Commit f4442ffc authored by John Chilton's avatar John Chilton
Browse files

Small tweaks toward more modern library API. 

- Use exception-aware API decorators for library contents API endpoints.
- Throw exceptions to handle permission and parameter errors for library upload paths with reusable validation functions.
- Re-arrange code to avoid working with empty paths and throw better configuration not allow exceptions.
parent ee297f02

lib/galaxy/actions/library.py

+50 −31
Original line number Diff line number Diff line
@@ -8,6 +8,11 @@ import os.path 
from markupsafe import escape



from galaxy import util

from galaxy.exceptions import (

    AdminRequiredException,

    ConfigDoesNotAllowException,

    RequestParameterInvalidException,

)

from galaxy.tools.actions import upload_common

from galaxy.tools.parameters import populate_state

from galaxy.util.path import (
@@ -19,6 +24,47 @@ from galaxy.util.path import ( 
log = logging.getLogger(__name__)





def validate_server_directory_upload(trans, server_dir):

    if server_dir in [None, 'None', '']:

        raise RequestParameterInvalidException("Invalid or unspecified server_dir parameter")



    if trans.user_is_admin():

        import_dir = trans.app.config.library_import_dir

        import_dir_desc = 'library_import_dir'

        if not import_dir:

            raise ConfigDoesNotAllowException('"library_import_dir" is not set in the Galaxy configuration')

    else:

        import_dir = trans.app.config.user_library_import_dir

        if not import_dir:

            raise ConfigDoesNotAllowException('"user_library_import_dir" is not set in the Galaxy configuration')

        if server_dir != trans.user.email:

            import_dir = os.path.join(import_dir, trans.user.email)

        import_dir_desc = 'user_library_import_dir'



    full_dir = os.path.join(import_dir, server_dir)

    unsafe = None

    if safe_relpath(server_dir):

        username = trans.user.username if trans.app.config.user_library_import_check_permissions else None

        if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist, username=username):

            for unsafe in unsafe_walk(full_dir, whitelist=[import_dir] + trans.app.config.user_library_import_symlink_whitelist):

                log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', unsafe, os.path.realpath(unsafe))

    else:

        log.error('User attempted to import a directory path that resolves to a path outside of their import dir: %s -> %s', server_dir, os.path.realpath(full_dir))

        unsafe = True

    if unsafe:

        raise RequestParameterInvalidException("Invalid server_dir specified")



    return full_dir, import_dir_desc





def validate_path_upload(trans):

    if not trans.app.config.allow_library_path_paste:

        raise ConfigDoesNotAllowException('"allow_path_paste" is not set to True in the Galaxy configuration file')



    if not trans.user_is_admin():

        raise AdminRequiredException('Uploading files via filesystem paths can only be performed by administrators')





class LibraryActions(object):

    """

    Mixin for controllers that provide library functionality.
@@ -42,38 +88,11 @@ class LibraryActions(object): 
        upload_option = kwd.get('upload_option', 'upload_file')

        response_code = 200

        if upload_option == 'upload_directory':

            if server_dir in [None, 'None', '']:

                response_code = 400

            if trans.user_is_admin():

                import_dir = trans.app.config.library_import_dir

                import_dir_desc = 'library_import_dir'

            else:

                import_dir = trans.app.config.user_library_import_dir

                if server_dir != trans.user.email:

                    import_dir = os.path.join(import_dir, trans.user.email)

                import_dir_desc = 'user_library_import_dir'

            full_dir = os.path.join(import_dir, server_dir)

            unsafe = None

            if safe_relpath(server_dir):

                username = trans.user.username if trans.app.config.user_library_import_check_permissions else None

                if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist):

                    for unsafe in unsafe_walk(full_dir, whitelist=[import_dir] + trans.app.config.user_library_import_symlink_whitelist, username=username):

                        log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', unsafe, os.path.realpath(unsafe))

            else:

                log.error('User attempted to import a directory path that resolves to a path outside of their import dir: %s -> %s', server_dir, os.path.realpath(full_dir))

                unsafe = True

            if unsafe:

                response_code = 403

                message = 'Invalid server_dir'

            if import_dir:

            full_dir, import_dir_desc = validate_server_directory_upload(trans, server_dir)

            message = 'Select a directory'

            else:

                response_code = 403

                message = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc

        elif upload_option == 'upload_paths':

            if not trans.app.config.allow_library_path_paste:

                response_code = 403

                message = '"allow_library_path_paste" is not defined in the Galaxy configuration file'

            # Library API already checked this - following check isn't actually needed.

            validate_path_upload(trans)

        # Some error handling should be added to this method.

        try:

            # FIXME: instead of passing params here ( which have been processed by util.Params(), the original kwd

lib/galaxy/webapps/galaxy/api/library_contents.py

+6 −11
Original line number Diff line number Diff line
@@ -12,9 +12,8 @@ from galaxy import ( 
    exceptions,

    managers,

    util,

    web

)

from galaxy.actions.library import LibraryActions

from galaxy.actions.library import LibraryActions, validate_path_upload

from galaxy.managers.collections_util import (

    api_payload_to_create_params,

    dictify_dataset_collection_instance
@@ -158,7 +157,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary 
            rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id'])

        return rval



    @web.expose_api

    @expose_api

    def create(self, trans, library_id, payload, **kwd):

        """

        create( self, trans, library_id, payload, **kwd )
@@ -314,12 +313,8 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary 
        if folder and last_used_build in ['None', None, '?']:

            last_used_build = folder.genome_build

        error = False

        if upload_option == 'upload_paths' and not trans.app.config.allow_library_path_paste:

            error = True

            message = '"allow_library_path_paste" is not defined in the Galaxy configuration file'

        elif upload_option == 'upload_paths' and not is_admin:

            error = True

            message = 'Uploading files via filesystem paths can only be performed by administrators'

        if upload_option == 'upload_paths':

            validate_path_upload(trans)  # Duplicate check made in _upload_dataset.

        elif upload_option not in ('upload_file', 'upload_directory', 'upload_paths'):

            error = True

            message = 'Invalid upload_option'
@@ -373,7 +368,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary 
            # for cross type comparisions, ie "True" == True

            yield prefix, ("%s" % (meta)).encode("utf8", errors='replace')



    @web.expose_api

    @expose_api

    def update(self, trans, id, library_id, payload, **kwd):

        """

        update( self, trans, id, library_id, payload, **kwd )
@@ -411,7 +406,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary 
        else:

            raise HTTPBadRequest('Malformed library content id ( %s ) specified, unable to decode.' % str(content_id))



    @web.expose_api

    @expose_api

    def delete(self, trans, library_id, id, **kwd):

        """

        delete( self, trans, library_id, id, **kwd )