Source code for galaxy.tools.actions.upload_common

import logging
import os
import tempfile
from dataclasses import dataclass
from io import StringIO
from json import (
    dump,
    dumps,
)
from typing import (
    Dict,
    List,
    Optional,
)

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 (
    stream_to_file,
    validate_non_local,
)
from galaxy.managers.context import ProvidesUserContext
from galaxy.model import (
    FormDefinition,
    LibraryDataset,
    LibraryFolder,
    Role,
)
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 f.file.name != "<fdopen>"
                local_filename = util.mkstemp_ln(f.file.name, "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"], trans.app.config.fetch_url_allowlist_ips)),
                    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)
        if template and template.fields:
            for field in template.fields:
                field_name = field["name"]  # type:ignore[index]
                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 = trans.app.model.HistoryDatasetAssociation(
        name=uploaded_dataset.name,
        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 = trans.app.security_agent.history_get_default_permissions(history)
    trans.app.security_agent.set_all_dataset_permissions(hda.dataset, 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 trans.app.security_agent.can_add_library_item(current_user_roles, 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 x.name == name]
            if matches:
                folder = matches[0]
            else:
                new_folder = LibraryFolder(name=name, description="Automatically created by upload tool")
                new_folder.genome_build = trans.app.genome_builds.default_value
                folder.add_folder(new_folder)
                trans.sa_session.add(new_folder)
                with transaction(trans.sa_session):
                    trans.sa_session.commit()
                trans.app.security_agent.copy_library_permissions(trans, folder, new_folder)
                folder = new_folder
    if library_bunch.replace_dataset:
        ld = library_bunch.replace_dataset
    else:
        ld = trans.app.model.LibraryDataset(folder=folder, name=uploaded_dataset.name)
        trans.sa_session.add(ld)
        with transaction(trans.sa_session):
            trans.sa_session.commit()
        trans.app.security_agent.copy_library_permissions(trans, folder, ld)
    ldda = trans.app.model.LibraryDatasetDatasetAssociation(
        name=uploaded_dataset.name,
        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(uploaded_dataset.name))[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):
        new_tags = tag_handler.parse_tags_list(tags_list)
        for tag in new_tags:
            tag_handler.apply_item_tag(item=ldda, user=trans.user, name=tag[0], value=tag[1], 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
    trans.app.security_agent.copy_library_permissions(trans, ld, ldda)
    if library_bunch.replace_dataset:
        # Copy the Dataset level permissions from replace_dataset to the new LibraryDatasetDatasetAssociation.dataset
        trans.app.security_agent.copy_dataset_permissions(
            library_bunch.replace_dataset.library_dataset_dataset_association.dataset, ldda.dataset
        )
    else:
        # Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset
        trans.app.security_agent.set_all_dataset_permissions(
            ldda.dataset, trans.app.security_agent.user_get_default_permissions(trans.user), 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 = ldda.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 = trans.app.model.FormValues(library_bunch.template, 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 = trans.app.model.LibraryDatasetDatasetInfoAssociation(
            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 = trans.app.model.DatasetPermissions(
                trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, 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)
        tags_raw = getattr(uploaded_dataset, "tags", None)
        if tags_raw:
            new_tags = tag_handler.parse_tags_list(tags_raw.split(","))
            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=True
                )
    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)
        uploaded_dataset.data = 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 = uploaded_dataset.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,
                dataset_id=data.dataset.id,
                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,
                name=uploaded_dataset.name,
                dataset_id=data.dataset.id,
                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,
                run_as_real_user=trans.app.config.external_chown_script is not None,
                check_content=trans.app.config.check_upload_content,
                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 trans.app.config.external_chown_script
                and not is_url(uploaded_dataset.path)
            ):
                external_chown(
                    uploaded_dataset.path,
                    trans.user.system_user_pwent(trans.app.config.real_system_username),
                    trans.app.config.external_chown_script,
                    description="uploaded file",
                )
        tool_params.append(params)
    with tempfile.NamedTemporaryFile(mode="w", prefix="upload_params_", delete=False) as fh:
        json_file_path = fh.name
        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.app.model.Job()
    trans.sa_session.add(job)
    job.galaxy_version = trans.app.config.version_major
    galaxy_session = trans.get_galaxy_session()
    if isinstance(galaxy_session, trans.model.GalaxySession):
        job.session_id = galaxy_session.id
    if trans.user is not None:
        job.user_id = trans.user.id
    if folder:
        job.library_folder_id = folder.id
    else:
        if not history:
            history = trans.history
        job.history_id = history.id
    job.tool_id = tool.id
    job.tool_version = tool.version
    job.dynamic_tool = tool.dynamic_tool

    for name, value in tool.params_to_strings(params, trans.app).items():
        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(LibraryFolder.name)
    )
    return trans.sa_session.scalars(stmt).unique().all()