Source code for galaxy.webapps.galaxy.controllers.data_manager

import logging
from json import loads

import paste.httpexceptions

from galaxy import web
from galaxy.util import (
    nice_size,
    unicodify,
)
from galaxy.webapps.base.controller import BaseUIController

log = logging.getLogger(__name__)


[docs]class DataManager(BaseUIController):
[docs]    @web.expose
    @web.json
    def data_managers_list(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized(
                "This Galaxy instance is not configured to allow non-admins to view the data manager."
            )
        message = kwd.get("message", "")
        status = kwd.get("status", "info")
        data_managers = []
        for data_manager_id, data_manager in sorted(
            trans.app.data_managers.data_managers.items(), key=lambda dm: dm[1].name
        ):
            data_managers.append(
                {
                    "toolUrl": web.url_for(controller="root", tool_id=data_manager.tool.id),
                    "id": data_manager_id,
                    "name": data_manager.name,
                    "description": data_manager.description.lower(),
                }
            )
        data_tables = []
        managed_table_names = trans.app.data_managers.managed_data_tables.keys()
        for table_name in sorted(trans.app.tool_data_tables.get_tables().keys()):
            data_tables.append({"name": table_name, "managed": True if table_name in managed_table_names else False})

        return {
            "dataManagers": data_managers,
            "dataTables": data_tables,
            "viewOnly": not_is_admin,
            "message": message,
            "status": status,
        }

[docs]    @web.expose
    @web.json
    def jobs_list(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized(
                "This Galaxy instance is not configured to allow non-admins to view the data manager."
            )
        message = kwd.get("message", "")
        status = kwd.get("status", "info")
        data_manager_id = kwd.get("id", None)
        data_manager = trans.app.data_managers.get_manager(data_manager_id)
        if data_manager is None:
            return {"message": f"Invalid Data Manager ({data_manager_id}) was requested", "status": "error"}
        jobs = []
        for assoc in trans.sa_session.query(trans.app.model.DataManagerJobAssociation).filter_by(
            data_manager_id=data_manager_id
        ):
            j = assoc.job
            jobs.append(
                {
                    "id": j.id,
                    "encId": trans.security.encode_id(j.id),
                    "runUrl": web.url_for(
                        controller="tool_runner", action="rerun", job_id=trans.security.encode_id(j.id)
                    ),
                    "user": j.history.user.email if j.history and j.history.user else "anonymous",
                    "updateTime": j.update_time.isoformat(),
                    "state": j.state,
                    "commandLine": j.command_line,
                    "jobRunnerName": j.job_runner_name,
                    "jobRunnerExternalId": j.job_runner_external_id,
                }
            )
        jobs.reverse()
        return {
            "dataManager": {
                "name": data_manager.name,
                "description": data_manager.description.lower(),
                "toolUrl": web.url_for(controller="root", tool_id=data_manager.tool.id),
            },
            "jobs": jobs,
            "viewOnly": not_is_admin,
            "message": message,
            "status": status,
        }

[docs]    @web.expose
    @web.json
    def job_info(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized(
                "This Galaxy instance is not configured to allow non-admins to view the data manager."
            )
        message = kwd.get("message", "")
        status = kwd.get("status", "info")
        job_id = kwd.get("id", None)
        try:
            job_id = trans.security.decode_id(job_id)
            job = trans.sa_session.query(trans.app.model.Job).get(job_id)
        except Exception as e:
            job = None
            log.error(f"Bad job id ({job_id}) passed to job_info: {e}")
        if not job:
            return {"message": f"Invalid job ({job_id}) was requested", "status": "error"}
        data_manager_id = job.data_manager_association.data_manager_id
        data_manager = trans.app.data_managers.get_manager(data_manager_id)
        hdas = [assoc.dataset for assoc in job.get_output_datasets()]
        hda_info = []
        data_manager_output = []
        error_messages = []
        for hda in hdas:
            hda_info.append(
                {
                    "id": hda.id,
                    "encId": trans.security.encode_id(hda.id),
                    "name": hda.name,
                    "created": unicodify(hda.create_time.strftime(trans.app.config.pretty_datetime_format)),
                    "fileSize": nice_size(hda.dataset.file_size),
                    "fileName": hda.file_name,
                    "infoUrl": web.url_for(
                        controller="dataset", action="show_params", dataset_id=trans.security.encode_id(hda.id)
                    ),
                }
            )
            try:
                data_manager_json = loads(open(hda.get_file_name()).read())
            except Exception as e:
                data_manager_json = {}
                error_messages.append(f"Unable to obtain data_table info for hda ({hda.id}): {e}")
            values = []
            for key, value in data_manager_json.get("data_tables", {}).items():
                values.append((key, value))
            data_manager_output.append(values)
        return {
            "jobId": job_id,
            "exitCode": job.exit_code,
            "runUrl": web.url_for(controller="tool_runner", action="rerun", job_id=trans.security.encode_id(job.id)),
            "commandLine": job.command_line,
            "dataManager": {
                "id": data_manager_id,
                "name": data_manager.name,
                "description": data_manager.description.lower(),
                "toolUrl": web.url_for(controller="root", tool_id=data_manager.tool.id),
            },
            "hdaInfo": hda_info,
            "dataManagerOutput": data_manager_output,
            "errorMessages": error_messages,
            "viewOnly": not_is_admin,
            "message": message,
            "status": status,
        }

[docs]    @web.expose
    @web.json
    def tool_data_table_info(self, trans, **kwd):
        return self.tool_data_table_info_1(trans, **kwd)

[docs]    def tool_data_table_info_1(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized(
                "This Galaxy instance is not configured to allow non-admins to view the data manager."
            )
        message = kwd.get("message", "")
        status = kwd.get("status", "info")
        data_table_name = kwd.get("table_name", None)
        if not data_table_name:
            return {"message": "No data table was requested.", "status": "error"}
        data_table = trans.app.tool_data_tables.get(data_table_name, None)
        if data_table is None:
            return {"message": f"Invalid data table '{data_table_name}' was requested.", "status": "error"}
        return {
            "dataTable": {
                "name": data_table.name,
                "columns": data_table.get_column_name_list(),
                "data": data_table.data,
            },
            "viewOnly": not_is_admin,
            "message": message,
            "status": status,
        }

[docs]    @web.expose
    @web.json
    @web.require_admin
    def reload_tool_data_tables(self, trans, table_name=None, **kwd):
        if table_name and isinstance(table_name, str):
            table_name = table_name.split(",")
        # Reload the tool data tables
        table_names = self.app.tool_data_tables.reload_tables(table_names=table_name)
        trans.app.queue_worker.send_control_task(
            "reload_tool_data_tables", noop_self=True, kwargs={"table_name": table_name}
        )
        data = None
        if table_names:
            message = "Reloaded data table{} '{}'.".format("s"[len(table_names) == 1 :], ", ".join(table_names))
            data = self.tool_data_table_info_1(trans, table_name=table_names[0], message=message, status="done")
        else:
            data = {"message": "No data tables have been reloaded.", "status": "error"}
        return data

[docs]    @web.expose
    @web.json
    @web.require_admin
    def tool_data_table_items(self, trans, **kwd):
        data = {"columns": [], "items": []}
        message = kwd.get("message", "")
        status = kwd.get("status", "info")
        table_name = kwd.get("table_name", None)

        if not table_name:
            return {
                "data": data,
                "message": "No Data table name provided.",
                "status": "warning",
            }

        data_table = trans.app.tool_data_tables.get(table_name, None)

        if data_table is None:
            return {"data": data, "message": f"Invalid Data table ({table_name}) was requested", "status": "error"}

        columns = data_table.get_column_name_list()
        rows = [dict(zip(columns, table_row)) for table_row in data_table.data]
        data["columns"] = columns
        data["items"] = rows

        return {"data": data, "message": message, "status": status}

[docs]    @web.expose
    @web.json
    @web.require_admin
    def reload_tool_data_table(self, trans, **kwd):
        table_name = kwd.get("table_name", None)

        if not table_name:
            return {
                "message": "No data table has been reloaded.",
                "status": "error",
            }

        redirect_url = web.url_for(
            controller="data_manager",
            action="tool_data_table_items",
            table_name=table_name,
            message=f'The data table "{table_name}" has been reloaded.',
            status="done",
        )

        return trans.response.send_redirect(redirect_url)