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https://github.com/galaxyproject/galaxy.git
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520 lines
25 KiB
Python
520 lines
25 KiB
Python
import logging
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import tool_shed.grids.admin_grids as admin_grids
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from galaxy import (
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util,
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web,
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)
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from galaxy.model.base import transaction
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from galaxy.util import inflector
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from galaxy.web.legacy_framework import grids
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from galaxy.webapps.base.controller import BaseUIController
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from tool_shed.metadata import repository_metadata_manager
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from tool_shed.util import (
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metadata_util,
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repository_util,
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shed_util_common as suc,
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)
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from tool_shed.util.admin_util import Admin
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from tool_shed.util.web_util import escape
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log = logging.getLogger(__name__)
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class AdminController(BaseUIController, Admin):
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user_list_grid = admin_grids.UserGrid()
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role_list_grid = admin_grids.RoleGrid()
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group_list_grid = admin_grids.GroupGrid()
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manage_category_grid = admin_grids.ManageCategoryGrid()
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repository_grid = admin_grids.AdminRepositoryGrid()
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repository_metadata_grid = admin_grids.RepositoryMetadataGrid()
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delete_operation = grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True)
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undelete_operation = grids.GridOperation(
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"Undelete", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True
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)
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purge_operation = grids.GridOperation(
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"Purge", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True
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)
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@web.expose
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@web.require_admin
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def browse_repositories(self, trans, **kwd):
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# We add parameters to the keyword dict in this method in order to rename the param
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# with an "f-" prefix, simulating filtering by clicking a search link. We have
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# to take this approach because the "-" character is illegal in HTTP requests.
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if "operation" in kwd:
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operation = kwd["operation"].lower()
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if operation == "view_or_manage_repository":
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return trans.response.send_redirect(
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web.url_for(controller="repository", action="browse_repositories", **kwd)
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)
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elif operation == "edit_repository":
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return trans.response.send_redirect(
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web.url_for(controller="repository", action="edit_repository", **kwd)
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)
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elif operation == "repositories_by_user":
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# Eliminate the current filters if any exist.
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for k in list(kwd.keys()):
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if k.startswith("f-"):
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del kwd[k]
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if "user_id" in kwd:
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user = suc.get_user(trans.app, kwd["user_id"])
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kwd["f-email"] = user.email
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del kwd["user_id"]
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else:
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# The received id is the repository id, so we need to get the id of the user
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# that uploaded the repository.
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repository_id = kwd.get("id", None)
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repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
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kwd["f-email"] = repository.user.email
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elif operation == "repositories_by_category":
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# Eliminate the current filters if any exist.
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for k in list(kwd.keys()):
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if k.startswith("f-"):
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del kwd[k]
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category_id = kwd.get("id", None)
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category = suc.get_category(trans.app, category_id)
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kwd["f-Category.name"] = category.name
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elif operation == "receive email alerts":
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if kwd["id"]:
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kwd["caller"] = "browse_repositories"
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return trans.response.send_redirect(
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web.url_for(controller="repository", action="set_email_alerts", **kwd)
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)
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else:
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del kwd["operation"]
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elif operation == "delete":
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return self.delete_repository(trans, **kwd)
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elif operation == "undelete":
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return self.undelete_repository(trans, **kwd)
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# The changeset_revision_select_field in the RepositoryGrid performs a refresh_on_change
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# which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One
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# of the many select fields on the grid performed the refresh_on_change, so we loop through
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# all of the received values to see which value is not the repository tip. If we find it, we
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# know the refresh_on_change occurred, and we have the necessary repository id and change set
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# revision to pass on.
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for k, v in kwd.items():
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changeset_revision_str = "changeset_revision_"
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if k.startswith(changeset_revision_str):
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repository_id = trans.security.encode_id(int(k.lstrip(changeset_revision_str)))
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repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
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if repository.tip() != v:
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return trans.response.send_redirect(
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web.url_for(
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controller="repository",
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action="browse_repositories",
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operation="view_or_manage_repository",
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id=trans.security.encode_id(repository.id),
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changeset_revision=v,
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)
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)
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# Render the list view
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return self.repository_grid(trans, **kwd)
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@web.expose
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@web.require_admin
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def browse_repository_metadata(self, trans, **kwd):
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if "operation" in kwd:
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operation = kwd["operation"].lower()
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if operation == "delete":
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return self.delete_repository_metadata(trans, **kwd)
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if operation == "view_or_manage_repository_revision":
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# The received id is a RepositoryMetadata object id, so we need to get the
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# associated Repository and redirect to view_or_manage_repository with the
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# changeset_revision.
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repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, kwd["id"])
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repository = repository_metadata.repository
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kwd["id"] = trans.security.encode_id(repository.id)
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kwd["changeset_revision"] = repository_metadata.changeset_revision
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kwd["operation"] = "view_or_manage_repository"
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return trans.response.send_redirect(
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web.url_for(controller="repository", action="browse_repositories", **kwd)
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)
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return self.repository_metadata_grid(trans, **kwd)
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@web.expose
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@web.require_admin
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def create_category(self, trans, **kwd):
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message = escape(kwd.get("message", ""))
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status = kwd.get("status", "done")
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name = kwd.get("name", "").strip()
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description = kwd.get("description", "").strip()
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if kwd.get("create_category_button", False):
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if not name or not description:
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message = "Enter a valid name and a description"
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status = "error"
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elif suc.get_category_by_name(trans.app, name):
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message = "A category with that name already exists"
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status = "error"
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else:
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# Create the category
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category = trans.app.model.Category(name=name, description=description)
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trans.sa_session.add(category)
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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# Update the Tool Shed's repository registry.
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trans.app.repository_registry.add_category_entry(category)
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message = f"Category '{escape(category.name)}' has been created"
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status = "done"
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trans.response.send_redirect(
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web.url_for(controller="admin", action="manage_categories", message=message, status=status)
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)
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return trans.fill_template(
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"/webapps/tool_shed/category/create_category.mako",
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name=name,
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description=description,
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message=message,
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status=status,
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)
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@web.expose
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@web.require_admin
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def delete_repository(self, trans, **kwd):
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message = escape(kwd.get("message", ""))
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status = kwd.get("status", "done")
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id = kwd.get("id", None)
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if id:
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# Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
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ids = util.listify(id)
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count = 0
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deleted_repositories = ""
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for repository_id in ids:
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repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
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if repository:
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if not repository.deleted:
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# Mark all installable repository_metadata records as not installable.
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for repository_metadata in repository.downloadable_revisions:
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repository_metadata.downloadable = False
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trans.sa_session.add(repository_metadata)
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# Mark the repository admin role as deleted.
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repository_admin_role = repository.admin_role
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if repository_admin_role is not None:
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repository_admin_role.deleted = True
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trans.sa_session.add(repository_admin_role)
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repository.deleted = True
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trans.sa_session.add(repository)
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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# Update the repository registry.
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trans.app.repository_registry.remove_entry(repository)
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count += 1
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deleted_repositories += f" {repository.name} "
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if count:
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message = "Deleted %d %s: %s" % (
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count,
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inflector.cond_plural(len(ids), "repository"),
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escape(deleted_repositories),
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)
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else:
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message = "All selected repositories were already marked deleted."
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else:
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message = "No repository ids received for deleting."
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status = "error"
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trans.response.send_redirect(
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web.url_for(
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controller="admin", action="browse_repositories", message=util.sanitize_text(message), status=status
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)
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)
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@web.expose
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@web.require_admin
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def delete_repository_metadata(self, trans, **kwd):
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message = escape(kwd.get("message", ""))
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status = kwd.get("status", "done")
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id = kwd.get("id", None)
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if id:
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ids = util.listify(id)
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count = 0
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for repository_metadata_id in ids:
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repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
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trans.sa_session.delete(repository_metadata)
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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count += 1
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if count:
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message = "Deleted %d repository metadata %s" % (count, inflector.cond_plural(len(ids), "record"))
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else:
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message = "No repository metadata ids received for deleting."
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status = "error"
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trans.response.send_redirect(
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web.url_for(
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controller="admin",
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action="browse_repository_metadata",
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message=util.sanitize_text(message),
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status=status,
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)
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)
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@web.expose
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@web.require_admin
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def edit_category(self, trans, **kwd):
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"""Handle requests to edit TS category name or description"""
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message = escape(kwd.get("message", ""))
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status = kwd.get("status", "done")
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id = kwd.get("id", None)
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if not id:
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message = "No category ids received for editing"
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trans.response.send_redirect(
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web.url_for(controller="admin", action="manage_categories", message=message, status="error")
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)
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category = suc.get_category(trans.app, id)
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original_category_name = str(category.name)
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original_category_description = str(category.description)
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if kwd.get("edit_category_button", False):
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flush_needed = False
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new_name = kwd.get("name", "").strip()
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new_description = kwd.get("description", "").strip()
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if original_category_name != new_name:
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if not new_name:
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message = "Enter a valid name"
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status = "error"
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elif original_category_name != new_name and suc.get_category_by_name(trans.app, new_name):
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message = "A category with that name already exists"
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status = "error"
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else:
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category.name = new_name
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flush_needed = True
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if original_category_description != new_description:
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category.description = new_description
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if not flush_needed:
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flush_needed = True
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if flush_needed:
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trans.sa_session.add(category)
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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if original_category_name != new_name:
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# Update the Tool Shed's repository registry.
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trans.app.repository_registry.edit_category_entry(original_category_name, new_name)
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message = f"The information has been saved for category '{escape(category.name)}'"
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status = "done"
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return trans.response.send_redirect(
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web.url_for(controller="admin", action="manage_categories", message=message, status=status)
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)
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return trans.fill_template(
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"/webapps/tool_shed/category/edit_category.mako", category=category, message=message, status=status
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)
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@web.expose
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@web.require_admin
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def manage_categories(self, trans, **kwd):
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if "f-free-text-search" in kwd:
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# Trick to enable searching repository name, description from the CategoryGrid.
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# What we've done is rendered the search box for the RepositoryGrid on the grid.mako
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# template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako.
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# Since we are searching repositories and not categories, redirect to browse_repositories().
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return trans.response.send_redirect(web.url_for(controller="admin", action="browse_repositories", **kwd))
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if "operation" in kwd:
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operation = kwd["operation"].lower()
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if operation == "create":
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return trans.response.send_redirect(web.url_for(controller="admin", action="create_category", **kwd))
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elif operation == "delete":
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return trans.response.send_redirect(
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web.url_for(controller="admin", action="mark_category_deleted", **kwd)
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)
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elif operation == "undelete":
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return trans.response.send_redirect(web.url_for(controller="admin", action="undelete_category", **kwd))
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elif operation == "purge":
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return trans.response.send_redirect(web.url_for(controller="admin", action="purge_category", **kwd))
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elif operation == "edit":
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return trans.response.send_redirect(web.url_for(controller="admin", action="edit_category", **kwd))
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return self.manage_category_grid(trans, **kwd)
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@web.expose
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@web.require_admin
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def regenerate_statistics(self, trans, **kwd):
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message = escape(kwd.get("message", ""))
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status = kwd.get("status", "done")
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if "regenerate_statistics_button" in kwd:
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trans.app.shed_counter.generate_statistics()
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message = "Successfully regenerated statistics"
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return trans.fill_template("/webapps/tool_shed/admin/statistics.mako", message=message, status=status)
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@web.expose
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@web.require_admin
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def manage_role_associations(self, trans, **kwd):
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"""Manage users, groups and repositories associated with a role."""
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role_id = kwd.get("id", None)
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role = repository_util.get_role_by_id(trans.app, role_id)
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# We currently only have a single role associated with a repository, the repository admin role.
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repository_role_association = role.repositories[0]
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repository = repository_role_association.repository
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associations_dict = repository_util.handle_role_associations(trans.app, role, repository, **kwd)
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in_users = associations_dict.get("in_users", [])
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out_users = associations_dict.get("out_users", [])
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in_groups = associations_dict.get("in_groups", [])
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out_groups = associations_dict.get("out_groups", [])
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message = associations_dict.get("message", "")
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status = associations_dict.get("status", "done")
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return trans.fill_template(
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"/webapps/tool_shed/role/role.mako",
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in_admin_controller=True,
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repository=repository,
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role=role,
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in_users=in_users,
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out_users=out_users,
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in_groups=in_groups,
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out_groups=out_groups,
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message=message,
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status=status,
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)
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@web.expose
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@web.require_admin
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def reset_metadata_on_selected_repositories_in_tool_shed(self, trans, **kwd):
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rmm = repository_metadata_manager.RepositoryMetadataManager(trans)
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if "reset_metadata_on_selected_repositories_button" in kwd:
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message, status = rmm.reset_metadata_on_selected_repositories(**kwd)
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else:
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message = escape(util.restore_text(kwd.get("message", "")))
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status = kwd.get("status", "done")
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repositories_select_field = rmm.build_repository_ids_select_field(
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name="repository_ids", multiple=True, display="checkboxes", my_writable=False
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)
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return trans.fill_template(
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"/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako",
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repositories_select_field=repositories_select_field,
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message=message,
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status=status,
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)
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@web.expose
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@web.require_admin
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def undelete_repository(self, trans, **kwd):
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message = escape(kwd.get("message", ""))
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id = kwd.get("id", None)
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if id:
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# Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
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ids = util.listify(id)
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count = 0
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undeleted_repositories = ""
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for repository_id in ids:
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repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
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if repository:
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if repository.deleted:
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# Inspect all repository_metadata records to determine those that are installable, and mark
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# them accordingly.
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for repository_metadata in repository.metadata_revisions:
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metadata = repository_metadata.metadata
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if metadata:
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if metadata_util.is_downloadable(metadata):
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repository_metadata.downloadable = True
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trans.sa_session.add(repository_metadata)
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# Mark the repository admin role as not deleted.
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repository_admin_role = repository.admin_role
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if repository_admin_role is not None:
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repository_admin_role.deleted = False
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trans.sa_session.add(repository_admin_role)
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repository.deleted = False
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trans.sa_session.add(repository)
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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if not repository.deprecated:
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# Update the repository registry.
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trans.app.repository_registry.add_entry(repository)
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count += 1
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undeleted_repositories += f" {repository.name}"
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if count:
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message = "Undeleted %d %s: %s" % (
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count,
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inflector.cond_plural(count, "repository"),
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undeleted_repositories,
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)
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else:
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message = "No selected repositories were marked deleted, so they could not be undeleted."
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else:
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message = "No repository ids received for undeleting."
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trans.response.send_redirect(
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web.url_for(
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controller="admin", action="browse_repositories", message=util.sanitize_text(message), status="done"
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)
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)
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@web.expose
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@web.require_admin
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def mark_category_deleted(self, trans, **kwd):
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# TODO: We should probably eliminate the Category.deleted column since it really makes no
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# sense to mark a category as deleted (category names and descriptions can be changed instead).
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# If we do this, and the following 2 methods can be eliminated.
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message = escape(kwd.get("message", ""))
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id = kwd.get("id", None)
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if id:
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ids = util.listify(id)
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message = "Deleted %d categories: " % len(ids)
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for category_id in ids:
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category = suc.get_category(trans.app, category_id)
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category.deleted = True
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trans.sa_session.add(category)
|
|
with transaction(trans.sa_session):
|
|
trans.sa_session.commit()
|
|
# Update the Tool Shed's repository registry.
|
|
trans.app.repository_registry.remove_category_entry(category)
|
|
message += f" {escape(category.name)} "
|
|
else:
|
|
message = "No category ids received for deleting."
|
|
trans.response.send_redirect(
|
|
web.url_for(
|
|
controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done"
|
|
)
|
|
)
|
|
|
|
@web.expose
|
|
@web.require_admin
|
|
def purge_category(self, trans, **kwd):
|
|
# This method should only be called for a Category that has previously been deleted.
|
|
# Purging a deleted Category deletes all of the following from the database:
|
|
# - RepoitoryCategoryAssociations where category_id == Category.id
|
|
message = escape(kwd.get("message", ""))
|
|
id = kwd.get("id", None)
|
|
if id:
|
|
ids = util.listify(id)
|
|
count = 0
|
|
purged_categories = ""
|
|
message = "Purged %d categories: " % len(ids)
|
|
for category_id in ids:
|
|
category = suc.get_category(trans.app, category_id)
|
|
if category.deleted:
|
|
# Delete RepositoryCategoryAssociations
|
|
for rca in category.repositories:
|
|
trans.sa_session.delete(rca)
|
|
with transaction(trans.sa_session):
|
|
trans.sa_session.commit()
|
|
purged_categories += f" {category.name} "
|
|
message = "Purged %d categories: %s" % (count, escape(purged_categories))
|
|
else:
|
|
message = "No category ids received for purging."
|
|
trans.response.send_redirect(
|
|
web.url_for(
|
|
controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done"
|
|
)
|
|
)
|
|
|
|
@web.expose
|
|
@web.require_admin
|
|
def undelete_category(self, trans, **kwd):
|
|
message = escape(kwd.get("message", ""))
|
|
id = kwd.get("id", None)
|
|
if id:
|
|
ids = util.listify(id)
|
|
count = 0
|
|
undeleted_categories = ""
|
|
for category_id in ids:
|
|
category = suc.get_category(trans.app, category_id)
|
|
if category.deleted:
|
|
category.deleted = False
|
|
trans.sa_session.add(category)
|
|
with transaction(trans.sa_session):
|
|
trans.sa_session.commit()
|
|
# Update the Tool Shed's repository registry.
|
|
trans.app.repository_registry.add_category_entry(category)
|
|
count += 1
|
|
undeleted_categories += f" {category.name}"
|
|
message = "Undeleted %d categories: %s" % (count, escape(undeleted_categories))
|
|
else:
|
|
message = "No category ids received for undeleting."
|
|
trans.response.send_redirect(
|
|
web.url_for(
|
|
controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done"
|
|
)
|
|
)
|