Repository:
+        if repository is None:
+            prefix = test_data_path.replace("_", "")
+            category_id = self.new_category(prefix=prefix).id
+            repository = self.new_repository(category_id, prefix=prefix)
+        self.setup_test_data_repo_by_id(test_data_path, repository, assert_ok=assert_ok, start=start, end=end)
         return repository
 
     def setup_column_maker_repo(self, prefix=DEFAULT_PREFIX) -> Repository:
@@ -152,7 +183,7 @@ def upload_revision_raw(
     def upload_revision(
         self, repository: HasRepositoryId, path: Traversable, commit_message: str = DEFAULT_COMMIT_MESSAGE
     ):
-        response = self.upload_revision_raw(repository, path, commit_message)
+        response = self.upload_revision_raw(repository, path, commit_message=commit_message)
         if response.status_code != 200:
             response_json = None
             err_msg = None