Unverified Commit 0f033804 authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_22.01' into release_22.05

parents c2aa3b73 5785342a

lib/galaxy/datatypes/binary.py

+4 −2
Original line number Diff line number Diff line
@@ -531,6 +531,8 @@ class BamNative(CompressedArchive, _BamOrSam): 
        file_paths = []

        rel_paths.append(f"{name or dataset.file_name}.{dataset.extension}")

        file_paths.append(dataset.file_name)

        # We may or may not have a bam index file (BamNative doesn't have it, but also index generation may have failed)

        if dataset.metadata.bam_index:

            rel_paths.append(f"{name or dataset.file_name}.{dataset.extension}.bai")

            file_paths.append(dataset.metadata.bam_index.file_name)

        return zip(file_paths, rel_paths)

lib/galaxy/webapps/base/webapp.py

+3 −7
Original line number Diff line number Diff line
@@ -14,10 +14,7 @@ from typing import ( 
    Any,

    Dict,

)

from urllib.parse import (

    urljoin,

    urlparse,

)

from urllib.parse import urlparse



import mako.lookup

import mako.runtime
@@ -466,7 +463,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo 
                if name not in self.request.cookies and TOOL_RUNNER_SESSION_COOKIE in self.request.cookies:

                    # TOOL_RUNNER_SESSION_COOKIE value is the encoded galaxysession cookie.

                    # We decode it here and pretend it's the galaxysession

                    tool_runner_path = urljoin(self.app.config.galaxy_url_prefix, "tool_runner")

                    tool_runner_path = url_for(controller="tool_runner")

                    if self.request.path.startswith(tool_runner_path):

                        return self.security.decode_guid(self.request.cookies[TOOL_RUNNER_SESSION_COOKIE].value)

                return self.request.cookies[name].value
@@ -482,13 +479,12 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo 
            self._set_cookie(

                value,

                name=TOOL_RUNNER_SESSION_COOKIE,

                path=urljoin(path, "tool_runner"),

                path=url_for(controller="tool_runner"),

                age=age,

                version=version,

                encode_value=True,

            )

            tool_runner_cookie = self.response.cookies[TOOL_RUNNER_SESSION_COOKIE]

            tool_runner_cookie["path"] = urljoin(path, "tool_runner")

            tool_runner_cookie["SameSite"] = "None"

            tool_runner_cookie["secure"] = True

lib/galaxy/webapps/galaxy/controllers/dataset.py

+7 −32
Original line number Diff line number Diff line
@@ -863,14 +863,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
        id = None

        try:

            id = self.decode_id(dataset_id)

            hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)

            assert hda, f"Invalid HDA: {id}"

            # Walk up parent datasets to find the containing history

            topmost_parent = hda

            while topmost_parent.parent:

                topmost_parent = topmost_parent.parent

            assert topmost_parent in trans.history.datasets, "Data does not belong to current history"

            # Mark deleted and cleanup

            hda = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)

            hda.mark_deleted()

            hda.clear_associated_files()

            trans.log_event(f"Dataset id {str(id)} marked as deleted")
@@ -889,17 +882,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
        id = None

        try:

            id = self.decode_id(dataset_id)

            history = trans.get_history()

            hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)

            assert hda and hda.undeletable, f"Invalid HDA: {id}"

            # Walk up parent datasets to find the containing history

            topmost_parent = hda

            while topmost_parent.parent:

                topmost_parent = topmost_parent.parent

            assert topmost_parent in history.datasets, "Data does not belong to current history"

            # Mark undeleted

            hda.mark_undeleted()

            trans.sa_session.flush()

            item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)

            self.hda_manager.undelete(item)

            trans.log_event(f"Dataset id {str(id)} has been undeleted")

        except Exception:

            msg = f"HDA undeletion failed (encoded: {dataset_id}, decoded: {id})"
@@ -912,21 +896,12 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
    def _unhide(self, trans, dataset_id):

        try:

            id = self.decode_id(dataset_id)

        except Exception:

            return False

        history = trans.get_history()

        hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)

        if hda:

            # Walk up parent datasets to find the containing history

            topmost_parent = hda

            while topmost_parent.parent:

                topmost_parent = topmost_parent.parent

            assert topmost_parent in history.datasets, "Data does not belong to current history"

            # Mark undeleted

            hda.mark_unhidden()

            item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)

            item.mark_unhidden()

            trans.sa_session.flush()

            trans.log_event(f"Dataset id {str(id)} has been unhidden")

            return True

        except Exception:

            return False



    def _purge(self, trans, dataset_id):