def get_repo_info_dict(app, user, repository_id, changeset_revision):
repository = suc.get_repository_in_tool_shed(app, repository_id)
repo = hg_util.get_repo_for_repository(app,
repository=repository,
repo_path=None,
create=False)
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(
user, repository)
repository_metadata = suc.get_repository_metadata_by_changeset_revision(
app, repository_id, changeset_revision)
if not repository_metadata:
# The received changeset_revision is no longer installable, so get the next changeset_revision
# in the repository's changelog. This generally occurs only with repositories of type
# repository_suite_definition or tool_dependency_definition.
next_downloadable_changeset_revision = \
suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
if next_downloadable_changeset_revision:
repository_metadata = suc.get_repository_metadata_by_changeset_revision(
app, repository_id, next_downloadable_changeset_revision)
if repository_metadata:
# For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
# is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
# returned repo_info_dict.
metadata = repository_metadata.metadata
if 'tools' in metadata:
includes_tools = True
else:
includes_tools = False
includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
repository_dependencies_dict = metadata.get('repository_dependencies',
{})
repository_dependencies = repository_dependencies_dict.get(
'repository_dependencies', [])
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
suc.get_repository_dependency_types( repository_dependencies )
if 'tool_dependencies' in metadata:
includes_tool_dependencies = True
else:
includes_tool_dependencies = False
else:
# Here's where we may have to handle enhancements to the callers. See above comment.
includes_tools = False
has_repository_dependencies = False
has_repository_dependencies_only_if_compiling_contained_td = False
includes_tool_dependencies = False
includes_tools_for_display_in_tool_panel = False
ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
repo_info_dict = create_repo_info_dict(
app=app,
repository_clone_url=repository_clone_url,
changeset_revision=changeset_revision,
ctx_rev=str(ctx.rev()),
repository_owner=repository.user.username,
repository_name=repository.name,
repository=repository,
repository_metadata=repository_metadata,
tool_dependencies=None,
repository_dependencies=None)
return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
def handle_request(self, trans, **kwd):
# The os command that results in this method being called will look something like:
# hg clone http://[email protected]:9009/repos/test/convert_characters1
hg_version = mercurial.__version__.version
cmd = kwd.get("cmd", None)
hgweb_config = trans.app.hgweb_config_manager.hgweb_config
def make_web_app():
hgwebapp = hgwebdir(hgweb_config)
return hgwebapp
wsgi_app = wsgiapplication(make_web_app)
if hg_version >= "2.2.3" and cmd == "pushkey":
# When doing an "hg push" from the command line, the following commands, in order, will be
# retrieved from environ, depending upon the mercurial version being used. In mercurial
# version 2.2.3, section 15.2. Command changes includes a new feature:
# pushkey: add hooks for pushkey/listkeys
# (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29).
# We require version 2.2.3 since the pushkey hook was added in that version.
# If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey
path_info = kwd.get("path_info", None)
if path_info:
owner, name = path_info.split("/")
repository = get_repository_by_name_and_owner(trans.app, name, owner)
if repository:
if hg_version >= "2.2.3":
# Update the repository on disk to the tip revision, because the web upload
# form uses the on-disk working directory. If the repository is not updated
# on disk, pushing from the command line and then uploading via the web
# interface will result in a new head being created.
repo = hg.repository(ui.ui(), repository.repo_path(trans.app))
update_repository(repo, ctx_rev=None)
repository_clone_url = generate_clone_url_for_repository_in_tool_shed(trans.user, repository)
# Set metadata using the repository files on disk.
rmm = repository_metadata_manager.RepositoryMetadataManager(
app=trans.app,
user=trans.user,
repository=repository,
changeset_revision=repository.tip(trans.app),
repository_clone_url=repository_clone_url,
relative_install_dir=repository.repo_path(trans.app),
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=False,
)
error_message, status = rmm.set_repository_metadata(trans.request.host)
if status == "ok" and error_message:
log.debug(
"Successfully reset metadata on repository %s owned by %s, but encountered problem: %s"
% (str(repository.name), str(repository.user.username), error_message)
)
elif status != "ok" and error_message:
log.debug(
"Error resetting metadata on repository %s owned by %s: %s"
% (str(repository.name), str(repository.user.username), error_message)
)
return wsgi_app
def handle_request(self, trans, **kwd):
# The os command that results in this method being called will look something like:
# hg clone http://[email protected]:9009/repos/test/convert_characters1
hg_version = mercurial.__version__.version
cmd = kwd.get('cmd', None)
hgweb_config = trans.app.hgweb_config_manager.hgweb_config
def make_web_app():
hgwebapp = hgwebdir(hgweb_config)
return hgwebapp
wsgi_app = wsgiapplication(make_web_app)
if hg_version >= '2.2.3' and cmd == 'pushkey':
# When doing an "hg push" from the command line, the following commands, in order, will be
# retrieved from environ, depending upon the mercurial version being used. In mercurial
# version 2.2.3, section 15.2. Command changes includes a new feature:
# pushkey: add hooks for pushkey/listkeys
# (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29).
# We require version 2.2.3 since the pushkey hook was added in that version.
# If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey
path_info = kwd.get('path_info', None)
if path_info:
owner, name = path_info.split('/')
repository = get_repository_by_name_and_owner(
trans.app, name, owner)
if repository:
if hg_version >= '2.2.3':
# Update the repository on disk to the tip revision, because the web upload
# form uses the on-disk working directory. If the repository is not updated
# on disk, pushing from the command line and then uploading via the web
# interface will result in a new head being created.
repo = hg.repository(ui.ui(),
repository.repo_path(trans.app))
update_repository(repo, ctx_rev=None)
repository_clone_url = generate_clone_url_for_repository_in_tool_shed(
trans.user, repository)
# Set metadata using the repository files on disk.
rmm = repository_metadata_manager.RepositoryMetadataManager(
app=trans.app,
user=trans.user,
repository=repository,
changeset_revision=repository.tip(trans.app),
repository_clone_url=repository_clone_url,
relative_install_dir=repository.repo_path(
trans.app),
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=False)
error_message, status = rmm.set_repository_metadata(
trans.request.host)
if status == 'ok' and error_message:
log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \
( str( repository.name ), str( repository.user.username ), error_message ) )
elif status != 'ok' and error_message:
log.debug( "Error resetting metadata on repository %s owned by %s: %s" % \
( str( repository.name ), str( repository.user.username ), error_message ) )
return wsgi_app
def get_repo_info_dict( app, user, repository_id, changeset_revision ):
repository = suc.get_repository_in_tool_shed( app, repository_id )
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
repository_id,
changeset_revision )
if not repository_metadata:
# The received changeset_revision is no longer installable, so get the next changeset_revision
# in the repository's changelog. This generally occurs only with repositories of type
# repository_suite_definition or tool_dependency_definition.
next_downloadable_changeset_revision = \
suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
if next_downloadable_changeset_revision:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
repository_id,
next_downloadable_changeset_revision )
if repository_metadata:
# For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
# is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
# returned repo_info_dict.
metadata = repository_metadata.metadata
if 'tools' in metadata:
includes_tools = True
else:
includes_tools = False
includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
repository_dependencies_dict = metadata.get( 'repository_dependencies', {} )
repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
suc.get_repository_dependency_types( repository_dependencies )
if 'tool_dependencies' in metadata:
includes_tool_dependencies = True
else:
includes_tool_dependencies = False
else:
# Here's where we may have to handle enhancements to the callers. See above comment.
includes_tools = False
has_repository_dependencies = False
has_repository_dependencies_only_if_compiling_contained_td = False
includes_tool_dependencies = False
includes_tools_for_display_in_tool_panel = False
ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
repo_info_dict = create_repo_info_dict( app=app,
repository_clone_url=repository_clone_url,
changeset_revision=changeset_revision,
ctx_rev=str( ctx.rev() ),
repository_owner=repository.user.username,
repository_name=repository.name,
repository=repository,
repository_metadata=repository_metadata,
tool_dependencies=None,
repository_dependencies=None )
return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
def json(self, trans, **kwd):
"""
GET /api/tools/json
Get the tool form JSON for a tool in a repository.
:param guid: the GUID of the tool
:param guid: str
:param tsr_id: the ID of the repository
:param tsr_id: str
:param changeset: the changeset at which to load the tool json
:param changeset: str
"""
guid = kwd.get('guid', None)
tsr_id = kwd.get('tsr_id', None)
changeset = kwd.get('changeset', None)
if None in [changeset, tsr_id, guid]:
message = 'Changeset, repository ID, and tool GUID are all required parameters.'
trans.response.status = 400
return {'status': 'error', 'message': message}
tsucm = ToolShedUtilityContainerManager(trans.app)
repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(repository.user, repository)
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, tsr_id, changeset)
toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url)
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
containers_dict = tsucm.build_repository_containers(repository,
changeset,
repository_dependencies,
repository_metadata)
found_tool = None
for folder in containers_dict['valid_tools'].folders:
if hasattr(folder, 'valid_tools'):
for tool in folder.valid_tools:
tool.id = tool.tool_id
tool_guid = suc.generate_tool_guid(repository_clone_url, tool)
if tool_guid == guid:
found_tool = tool
break
if found_tool is None:
message = 'Unable to find tool with guid %s in repository %s.' % (guid, repository.name)
trans.response.status = 404
return {'status': 'error', 'message': message}
tv = tool_validator.ToolValidator(trans.app)
repository, tool, message = tv.load_tool_from_changeset_revision(tsr_id,
changeset,
found_tool.tool_config)
if message:
status = 'error'
return dict(message=message, status=status)
tool_help = ''
if tool.help:
tool_help = tool.help.render(static_path=web.url_for('/static'), host_url=web.url_for('/', qualified=True))
tool_help = util.unicodify(tool_help, 'utf-8')
tool_dict = tool.to_dict(trans)
tool_dict['inputs'] = {}
tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs'])
tool_dict.update({
'help' : tool_help,
'citations' : bool(tool.citations),
'biostar_url' : trans.app.config.biostar_url,
'requirements' : [{'name' : r.name, 'version' : r.version} for r in tool.requirements],
'state_inputs' : params_to_strings(tool.inputs, {}, trans.app),
'display' : tool.display_interface,
'action' : web.url_for(tool.action),
'method' : tool.method,
'enctype' : tool.enctype
})
return json.dumps(tool_dict)
def json(self, trans, **kwd):
"""
GET /api/tools/json
Get the tool form JSON for a tool in a repository.
:param guid: the GUID of the tool
:param guid: str
:param tsr_id: the ID of the repository
:param tsr_id: str
:param changeset: the changeset at which to load the tool json
:param changeset: str
"""
guid = kwd.get('guid', None)
tsr_id = kwd.get('tsr_id', None)
changeset = kwd.get('changeset', None)
if None in [changeset, tsr_id, guid]:
message = 'Changeset, repository ID, and tool GUID are all required parameters.'
trans.response.status = 400
return {'status': 'error', 'message': message}
tsucm = ToolShedUtilityContainerManager(trans.app)
repository = repository_util.get_repository_in_tool_shed(
self.app, tsr_id)
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(
repository.user, repository)
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
trans.app, tsr_id, changeset)
toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
rb = relation_builder.RelationBuilder(trans.app, repository,
repository_metadata,
toolshed_base_url)
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision(
)
containers_dict = tsucm.build_repository_containers(
repository, changeset, repository_dependencies,
repository_metadata)
found_tool = None
for folder in containers_dict['valid_tools'].folders:
if hasattr(folder, 'valid_tools'):
for tool in folder.valid_tools:
tool.id = tool.tool_id
tool_guid = suc.generate_tool_guid(repository_clone_url,
tool)
if tool_guid == guid:
found_tool = tool
break
if found_tool is None:
message = f'Unable to find tool with guid {guid} in repository {repository.name}.'
trans.response.status = 404
return {'status': 'error', 'message': message}
with ValidationContext.from_app(trans.app) as validation_context:
tv = tool_validator.ToolValidator(validation_context)
repository, tool, valid, message = tv.load_tool_from_changeset_revision(
tsr_id, changeset, found_tool.tool_config)
if message or not valid:
status = 'error'
return dict(message=message, status=status)
tool_help = ''
if tool.help:
tool_help = tool.help.render(static_path=web.url_for('/static'),
host_url=web.url_for('/',
qualified=True))
tool_help = util.unicodify(tool_help, 'utf-8')
tool_dict = tool.to_dict(trans)
tool_dict['inputs'] = {}
tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs'])
tool_dict.update({
'help':
tool_help,
'citations':
bool(tool.citations),
'requirements': [{
'name': r.name,
'version': r.version
} for r in tool.requirements],
'state_inputs':
params_to_strings(tool.inputs, {}, trans.app),
'display':
tool.display_interface,
'action':
web.url_for(tool.action),
'method':
tool.method,
'enctype':
tool.enctype
})
return json.dumps(tool_dict)
