diff env/lib/python3.9/site-packages/planemo/commands/cmd_shed_update.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/planemo/commands/cmd_shed_update.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,151 @@
+"""Module describing the planemo ``shed_update`` command."""
+import sys
+
+import click
+
+from planemo import options
+from planemo import shed
+from planemo.cli import command_function
+from planemo.io import (
+    captured_io_for_xunit,
+    error,
+    info,
+)
+from planemo.reports.xunit_handler import handle_report_xunit_kwd
+
+
[e-mail]("shed_update")
[e-mail]_xunit()
[e-mail]_publish_options()
[e-mail]_upload_options()
[e-mail]_skip_upload()
[e-mail]_skip_metadata()
+@command_function
+def cli(ctx, paths, **kwds):
+    """Update Tool Shed repository.
+
+    By default this command will update both repository metadata
+    from ``.shed.yml`` and upload new contents from the repository
+    directory.
+
+    \b
+        % planemo shed_update
+
+    This will update the main tool shed with the repository defined
+    by a ``.shed.yml`` file in the current working directory. Both
+    the location of the ``.shed.yml`` and the tool shed to upload to
+    can be easily configured. For instance, the following command can
+    be used if ``.shed.yml`` if contained in ``path/to/repo`` and the
+    desire is to update the test tool shed.
+
+    \b
+        % planemo shed_update --shed_target testtoolshed path/to/repo
+
+    Another important option is ``--check_diff`` - this doesn't affect the
+    updating of shed metadata but it will check for differences before
+    uploading new contents to the tool shed. This may important because the
+    tool shed will automatically populate certain attributes in tool shed
+    artifact files (such as ``tool_dependencies.xml``) and this may
+    cause unwanted installable revisions to be created when there are no
+    important changes.
+
+    The lower-level ``shed_upload`` command should be used instead if
+    the repository doesn't define complete metadata in a ``.shed.yml``.
+    """
+    # In a little bit of cheating, we're defining this variable here to collect
+    # a "report" on the shed_update command
+    collected_data = {
+        'results': {
+            'total': 0,
+            'errors': 0,
+            'failures': 0,
+            'skips': 0,
+        },
+        'suitename': 'update',
+        'tests': [],
+    }
+
+    shed_context = shed.get_shed_context(ctx, **kwds)
+
+    def update(realized_repository):
+        collected_data['results']['total'] += 1
+        skip_upload = kwds["skip_upload"]
+        skip_metadata = kwds["skip_metadata"]
+        upload_ret_code = 0
+        upload_ok = True
+
+        captured_io = {}
+        if not skip_upload:
+            with captured_io_for_xunit(kwds, captured_io):
+                upload_ret_code = shed.upload_repository(
+                    ctx, realized_repository, **kwds
+                )
+                upload_ok = not upload_ret_code
+
+        repo_result = {
+            'classname': realized_repository.name,
+            'time': captured_io.get("time", None),
+            'name': 'shed-update',
+            'stdout': captured_io.get("stdout", None),
+            'stderr': captured_io.get("stderr", None),
+        }
+
+        # Now that we've uploaded (or skipped appropriately), collect results.
+        if upload_ret_code == 2:
+            collected_data['results']['failures'] += 1
+            message = "Failed to update repository '%s' as it does not exist on the %s." % (realized_repository.name, shed_context.label)
+            repo_result.update({
+                'errorType': 'FailedUpdate',
+                'errorMessage': message,
+            })
+            collected_data['tests'].append(repo_result)
+            error(message)
+            return upload_ret_code
+
+        exit = 0
+        metadata_ok = True
+        repository_destination_label = "repository '%s' on the %s" % (realized_repository.name, shed_context.label)
+        if not skip_metadata:
+            repo_id = shed.handle_force_create(realized_repository, ctx, shed_context, **kwds)
+            # failing to create the repo, give up
+            if repo_id is None:
+                exit = shed.report_non_existent_repository(realized_repository)
+                metadata_ok = False
+                error("Failed to update metadata for %s." % repository_destination_label)
+            else:
+                metadata_ok = realized_repository.update(ctx, shed_context, repo_id)
+                if metadata_ok:
+                    info("Repository metadata updated successfully for %s." % repository_destination_label)
+        else:
+            info("Skipping metadata update for %s" % repository_destination_label)
+
+        if metadata_ok and upload_ok:
+            pass
+        elif upload_ok:
+            collected_data['results']['skips'] += 1
+            repo_result.update({
+                'errorType': 'FailedMetadata',
+                'errorMessage': 'Failed to update repository metadata',
+            })
+            if not skip_upload:
+                error("Repository contents updated but failed to update metadata for %s." % repository_destination_label)
+            exit = exit or 1
+        else:
+            collected_data['results']['failures'] += 1
+            repo_result.update({
+                'errorType': 'FailedUpdate',
+                'errorMessage': 'Failed to update repository',
+            })
+            if metadata_ok:
+                error("Failed to update repository contents for %s." % repository_destination_label)
+            else:
+                error("Failed to update repository contents and metadata for %s." % repository_destination_label)
+            exit = exit or 1
+        collected_data['tests'].append(repo_result)
+        return exit
+
+    exit_code = shed.for_each_repository(ctx, update, paths, **kwds)
+
+    handle_report_xunit_kwd(kwds, collected_data)
+
+    sys.exit(exit_code)