Add galaxykit collection upload --skip-upload, --template

galaxykit/client.py

@@ -100,6 +100,9 @@ def __init__(
         self._container_tls_verify = container_tls_verify
         self.gw_root_url = gw_root_url
 
+        if not https_verify:
+            requests.packages.urllib3.disable_warnings()
+
         if auth and not github_social_auth and not gw_auth:
             if isinstance(auth, dict):
                 self.username = auth.get("username")

galaxykit/collections.py

@@ -54,37 +54,70 @@ def get_all_collections(client):
     return client.get(url)
 
 
+def create_test_collection(
+    namespace=None,
+    name=None,
+    version="1.0.0",
+    tags=None,
+    template="skeleton",
+):
+    config = {
+        "namespace": namespace,
+        "version": version,
+    }
+
+    if name is not None:
+        config["name"] = name
+
+    # cloud importer config requires at least one tag
+    if tags is not None:
+        config["tags"] = tags
+
+    return build_collection(template, config=config)
+
+
+def save_test_collection(
+    namespace=None,
+    collection_name=None,
+    version="1.0.0",
+    tags=["tools"],
+    template="skeleton",
+):
+    """
+    Saves (locally) a test collection generated with orionutils
+    """
+    artifact = create_test_collection(
+        namespace, collection_name, version, tags, template
+    )
+
+    return {
+        "namespace": artifact.namespace,
+        "name": artifact.name,
+        "version": artifact.version,
+        "published": artifact.published,
+        "filename": artifact.filename,
+    }
+
+
 def upload_test_collection(
     client,
     namespace=None,
     collection_name=None,
     version="1.0.0",
     path="staging",
     tags=["tools"],
+    template="skeleton",
 ):
     """
     Uploads a test collection generated with orionutils
     """
-    config = {
-        "namespace": namespace or client.username,
-        "version": version,
-    }
-    if collection_name is not None:
-        config["name"] = collection_name
-    # cloud importer config requires at least one tag
-    config["tags"] = tags
-    artifact = build_collection("skeleton", config=config)
-    upload_resp_url = upload_artifact(config, client, artifact, path=path)["task"]
+    artifact = create_test_collection(
+        namespace or client.username, collection_name, version, tags, template
+    )
+
+    resp = upload_artifact(None, client, artifact, path=path)
+    wait_for_task(client, resp)
 
-    ready = False
-    state = ""
-    while not ready:
-        sleep(1)
-        task_resp = client.get(upload_resp_url)
-        state = task_resp["state"]
-        ready = state in ["completed", "failed"]
-    if state == "failed":
-        raise GalaxyClientError(json.dumps(task_resp))
     return {
         "namespace": artifact.namespace,
         "name": artifact.name,
@@ -106,9 +139,7 @@ def upload_artifact(
     """
     Publishes a collection to a Galaxy server and returns the import task URI.
 
-    :param config: a configuration object to describe the artifact to be uploaded.
-        Example:
-            {"namespace": "foo", "name": "bar"}
+    :param config: unused, left for compatibility
     :param client: a GalaxyClient object. Must be authenticated.
     :param artifact: the collection artifact to be uploaded. Expects structure to be that
         of collections produced using the orionutils build_collection function.
@@ -206,6 +237,18 @@ def to_bytes(s, errors=None):
     return resp
 
 
+def approve_collection(client, namespace, collection_name, version):
+    return move_or_copy_collection(
+        client,
+        namespace,
+        collection_name,
+        version,
+        source="staging",
+        destination="published",
+        operation="move",
+    )
+
+
 def move_or_copy_collection(
     client,
     namespace,
@@ -270,6 +313,15 @@ def deprecate_collection(client, namespace, collection, repository):
     return resp
 
 
+def undeprecate_collection(client, namespace, collection, repository):
+    logger.debug(f"Undeprecating {collection} in {namespace} on {client.galaxy_root}")
+    url = f"v3/plugin/ansible/content/{repository}/collections/index/{namespace}/{collection}/"
+    body = {"deprecated": False}
+    resp = client.patch(url, body)
+    wait_for_task(client, resp)
+    return resp
+
+
 def collection_sign(
     client,
     repository,

galaxykit/command.py

@@ -97,6 +97,16 @@ def report_error(resp):
                         "nargs": "*",
                         "default": None,
                     },
+                    "--skip-upload": {
+                        "help": "Save to a local file instead of uploading.",
+                        "action": "store_true",
+                        "default": False,
+                    },
+                    "--template": {
+                        "help": "orionutils collection template",
+                        "nargs": "?",
+                        "default": "skeleton",
+                    },
                 },
             },
             "move": {
@@ -149,6 +159,27 @@ def report_error(resp):
                     "collection_name": {},
                 },
             },
+            "approve": {
+                "args": {
+                    "namespace": {},
+                    "collection_name": {},
+                    "version": {},
+                },
+            },
+            "deprecate": {
+                "args": {
+                    "namespace": {},
+                    "collection_name": {},
+                    "repository": {"nargs": "?", "default": "published"},
+                },
+            },
+            "undeprecate": {
+                "args": {
+                    "namespace": {},
+                    "collection_name": {},
+                    "repository": {"nargs": "?", "default": "published"},
+                },
+            },
         },
     },
     "namespace": {
@@ -296,6 +327,9 @@ def report_error(resp):
     "registry": {
         "help": "Remote Registry",
         "ops": {
+            "list": {
+                "args": None,
+            },
             "delete": {
                 "args": {
                     "name": {},
@@ -888,7 +922,16 @@ def main():
                         sys.exit(EXIT_NOT_FOUND)
 
         elif args.kind == "registry":
-            if args.operation == "delete":
+            if args.operation == "list":
+                try:
+                    resp = registries.list_registries(client)
+                    for name in map(lambda r: r["name"], resp):
+                        print(name)
+                except ValueError as e:
+                    if not args.ignore:
+                        logger.error(e)
+                        sys.exit(EXIT_NOT_FOUND)
+            elif args.operation == "delete":
                 name = args.name
                 try:
                     resp = registries.delete_registry(client, name)
@@ -1008,22 +1051,42 @@ def main():
             if args.operation == "list":
                 print(json.dumps(collections.get_collection_list(client)))
             elif args.operation == "upload":
-                namespace, collection_name, version, path, tags = (
+                (
+                    namespace,
+                    collection_name,
+                    version,
+                    path,
+                    tags,
+                    skip_upload,
+                    template,
+                ) = (
                     args.namespace or client.username,
                     args.collection_name,
                     args.version or "1.0.0",
                     args.path or "staging",
                     args.tags or ["tools"],
+                    args.skip_upload or False,
+                    args.template or "skeleton",
                 )
-                resp = namespaces.create_namespace(client, namespace, None)
-                artifact = collections.upload_test_collection(
-                    client,
-                    namespace=namespace,
-                    collection_name=collection_name,
-                    version=version,
-                    path=path,
-                    tags=tags,
-                )
+                if not skip_upload:
+                    namespaces.create_namespace(client, namespace, None)
+                    artifact = collections.upload_test_collection(
+                        client,
+                        namespace=namespace,
+                        collection_name=collection_name,
+                        version=version,
+                        path=path,
+                        tags=tags,
+                        template=template,
+                    )
+                else:
+                    artifact = collections.save_test_collection(
+                        namespace=namespace,
+                        collection_name=collection_name,
+                        version=version,
+                        tags=tags,
+                        template=template,
+                    )
                 print(json.dumps(artifact))
             elif args.operation == "move":
                 namespace, collection_name, version, source, destination = (
@@ -1115,6 +1178,42 @@ def main():
                     if not args.ignore:
                         logger.error(e)
                         sys.exit(EXIT_NOT_FOUND)
+            elif args.operation == "approve":
+                namespace, collection_name, version = (
+                    args.namespace,
+                    args.collection_name,
+                    args.version,
+                )
+                collections.approve_collection(
+                    client,
+                    namespace,
+                    collection_name,
+                    version,
+                )
+            elif args.operation == "deprecate":
+                namespace, collection_name, repository = (
+                    args.namespace,
+                    args.collection_name,
+                    args.repository or "published",
+                )
+                collections.deprecate_collection(
+                    client,
+                    namespace,
+                    collection_name,
+                    repository,
+                )
+            elif args.operation == "undeprecate":
+                namespace, collection_name, repository = (
+                    args.namespace,
+                    args.collection_name,
+                    args.repository or "published",
+                )
+                collections.undeprecate_collection(
+                    client,
+                    namespace,
+                    collection_name,
+                    repository,
+                )
         elif args.kind == "url":
             if args.operation == "get":
                 url = args.url

galaxykit/registries.py

@@ -39,3 +39,12 @@ def create_registry(client, name, url):
         "url": url,
     }
     return client.post(post_url, registry)
+
+
+def list_registries(client):
+    """
+    List registries
+    """
+    url = f"_ui/v1/execution-environments/registries/?limit=100"
+    resp = client.get(url)
+    return resp["data"]

galaxykit/utils.py

@@ -3,7 +3,6 @@
 import json
 import re
 import time
-from urllib import request
 from urllib.parse import urljoin
 
 import requests