def cli(ctx, paths, **kwds):
"""Update repository in shed from a ``.shed.yml`` file.
By default this command will update both repository metadata
from ``.shed.yml`` and upload new contents from the repository
directory.
::
% 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.
::
% 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,
},
'tests': [],
}
shed_context = shed.get_shed_context(ctx, **kwds)
def update(realized_repository):
collected_data['results']['total'] += 1
upload_ret_code = 0
upload_ok = True
if not kwds["skip_upload"]:
upload_ret_code = shed.upload_repository(ctx, realized_repository,
**kwds)
upload_ok = not upload_ret_code
if upload_ret_code == 2:
collected_data['results']['failures'] += 1
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 2,
})
error("Failed to update repository it does not exist "
"in target ToolShed.")
return upload_ret_code
repo_id = realized_repository.find_repository_id(ctx, shed_context)
metadata_ok = True
if not kwds["skip_metadata"]:
metadata_ok = realized_repository.update(ctx, shed_context,
repo_id)
if metadata_ok:
info("Repository metadata updated.")
else:
error("Failed to update repository metadata.")
if metadata_ok and upload_ok:
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 0,
})
return 0
elif upload_ok:
collected_data['results']['skips'] += 1
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 3,
})
error("Repo updated but metadata was not.")
return 1
else:
collected_data['results']['failures'] += 1
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 1,
})
error("Failed to update a repository.")
return 1
exit_code = shed.for_each_repository(ctx, update, paths, **kwds)
if kwds.get('report_xunit', False):
with open(kwds['report_xunit'], 'w') as handle:
handle.write(
build_report.template_data(collected_data,
template_name='update_xunit.tpl'))
sys.exit(exit_code)
def cli(ctx, paths, **kwds):
"""Update repository in shed from a ``.shed.yml`` file.
By default this command will update both repository metadata
from ``.shed.yml`` and upload new contents from the repository
directory.
::
% 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.
::
% 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,
},
'tests': [],
}
shed_context = shed.get_shed_context(ctx, **kwds)
def update(realized_repository):
collected_data['results']['total'] += 1
upload_ret_code = 0
upload_ok = True
if not kwds["skip_upload"]:
upload_ret_code = shed.upload_repository(
ctx, realized_repository, **kwds
)
upload_ok = not upload_ret_code
if upload_ret_code == 2:
collected_data['results']['failures'] += 1
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 2,
})
error("Failed to update repository it does not exist "
"in target ToolShed.")
return upload_ret_code
repo_id = realized_repository.find_repository_id(ctx, shed_context)
metadata_ok = True
if not kwds["skip_metadata"]:
metadata_ok = realized_repository.update(ctx, shed_context, repo_id)
if metadata_ok:
info("Repository metadata updated.")
else:
error("Failed to update repository metadata.")
if metadata_ok and upload_ok:
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 0,
})
return 0
elif upload_ok:
collected_data['results']['skips'] += 1
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 3,
})
error("Repo updated but metadata was not.")
return 1
else:
collected_data['results']['failures'] += 1
collected_data['tests'].append({
'classname': realized_repository.name,
'result': 1,
})
error("Failed to update a repository.")
return 1
exit_code = shed.for_each_repository(ctx, update, paths, **kwds)
if kwds.get('report_xunit', False):
with open(kwds['report_xunit'], 'w') as handle:
handle.write(build_report.template_data(
collected_data, template_name='update_xunit.tpl'))
sys.exit(exit_code)
def cli(ctx, paths, **kwds):
"""diff between local repository and Tool Shed.
By default, this will produce a diff between this repository and what
would be uploaded to the Tool Shed with the `shed_upload` command - but
this command can be made to compare other combinations of repositories.
Here are some examples::
% # diff for this repository and the main Tool Shed
% planemo shed_diff
% # diff for this repository and the test Tool Shed
% planemo shed_diff --shed_target testtoolshed
% # diff for the test Tool Shed and main Tool Shed
% planemo shed_diff --shed_target_source testtoolshed
% # diff for two an explicitly specified repositories (ignores
% # current project's shed YAML file.)
% planemo shed_diff --owner peterjc --name blast_rbh
--shed_target_source testtoolshed
This command will return an exit code of:
- 0 if there are no detected differences.
- 1 if there are differences.
- 2 if the target repository doesn't exist.
- >200 if there are errors attempting to perform a diff.
**Warning:** ``shed_diff`` doesn't inspect repository metadata, this
difference applies only to the file contents of files that would actually be
uploaded to the repository.
"""
# In a little bit of cheating, we're defining this variable here to collect
# a "report" on our shed_diff
collected_data = {
'results': {
'total': 0,
'errors': 0,
'failures': 0,
'skips': 0,
},
'suitename': 'shed_diff',
'tests': [],
}
def diff(realized_repository):
# We create a temporary redirection from kwds's
# output to our tempfile. This lets us capture the
# diff and redirect it to their requested location as
# well as to the XUnit report.
diff_output = tempfile.NamedTemporaryFile(mode='r')
user_requested_output = kwds.get('output', None)
# Replace their output handle with ours
kwds['output'] = diff_output.name
captured_io = {}
with captured_io_for_xunit(kwds, captured_io):
result = shed.diff_repo(ctx, realized_repository, **kwds)
# May be extraneous but just want to ensure entire file is written
# before a copy is made.
diff_output.flush()
# Redirect a copy to user_requested_output if they did:
if user_requested_output is not None:
shutil.copy(diff_output.name, user_requested_output)
else:
with open(diff_output.name, "r") as f:
sys.stdout.write(f.read())
# Rewind to the start of the file and read it in its entirety
diff_output.seek(0)
diff_output_contents = diff_output.read()
diff_output.close()
# Collect data about what happened
collected_data['results']['total'] += 1
xunit_case = {
'name': 'shed-diff',
'classname': realized_repository.name,
'time': captured_io["time"],
'stdout': captured_io["stdout"],
'stderr': captured_io["stderr"],
}
if result >= 200:
collected_data['results']['errors'] += 1
xunit_case.update({
'errorType': 'DiffError',
'errorMessage': 'Error diffing repositories',
'errorContent': escape(diff_output_contents),
'time': captured_io["time"],
})
elif result > 2:
collected_data['results']['failures'] += 1
xunit_case.update({
'errorType': 'PlanemoDiffError',
'errorMessage': 'Planemo error diffing repositories',
'errorContent': escape(diff_output_contents),
})
elif result == 2:
collected_data['results']['failures'] += 1
xunit_case.update({
'errorType': 'RepoDoesNotExist',
'errorMessage': 'Target Repository does not exist',
'errorContent': escape(diff_output_contents),
})
elif result == 1:
collected_data['results']['failures'] += 1
xunit_case.update({
'errorType': 'Different',
'errorMessage': 'Repository is different',
'errorContent': escape(diff_output_contents),
})
# Append our xunit test case
collected_data['tests'].append(xunit_case)
return result
exit_code = shed.for_each_repository(ctx, diff, paths, **kwds)
if kwds.get('report_xunit', False):
with open(kwds['report_xunit'], 'wb') as handle:
template_data = build_report.template_data(
collected_data,
template_name='xunit.tpl'
)
handle.write(template_data.encode('ascii', 'xmlcharrefreplace'))
sys.exit(exit_code)
def cli(ctx, paths, **kwds):
"""Update repository in shed from a ``.shed.yml`` file.
By default this command will update both repository metadata
from ``.shed.yml`` and upload new contents from the repository
directory.
::
% 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.
::
% 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
repo_result.update({
'errorType': 'FailedUpdate',
'errorMessage': 'Failed to update repository as it does not exist in target ToolShed',
})
collected_data['tests'].append(repo_result)
error("Failed to update repository it does not exist "
"in target ToolShed.")
return upload_ret_code
exit = 0
metadata_ok = True
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
else:
metadata_ok = realized_repository.update(ctx, shed_context, repo_id)
else:
info("Skipping repository metadata update.")
if not metadata_ok:
error("Failed to update repository metadata.")
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("Repo updated but metadata was not.")
exit = exit or 1
else:
collected_data['results']['failures'] += 1
repo_result.update({
'errorType': 'FailedUpdate',
'errorMessage': 'Failed to update repository',
})
error("Failed to update a repository.")
exit = exit or 1
collected_data['tests'].append(repo_result)
return exit
exit_code = shed.for_each_repository(ctx, update, paths, **kwds)
if kwds.get('report_xunit', False):
with open(kwds['report_xunit'], 'w') as handle:
handle.write(build_report.template_data(
collected_data, template_name='xunit.tpl')
.encode('ascii', 'xmlcharrefreplace'))
sys.exit(exit_code)
def cli(ctx, paths, **kwds):
"""Produce diff between local repository and Tool Shed contents.
By default, this will produce a diff between this repository and what
would be uploaded to the Tool Shed with the `shed_upload` command - but
this command can be made to compare other combinations of repositories.
Here are some examples::
% # diff for this repository and the main Tool Shed
% planemo shed_diff
% # diff for this repository and the test Tool Shed
% planemo shed_diff --shed_target testtoolshed
% # diff for the test Tool Shed and main Tool Shed
% planemo shed_diff --shed_target_source testtoolshed
% # diff for two an explicitly specified repositories (ignores
% # current project's shed YAML file.)
% planemo shed_diff --owner peterjc --name blast_rbh
--shed_target_source testtoolshed
This command will return an exit code of:
- 0 if there are no detected differences.
- 1 if there are differences.
- 2 if the target repository doesn't exist.
- >200 if there are errors attempting to perform a diff.
**Warning:** ``shed_diff`` doesn't inspect repository metadata, this
difference applies only to the file contents of files that would actually be
uploaded to the repository.
"""
# In a little bit of cheating, we're defining this variable here to collect
# a "report" on our shed_diff
collected_data = {
'results': {
'total': 0,
'errors': 0,
'failures': 0,
'skips': 0,
},
'tests': [],
}
def diff(realized_repository):
result = shed.diff_repo(ctx, realized_repository, **kwds)
# Collect data about what happened
collected_data['results']['total'] += 1
if result >= 200:
collected_data['results']['errors'] += 1
elif result > 0:
collected_data['results']['failures'] += 1
collected_data['tests'].append({
'classname': realized_repository.name,
'result': result,
})
return result
exit_code = shed.for_each_repository(ctx, diff, paths, **kwds)
if kwds.get('report_xunit', False):
with open(kwds['report_xunit'], 'w') as handle:
handle.write(
build_report.template_data(collected_data,
template_name='diff_xunit.tpl'))
sys.exit(exit_code)
def cli(ctx, paths, **kwds):
"""diff between local repository and Tool Shed.
By default, this will produce a diff between this repository and what
would be uploaded to the Tool Shed with the `shed_upload` command - but
this command can be made to compare other combinations of repositories.
Here are some examples::
% # diff for this repository and the main Tool Shed
% planemo shed_diff
% # diff for this repository and the test Tool Shed
% planemo shed_diff --shed_target testtoolshed
% # diff for the test Tool Shed and main Tool Shed
% planemo shed_diff --shed_target_source testtoolshed
% # diff for two an explicitly specified repositories (ignores
% # current project's shed YAML file.)
% planemo shed_diff --owner peterjc --name blast_rbh
--shed_target_source testtoolshed
This command will return an exit code of:
- 0 if there are no detected differences.
- 1 if there are differences.
- 2 if the target repository doesn't exist.
- >200 if there are errors attempting to perform a diff.
**Warning:** ``shed_diff`` doesn't inspect repository metadata, this
difference applies only to the file contents of files that would actually be
uploaded to the repository.
"""
# In a little bit of cheating, we're defining this variable here to collect
# a "report" on our shed_diff
collected_data = {
'results': {
'total': 0,
'errors': 0,
'failures': 0,
'skips': 0,
},
'suitename': 'shed_diff',
'tests': [],
}
def diff(realized_repository):
# We create a temporary redirection from kwds's
# output to our tempfile. This lets us capture the
# diff and redirect it to their requested location as
# well as to the XUnit report.
diff_output = tempfile.NamedTemporaryFile(mode='r')
user_requested_output = kwds.get('output', None)
# Replace their output handle with ours
kwds['output'] = diff_output.name
captured_io = {}
with captured_io_for_xunit(kwds, captured_io):
result = shed.diff_repo(ctx, realized_repository, **kwds)
# May be extraneous but just want to ensure entire file is written
# before a copy is made.
diff_output.flush()
# Redirect a copy to user_requested_output if they did:
if user_requested_output is not None:
shutil.copy(diff_output.name, user_requested_output)
else:
with open(diff_output.name, "r") as f:
sys.stdout.write(f.read())
# Rewind to the start of the file and read it in its entirety
diff_output.seek(0)
diff_output_contents = diff_output.read()
diff_output.close()
# Collect data about what happened
collected_data['results']['total'] += 1
xunit_case = {
'name': 'shed-diff',
'classname': realized_repository.name,
'time': captured_io["time"],
'stdout': captured_io["stdout"],
'stderr': captured_io["stderr"],
}
if result >= 200:
collected_data['results']['errors'] += 1
xunit_case.update({
'errorType': 'DiffError',
'errorMessage': 'Error diffing repositories',
'errorContent': escape(diff_output_contents),
'time': captured_io["time"],
})
elif result > 2:
collected_data['results']['failures'] += 1
xunit_case.update({
'errorType': 'PlanemoDiffError',
'errorMessage': 'Planemo error diffing repositories',
'errorContent': escape(diff_output_contents),
})
elif result == 2:
collected_data['results']['failures'] += 1
xunit_case.update({
'errorType': 'RepoDoesNotExist',
'errorMessage': 'Target Repository does not exist',
'errorContent': escape(diff_output_contents),
})
elif result == 1:
collected_data['results']['failures'] += 1
xunit_case.update({
'errorType': 'Different',
'errorMessage': 'Repository is different',
'errorContent': escape(diff_output_contents),
})
# Append our xunit test case
collected_data['tests'].append(xunit_case)
return result
exit_code = shed.for_each_repository(ctx, diff, paths, **kwds)
if kwds.get('report_xunit', False):
with open(kwds['report_xunit'], 'wb') as handle:
template_data = build_report.template_data(
collected_data, template_name='xunit.tpl')
handle.write(template_data.encode('ascii', 'xmlcharrefreplace'))
sys.exit(exit_code)
def cli(ctx, paths, **kwds):
"""Update repository in shed from a ``.shed.yml`` file.
By default this command will update both repository metadata
from ``.shed.yml`` and upload new contents from the repository
directory.
::
% 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.
::
% 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
repo_result.update({
'errorType':
'FailedUpdate',
'errorMessage':
'Failed to update repository as it does not exist in target ToolShed',
})
collected_data['tests'].append(repo_result)
error("Failed to update repository it does not exist "
"in target ToolShed.")
return upload_ret_code
exit = 0
metadata_ok = True
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
else:
metadata_ok = realized_repository.update(
ctx, shed_context, repo_id)
else:
info("Skipping repository metadata update.")
if not metadata_ok:
error("Failed to update repository metadata.")
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("Repo updated but metadata was not.")
exit = exit or 1
else:
collected_data['results']['failures'] += 1
repo_result.update({
'errorType': 'FailedUpdate',
'errorMessage': 'Failed to update repository',
})
error("Failed to update a repository.")
exit = exit or 1
collected_data['tests'].append(repo_result)
return exit
exit_code = shed.for_each_repository(ctx, update, paths, **kwds)
if kwds.get('report_xunit', False):
with open(kwds['report_xunit'], 'w') as handle:
handle.write(
build_report.template_data(collected_data,
template_name='xunit.tpl').encode(
'ascii', 'xmlcharrefreplace'))
sys.exit(exit_code)
