def load_tool_elements_from_path(path, recursive, register_load_errors=False):
return loader_directory.load_tool_elements_from_path(
path,
_load_exception_handler,
recursive=recursive,
register_load_errors=register_load_errors,
)
def load_tool_elements_from_path(path, recursive, register_load_errors=False):
"""Generator for tool XML elements on a path."""
return loader_directory.load_tool_elements_from_path(
path,
_load_exception_handler,
recursive=recursive,
register_load_errors=register_load_errors,
)
def collect_conda_targets(path, found_tool_callback=None, conda_context=None):
conda_targets = []
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
if found_tool_callback:
found_tool_callback(tool_path)
requirements, containers = parse_requirements_from_xml(tool_xml)
conda_targets.extend(conda_util.requirements_to_conda_targets(requirements))
return conda_targets
def collect_conda_targets(path, found_tool_callback=None, conda_context=None):
conda_targets = []
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
if found_tool_callback:
found_tool_callback(tool_path)
requirements, containers = parse_requirements_from_xml(tool_xml)
conda_targets.extend(conda_util.requirements_to_conda_targets(requirements))
return conda_targets
def load_tool_elements_from_path(path, recursive, register_load_errors=False):
"""Generator for tool XML elements on a path."""
return loader_directory.load_tool_elements_from_path(
path,
_load_exception_handler,
recursive=recursive,
register_load_errors=register_load_errors,
)
def load_one_dir( path ):
tools_in_dir = []
tool_elems = load_tool_elements_from_path( path )
if tool_elems:
for elem in tool_elems:
root = elem[1].getroot()
if root.tag == 'tool':
tool = {}
if root.find( 'help' ) is not None:
tool.update( dict( help=root.find( 'help' ).text ) )
if root.find( 'description' ) is not None:
tool.update( dict( description=root.find( 'description' ).text ) )
tool.update( dict( id=root.attrib.get( 'id' ),
name=root.attrib.get( 'name' ),
version=root.attrib.get( 'version' ) ) )
tools_in_dir.append( tool )
return tools_in_dir
def load_one_dir(path):
tools_in_dir = []
tool_elems = load_tool_elements_from_path(path)
if tool_elems:
for elem in tool_elems:
root = elem[1].getroot()
if root.tag == 'tool':
tool = {}
if root.find('help') is not None:
tool.update(dict(help=root.find('help').text))
if root.find('description') is not None:
tool.update(
dict(description=root.find('description').text))
tool.update(
dict(id=root.attrib.get('id'),
name=root.attrib.get('name'),
version=root.attrib.get('version')))
tools_in_dir.append(tool)
return tools_in_dir
def cli(ctx, path, brew=None):
"""Install tool requirements using brew. (**Experimental**)
An experimental approach to versioning brew recipes will be used.
See full discussion on the homebrew-science issues page here -
https://github.com/Homebrew/homebrew-science/issues/1191. Information
on the implementation can be found at
https://github.com/jmchilton/platform-brew
until a more permanent project home is setup.
"""
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
ctx.log('Brewing requirements from tool %s',
click.format_filename(tool_path))
mock_args = bunch.Bunch(brew=brew)
brew_context = brew_exts.BrewContext(mock_args)
requirements, containers = parse_requirements_from_xml(tool_xml)
for recipe_context in brew_util.requirements_to_recipe_contexts(
requirements, brew_context):
brew_exts.versioned_install(recipe_context)
def cli(ctx, path, brew=None):
"""Install tool requirements using brew. (**Experimental**)
An experimental approach to versioning brew recipes will be used.
See full discussion on the homebrew-science issues page here -
https://github.com/Homebrew/homebrew-science/issues/1191. Information
on the implementation can be found at
https://github.com/jmchilton/platform-brew
until a more permanent project home is setup.
"""
for (tool_path, tool_xml) in load_tool_elements_from_path(path):
ctx.log('Brewing requirements from tool %s',
click.format_filename(tool_path))
mock_args = bunch.Bunch(brew=brew)
brew_context = brew_exts.BrewContext(mock_args)
requirements, containers = parse_requirements_from_xml(tool_xml)
for recipe_context in brew_util.requirements_to_recipe_contexts(
requirements,
brew_context
):
brew_exts.versioned_install(recipe_context)
def get_repos( sa_session, path_to_repositories ):
"""
Load repos from DB and included tools from .xml configs.
"""
results = []
for repo in sa_session.query( model.Repository ).filter_by( deleted=False ).filter_by( deprecated=False ).filter( model.Repository.type != 'tool_dependency_definition' ):
repo_id = repo.id
name = repo.name
description = repo.description
long_description = repo.long_description
homepage_url = repo.homepage_url
remote_repository_url = repo.remote_repository_url
times_downloaded = repo.times_downloaded
if not isinstance( times_downloaded, ( int, long ) ):
times_downloaded = 0
repo_owner_username = ''
if repo.user_id is not None:
user = sa_session.query( model.User ).filter( model.User.id == repo.user_id ).one()
repo_owner_username = user.username
approved = 'no'
for review in repo.reviews:
if review.approved == 'yes':
approved = 'yes'
break
# Format the time since last update to be nicely readable.
last_updated = pretty_print_time_interval( repo.update_time )
full_last_updated = repo.update_time.strftime( "%Y-%m-%d %I:%M %p" )
# Parse all the tools within repo for separate index.
tools_list = []
path = os.path.join( path_to_repositories, *model.directory_hash_id( repo.id ))
path = os.path.join( path, "repo_%d" % repo.id )
if os.path.exists(path):
tool_elems = load_tool_elements_from_path(path)
if tool_elems:
for elem in tool_elems:
root = elem[1].getroot()
if root.tag == 'tool':
tool = {}
if root.find('help') is not None:
tool.update( dict( help=root.find( 'help' ).text ) )
if root.find('description') is not None:
tool.update( dict( description=root.find( 'description' ).text ) )
tool.update( dict( id=root.attrib.get('id'),
name=root.attrib.get('name'),
version=root.attrib.get('version') ) )
tools_list.append( tool )
results.append(dict( id=repo_id,
name=name,
description=description,
long_description=long_description,
homepage_url=homepage_url,
remote_repository_url=remote_repository_url,
repo_owner_username=repo_owner_username,
times_downloaded=times_downloaded,
approved=approved,
last_updated=last_updated,
full_last_updated=full_last_updated,
tools_list=tools_list ) )
return results
def load_tool_elements_from_path(path, recursive):
return loader_directory.load_tool_elements_from_path(
path,
load_exception_handler,
recursive,
)
