Merge branch 'release_22.05' into dev

client/src/components/providers/StoredWorkflowsProvider.js

@@ -21,7 +21,7 @@ export function storedWorkflowsProvider(ctx, callback, extraParams = {}) {
 }
 
 async function storedWorkflowDetails({ storedWorkflowId }) {
-    const url = `${getAppRoot()}api/workflows/${storedWorkflowId}?instance=true`;
+    const url = `${getAppRoot()}api/workflows/${storedWorkflowId}`;
     try {
         const { data } = await axios.get(url);
         return data;

lib/galaxy/jobs/handler.py

@@ -738,7 +738,7 @@ class JobHandlerQueue(Monitors):
                 # History is job.state_history
                 started = None
                 finished = None
-                for history in sorted(job.state_history, key=lambda h: h.update_time):
+                for history in sorted(job.state_history, key=lambda h: h.create_time):
                     if history.state == "running":
                         started = history.create_time
                     elif history.state == "ok":

lib/galaxy/tool_util/deps/conda_util.py

@@ -31,12 +31,10 @@ SHELL_UNSAFE_PATTERN = re.compile(r"[\s\"']")
 
 IS_OS_X = sys.platform == "darwin"
 
-# BSD 3-clause
-CONDA_LICENSE = "http://docs.continuum.io/anaconda/eula"
 VERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@(.*)")
 UNVERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@_uv_")
 USE_PATH_EXEC_DEFAULT = False
-CONDA_VERSION = "4.6.14"
+CONDA_PACKAGE_SPECS = ("conda=4.6.14", "'pyopenssl>=22.1.0'")
 CONDA_BUILD_VERSION = "3.17.8"
 USE_LOCAL_DEFAULT = False
 
@@ -113,7 +111,6 @@ class CondaContext(installable.InstallableContext):
             self.conda_exec = self._bin("conda")
         self.ensure_channels: List[str] = listify(ensure_channels)
         self._conda_version = None
-        self._miniconda_version = None
         self._conda_build_available = None
         self.use_local = use_local
 
@@ -130,35 +127,16 @@ class CondaContext(installable.InstallableContext):
         return self._conda_build_available
 
     def _guess_conda_properties(self):
-        conda_meta_path = self._conda_meta_path
-        # Perhaps we should call "conda info --json" and parse it but for now we are going
-        # to assume the default.
-        conda_version = packaging.version.parse(CONDA_VERSION)
-        conda_build_available = False
-        miniconda_version = "3"
-
-        if os.path.exists(conda_meta_path):
-            for package in os.listdir(conda_meta_path):
-                package_parts = package.split("-")
-                if len(package_parts) < 3:
-                    continue
-                package = "-".join(package_parts[:-2])
-                version = package_parts[-2]
-                # build = package_parts[-1]
-                if package == "conda":
-                    conda_version = packaging.version.parse(version)
-                if package == "python" and version.startswith("2"):
-                    miniconda_version = "2"
-                if package == "conda-build":
-                    conda_build_available = True
-
-        self._conda_version = conda_version
-        self._miniconda_version = miniconda_version
-        self._conda_build_available = conda_build_available
-
-    @property
-    def _conda_meta_path(self):
-        return os.path.join(self.conda_prefix, "conda-meta")
+        info = self.conda_info()
+        self._conda_version = packaging.version.parse(info["conda_version"])
+        self._conda_build_available = False
+        conda_build_version = info.get("conda_build_version")
+        if conda_build_version != "not installed":
+            try:
+                self._conda_version = packaging.version.parse(conda_build_version)
+                self._conda_build_available = True
+            except Exception:
+                pass
 
     @property
     def _override_channels_args(self):
@@ -262,6 +240,8 @@ class CondaContext(installable.InstallableContext):
         Return the process exit code (i.e. 0 in case of success).
         """
         create_args = ["-y", "--quiet"]
+        if self.conda_version >= packaging.version.parse("4.7.5"):
+            create_args.append("--strict-channel-priority")
         if allow_local and self.use_local:
             create_args.extend(["--use-local"])
         create_args.extend(self._override_channels_args)
@@ -283,6 +263,8 @@ class CondaContext(installable.InstallableContext):
         Return the process exit code (i.e. 0 in case of success).
         """
         install_args = ["-y"]
+        if self.conda_version >= packaging.version.parse("4.7.5"):
+            install_args.append("--strict-channel-priority")
         if allow_local and self.use_local:
             install_args.append("--use-local")
         install_args.extend(self._override_channels_args)
@@ -447,9 +429,7 @@ def install_conda(conda_context, force_conda_build=False):
         script_path = temp.name
     download_cmd = commands.download_command(conda_link(), to=script_path)
     install_cmd = ["bash", script_path, "-b", "-p", conda_context.conda_prefix]
-    package_targets = [
-        f"conda={CONDA_VERSION}",
-    ]
+    package_targets = list(CONDA_PACKAGE_SPECS)
     if force_conda_build or conda_context.use_local:
         package_targets.append(f"conda-build={CONDA_BUILD_VERSION}")
     log.info("Installing conda, this may take several minutes.")

lib/galaxy/tool_util/deps/views.py

@@ -340,7 +340,7 @@ class ContainerResolutionView:
     def show(self, index):
         return self._container_resolver(index).to_dict()
 
-    def resolve(self, **kwds):
+    def resolve(self, index=None, **kwds):
         find_best_kwds = {
             "install": False,
             "enabled_container_types": ["docker", "singularity"],
@@ -348,8 +348,8 @@ class ContainerResolutionView:
             "session": kwds.get("session"),
         }
 
-        if "index" in kwds:
-            find_best_kwds["index"] = int(kwds["index"])
+        if index is not None:
+            find_best_kwds["index"] = int(index)
         if "container_type" in kwds:
             find_best_kwds["enabled_container_types"] = [kwds["container_type"]]
         if "resolver_type" in kwds:

lib/galaxy_test/api/test_container_resolution.py

@@ -1,7 +1,8 @@
+from galaxy_test.base.populators import skip_without_tool
 from ._framework import ApiTestCase
 
 
-class ContainerResolutionApiTestCase(ApiTestCase):
+class TestContainerResolutionApi(ApiTestCase):
     def test_index(self):
         response = self._get("container_resolvers", admin=True)
         assert response.status_code == 200
@@ -11,3 +12,15 @@ class ContainerResolutionApiTestCase(ApiTestCase):
         response = self._get("container_resolvers/0", admin=True)
         assert response.status_code == 200
         assert isinstance(response.json(), dict)
+
+    @skip_without_tool("cat1")
+    def test_resolve(self):
+        tool_id = "cat1"
+
+        # no index
+        response = self._get(f"container_resolvers/resolve?tool_id={tool_id}", admin=True)
+        assert response.status_code == 200
+
+        # with index
+        response = self._get(f"container_resolvers/0/resolve?tool_id={tool_id}", admin=True)
+        assert response.status_code == 200