Source code for

import logging
import os
import tempfile
from dataclasses import dataclass
from io import StringIO
from json import (
from typing import (

from sqlalchemy import select
from sqlalchemy.orm import joinedload
from webob.compat import cgi_FieldStorage

from galaxy import util
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.files.uris import (
from galaxy.managers.context import ProvidesUserContext
from galaxy.model import (
from galaxy.model.base import transaction
from galaxy.util import is_url
from galaxy.util.path import external_chown

log = logging.getLogger(__name__)

[docs]def validate_datatype_extension(datatypes_registry, ext): if ext and ext not in ("auto", "data") and not datatypes_registry.get_datatype_by_extension(ext): raise RequestParameterInvalidException(f"Requested extension '{ext}' unknown, cannot upload dataset.")
[docs]def persist_uploads(params, trans): """ Turn any uploads in the submitted form to persisted files. """ if "files" in params: new_files = [] for upload_dataset in params["files"]: f = upload_dataset["file_data"] if isinstance(f, cgi_FieldStorage): assert not isinstance(f.file, StringIO) assert != "<fdopen>" local_filename = util.mkstemp_ln(, "upload_file_data_") f.file.close() upload_dataset["file_data"] = dict(filename=f.filename, local_filename=local_filename) elif isinstance(f, dict) and "local_filename" not in f: raise Exception("Uploaded file was encoded in a way not understood by Galaxy.") if ( "url_paste" in upload_dataset and upload_dataset["url_paste"] and upload_dataset["url_paste"].strip() != "" ): upload_dataset["url_paste"] = stream_to_file( StringIO(validate_non_local(upload_dataset["url_paste"],, prefix="strio_url_paste_", ) else: upload_dataset["url_paste"] = None new_files.append(upload_dataset) params["files"] = new_files return params
[docs]@dataclass class LibraryParams: roles: List[Role] tags: Optional[List[str]] template: Optional[FormDefinition] template_field_contents: Dict[str, str] folder: LibraryFolder message: str replace_dataset: Optional[LibraryDataset]
[docs]def handle_library_params( trans, params, folder_id: int, replace_dataset: Optional[LibraryDataset] = None ) -> LibraryParams: session = trans.sa_session # FIXME: the received params has already been parsed by util.Params() by the time it reaches here, # so no complex objects remain. This is not good because it does not allow for those objects to be # manipulated here. The received params should be the original kwd from the initial request. message = params.get("ldda_message", "") # See if we have any template field contents template_field_contents = {} template_id = params.get("template_id", None) folder = session.get(LibraryFolder, folder_id) # We are inheriting the folder's info_association, so we may have received inherited contents or we may have redirected # here after the user entered template contents ( due to errors ). template: Optional[FormDefinition] = None if template_id not in [None, "None"]: template = session.get(FormDefinition, template_id) assert template for field in template.fields: field_name = field["name"] if params.get(field_name, False): field_value = util.restore_text(params.get(field_name, "")) template_field_contents[field_name] = field_value roles: List[Role] = [] for role_id in util.listify(params.get("roles", [])): role = session.get(Role, role_id) roles.append(role) tags = params.get("tags", None) return LibraryParams( folder=folder, message=message, roles=roles, tags=tags, template=template, template_field_contents=template_field_contents, replace_dataset=replace_dataset, )
def __new_history_upload(trans, uploaded_dataset, history=None, state=None): if not history: history = trans.history hda =, extension=uploaded_dataset.file_type, dbkey=uploaded_dataset.dbkey, history=history, create_dataset=True, sa_session=trans.sa_session, ) trans.sa_session.add(hda) if state: hda.state = state else: hda.state = hda.states.QUEUED history.add_dataset(hda, genome_build=uploaded_dataset.dbkey, quota=False) permissions =, permissions, new=True, flush=False) with transaction(trans.sa_session): trans.sa_session.commit() return hda def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_handler, state=None): current_user_roles = trans.get_current_user_roles() if not ( (trans.user_is_admin and cntrller in ["library_admin", "api"]) or, library_bunch.folder) ): # This doesn't have to be pretty - the only time this should happen is if someone's being malicious. raise Exception("User is not authorized to add datasets to this library.") folder = library_bunch.folder if uploaded_dataset.get("in_folder", False): # Create subfolders if desired for name in uploaded_dataset.in_folder.split(os.path.sep): trans.sa_session.refresh(folder) matches = [x for x in active_folders(trans, folder) if == name] if matches: folder = matches[0] else: new_folder = LibraryFolder(name=name, description="Automatically created by upload tool") new_folder.genome_build = folder.add_folder(new_folder) trans.sa_session.add(new_folder) with transaction(trans.sa_session): trans.sa_session.commit(), folder, new_folder) folder = new_folder if library_bunch.replace_dataset: ld = library_bunch.replace_dataset else: ld =, trans.sa_session.add(ld) with transaction(trans.sa_session): trans.sa_session.commit(), folder, ld) ldda =, extension=uploaded_dataset.file_type, dbkey=uploaded_dataset.dbkey, library_dataset=ld, user=trans.user, create_dataset=True, sa_session=trans.sa_session, ) if uploaded_dataset.get("tag_using_filenames", False): tag_from_filename = os.path.splitext(os.path.basename([0] tag_handler.apply_item_tag(item=ldda, user=trans.user, name="name", value=tag_from_filename, flush=False) if tags_list := uploaded_dataset.get("tags", False): for tag in tags_list: tag_handler.apply_item_tag(item=ldda, user=trans.user, name="name", value=tag, flush=False) trans.sa_session.add(ldda) if state: ldda.state = state else: ldda.state = ldda.states.QUEUED ldda.message = library_bunch.message with transaction(trans.sa_session): trans.sa_session.commit() # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset, ld, ldda) if library_bunch.replace_dataset: # Copy the Dataset level permissions from replace_dataset to the new LibraryDatasetDatasetAssociation.dataset library_bunch.replace_dataset.library_dataset_dataset_association.dataset, ldda.dataset ) else: # Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset ldda.dataset,, new=True ) folder.add_library_dataset(ld, genome_build=uploaded_dataset.dbkey) trans.sa_session.add(folder) with transaction(trans.sa_session): trans.sa_session.commit() ld.library_dataset_dataset_association_id = trans.sa_session.add(ld) with transaction(trans.sa_session): trans.sa_session.commit() # Handle template included in the upload form, if any. If the upload is not asynchronous ( e.g., URL paste ), # then the template and contents will be included in the library_bunch at this point. If the upload is # asynchronous ( e.g., uploading a file ), then the template and contents will be included in the library_bunch # in the get_uploaded_datasets() method below. if library_bunch.template and library_bunch.template_field_contents: # Since information templates are inherited, the template fields can be displayed on the upload form. # If the user has added field contents, we'll need to create a new form_values and info_association # for the new library_dataset_dataset_association object. # Create a new FormValues object, using the template we previously retrieved form_values =, library_bunch.template_field_contents) trans.sa_session.add(form_values) with transaction(trans.sa_session): trans.sa_session.commit() # Create a new info_association between the current ldda and form_values # TODO: Currently info_associations at the ldda level are not inheritable to the associated LibraryDataset, # we need to figure out if this is optimal info_association = ldda, library_bunch.template, form_values ) trans.sa_session.add(info_association) with transaction(trans.sa_session): trans.sa_session.commit() # If roles were selected upon upload, restrict access to the Dataset to those roles if library_bunch.roles: for role in library_bunch.roles: dp =, ldda.dataset, role ) trans.sa_session.add(dp) with transaction(trans.sa_session): trans.sa_session.commit() return ldda
[docs]def new_upload( trans: ProvidesUserContext, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None, tag_list=None ): tag_handler = trans.tag_handler if library_bunch: upload_target_dataset_instance = __new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, tag_handler, state ) if library_bunch.tags and not uploaded_dataset.tags: new_tags = tag_handler.parse_tags_list(library_bunch.tags) for tag in new_tags: tag_handler.apply_item_tag( user=trans.user, item=upload_target_dataset_instance, name=tag[0], value=tag[1], flush=False ) else: upload_target_dataset_instance = __new_history_upload(trans, uploaded_dataset, history=history, state=state) if tag_list: tag_handler.add_tags_from_list(trans.user, upload_target_dataset_instance, tag_list, flush=False) return upload_target_dataset_instance
[docs]def get_uploaded_datasets(trans, cntrller, params, dataset_upload_inputs, library_bunch=None, history=None): uploaded_datasets = [] for dataset_upload_input in dataset_upload_inputs: uploaded_datasets.extend(dataset_upload_input.get_uploaded_datasets(trans, params)) for uploaded_dataset in uploaded_datasets: data = new_upload(trans, cntrller, uploaded_dataset, library_bunch=library_bunch, history=history) = data return uploaded_datasets
[docs]def create_paramfile(trans, uploaded_datasets): """ Create the upload tool's JSON "param" file. """ tool_params = [] json_file_path = None for uploaded_dataset in uploaded_datasets: data = if uploaded_dataset.type == "composite": # we need to init metadata before the job is dispatched data.init_meta() for meta_name, meta_value in uploaded_dataset.metadata.items(): setattr(data.metadata, meta_name, meta_value) trans.sa_session.add(data) with transaction(trans.sa_session): trans.sa_session.commit() params = dict( file_type=uploaded_dataset.file_type,, dbkey=uploaded_dataset.dbkey, type=uploaded_dataset.type, metadata=uploaded_dataset.metadata, primary_file=uploaded_dataset.primary_file, composite_file_paths=uploaded_dataset.composite_files, composite_files={k: v.__dict__ for k, v in data.datatype.get_composite_files(data).items()}, ) else: try: is_binary = uploaded_dataset.datatype.is_binary except Exception: is_binary = None try: link_data_only = uploaded_dataset.link_data_only except Exception: link_data_only = "copy_files" try: uuid_str = uploaded_dataset.uuid except Exception: uuid_str = None try: purge_source = uploaded_dataset.purge_source except Exception: purge_source = True try: user_ftp_dir = os.path.abspath(trans.user_ftp_dir) except Exception: user_ftp_dir = None if user_ftp_dir and uploaded_dataset.path.startswith(user_ftp_dir): uploaded_dataset.type = "ftp_import" params = dict( file_type=uploaded_dataset.file_type, ext=uploaded_dataset.ext,,, dbkey=uploaded_dataset.dbkey, type=uploaded_dataset.type, is_binary=is_binary, link_data_only=link_data_only, uuid=uuid_str, to_posix_lines=getattr(uploaded_dataset, "to_posix_lines", True), auto_decompress=getattr(uploaded_dataset, "auto_decompress", True), purge_source=purge_source, space_to_tab=uploaded_dataset.space_to_tab, is not None,, path=uploaded_dataset.path, ) # TODO: This will have to change when we start bundling inputs. # Also, in_place above causes the file to be left behind since the # user cannot remove it unless the parent directory is writable. if ( link_data_only == "copy_files" and trans.user and and not is_url(uploaded_dataset.path) ): external_chown( uploaded_dataset.path, trans.user.system_user_pwent(,, description="uploaded file", ) tool_params.append(params) with tempfile.NamedTemporaryFile(mode="w", prefix="upload_params_", delete=False) as fh: json_file_path = dump(tool_params, fh) return json_file_path
[docs]def create_job(trans, params, tool, json_file_path, outputs, folder=None, history=None, job_params=None): """ Create the upload job. """ job = trans.sa_session.add(job) job.galaxy_version = galaxy_session = trans.get_galaxy_session() if isinstance(galaxy_session, trans.model.GalaxySession): job.session_id = if trans.user is not None: job.user_id = if folder: job.library_folder_id = else: if not history: history = trans.history job.history_id = job.tool_id = job.tool_version = tool.version job.dynamic_tool = tool.dynamic_tool for name, value in tool.params_to_strings(params, job.add_parameter(name, value) job.add_parameter("paramfile", dumps(json_file_path)) for i, output_object in enumerate(outputs): output_name = "output%i" % i if hasattr(output_object, "collection"): job.add_output_dataset_collection(output_name, output_object) output_object.job = job else: dataset = output_object if folder: job.add_output_library_dataset(output_name, dataset) else: job.add_output_dataset(output_name, dataset) job.set_state(job.states.NEW) if job_params: for name, value in job_params.items(): job.add_parameter(name, value) output = {} for i, v in enumerate(outputs): if not hasattr(output_object, "collection_type"): output["output%i" % i] = v return job, output
[docs]def active_folders(trans, folder): # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues). # Much faster way of retrieving all active sub-folders within a given folder than the # performance of the mapper. This query also eagerloads the permissions on each folder. stmt = ( select(LibraryFolder) .filter_by(parent=folder, deleted=False) .options(joinedload(LibraryFolder.actions)) .order_by( ) return trans.sa_session.scalars(stmt).unique().all()