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Drop old repositories, group repo functions in one module
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,164 @@ | ||
| from typing import Any | ||
| from typing import Optional | ||
|
|
||
| from sqlalchemy import select | ||
| from sqlalchemy import ( | ||
| cast, | ||
| false, | ||
| func, | ||
| Integer, | ||
| null, | ||
| or_, | ||
| select, | ||
| true, | ||
| update, | ||
| ) | ||
| from sqlalchemy.orm import Session | ||
|
|
||
| from galaxy.model import Base | ||
| from galaxy.model import ( | ||
| APIKeys, | ||
| Group, | ||
| GroupRoleAssociation, | ||
| HistoryDatasetAssociation, | ||
| Job, | ||
| PageRevision, | ||
| Quota, | ||
| StoredWorkflowUserShareAssociation, | ||
| User, | ||
| UserGroupAssociation, | ||
| YIELD_PER_ROWS, | ||
| ) | ||
| from galaxy.model.tool_shed_install import ToolShedRepository | ||
|
|
||
| MappedType = Base | ||
|
|
||
| # all models | ||
| def get_all(session: Session, model_class): | ||
| return session.scalars(select(model_class)).all() | ||
|
|
||
| class ModelRepository: | ||
| def __init__(self, session: Session, model_class: MappedType): | ||
| self.session = session | ||
| self.model_class = model_class | ||
|
|
||
| def get_all(self): | ||
| return self.session.scalars(select(self.model_class)).all() | ||
| # api_keys | ||
| def get_api_key(session: Session, user_id: int): | ||
| stmt = select(APIKeys).filter_by(user_id=user_id, deleted=False).order_by(APIKeys.create_time.desc()).limit(1) | ||
| return session.scalars(stmt).first() | ||
|
|
||
|
|
||
| def mark_all_api_keys_as_deleted(session: Session, user_id: int): | ||
| stmt = ( | ||
| update(APIKeys) | ||
| .where(APIKeys.user_id == user_id) | ||
| .where(APIKeys.deleted == false()) | ||
| .values(deleted=True) | ||
| .execution_options(synchronize_session="evaluate") | ||
| ) | ||
| return session.execute(stmt) | ||
|
|
||
|
|
||
| # groups | ||
| def get_group_by_name(session: Session, name: str): | ||
| stmt = select(Group).filter(Group.name == name).limit(1) | ||
| return session.scalars(stmt).first() | ||
|
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||
|
|
||
| def get_not_deleted_groups(session: Session): | ||
| stmt = select(Group).where(Group.deleted == false()) | ||
| return session.scalars(stmt) | ||
|
|
||
|
|
||
| # hdas | ||
| def get_fasta_hdas_by_history(session: Session, history_id: int): | ||
| stmt = ( | ||
| select(HistoryDatasetAssociation) | ||
| .filter_by(history_id=history_id, extension="fasta", deleted=False) | ||
| .order_by(HistoryDatasetAssociation.hid.desc()) | ||
| ) | ||
| return session.scalars(stmt).all() | ||
|
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||
|
|
||
| def get_len_files_by_history(session: Session, history_id: int): | ||
| stmt = select(HistoryDatasetAssociation).filter_by(history_id=history_id, extension="len", deleted=False) | ||
| return session.scalars(stmt) | ||
|
|
||
|
|
||
| # jobs | ||
| def get_jobs_to_check_at_startup(session: Session, track_jobs_in_database: bool, config): | ||
| if track_jobs_in_database: | ||
| in_list = (Job.states.QUEUED, Job.states.RUNNING, Job.states.STOPPED) | ||
| else: | ||
| in_list = (Job.states.NEW, Job.states.QUEUED, Job.states.RUNNING) | ||
|
|
||
| stmt = ( | ||
| select(Job) | ||
| .execution_options(yield_per=YIELD_PER_ROWS) | ||
| .filter(Job.state.in_(in_list) & (Job.handler == config.server_name)) | ||
| ) | ||
| if config.user_activation_on: | ||
| # Filter out the jobs of inactive users. | ||
| stmt = stmt.outerjoin(User).filter(or_((Job.user_id == null()), (User.active == true()))) | ||
|
|
||
| return session.scalars(stmt) | ||
|
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||
|
|
||
| # page_revisions | ||
| def get_page_revision(session: Session, page_id: int): | ||
| stmt = select(PageRevision).filter_by(page_id=page_id) | ||
| return session.scalars(stmt) | ||
|
|
||
|
|
||
| # quotas | ||
| def get_quotas(session: Session, deleted: bool = False): | ||
| is_deleted = true() | ||
| if not deleted: | ||
| is_deleted = false() | ||
| stmt = select(Quota).where(Quota.deleted == is_deleted) | ||
| return session.scalars(stmt) | ||
|
|
||
|
|
||
| # roles | ||
| def get_group_role(session: Session, group, role) -> Optional[GroupRoleAssociation]: | ||
| stmt = ( | ||
| select(GroupRoleAssociation).where(GroupRoleAssociation.group == group).where(GroupRoleAssociation.role == role) | ||
| ) | ||
| return session.execute(stmt).scalar_one_or_none() | ||
|
|
||
|
|
||
| # tool_shed_repositories | ||
| def get_tool_shed_repositories(session: Session, **kwd): | ||
| stmt = select(ToolShedRepository) | ||
| for key, value in kwd.items(): | ||
| if value is not None: | ||
| column = ToolShedRepository.table.c[key] | ||
| stmt = stmt.filter(column == value) | ||
| stmt = stmt.order_by(ToolShedRepository.name).order_by(cast(ToolShedRepository.ctx_rev, Integer).desc()) | ||
| return session.scalars(stmt).all() | ||
|
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||
|
|
||
| # users | ||
| def get_group_user(session: Session, user, group) -> Optional[UserGroupAssociation]: | ||
| stmt = ( | ||
| select(UserGroupAssociation).where(UserGroupAssociation.user == user).where(UserGroupAssociation.group == group) | ||
| ) | ||
| return session.execute(stmt).scalar_one_or_none() | ||
|
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||
|
|
||
| def get_users_by_ids(session: Session, user_ids): | ||
| stmt = select(User).where(User.id.in_(user_ids)) | ||
| return session.scalars(stmt).all() | ||
|
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||
|
|
||
| # The get_user_by_email and get_user_by_username functions may be called from | ||
| # the tool_shed app, which has its own User model, which is different from | ||
| # galaxy.model.User. In that case, the tool_shed user model should be passed as | ||
| # the model_class argument. | ||
| def get_user_by_email(session, email: str, model_class=User): | ||
| stmt = select(model_class).filter(model_class.email == email).limit(1) | ||
| return session.scalars(stmt).first() | ||
|
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||
|
|
||
| def get_user_by_username(session, username: str, model_class=User): | ||
| stmt = select(model_class).filter(model_class.username == username).limit(1) | ||
| return session.scalars(stmt).first() | ||
|
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||
|
|
||
| # workflows | ||
| def count_stored_workflow_user_assocs(session: Session, user, stored_workflow) -> int: | ||
| stmt = select(StoredWorkflowUserShareAssociation).filter_by(user=user, stored_workflow=stored_workflow) | ||
| stmt = select(func.count()).select_from(stmt) | ||
| return session.scalar(stmt) |
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