WIP: created draft for generic analysis method

src/caosadvancedtools/serverside/generic_analysis.py

+# encoding: utf-8
+#
+# Copyright (C) 2021 Alexander Schlemmer <alexander.schlemmer@ds.mpg.de>
+# Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+#
+# See: https://gitlab.indiscale.com/caosdb/src/caosdb-advanced-user-tools/-/issues/55
+
+# This source file is work in progress and currently untested.
+
+import importlib
+import argparse
+import caosdb as db
+
+def _parse_arguments():
+    """Parses the command line arguments.
+    """
+    parser = argparse.ArgumentParser(description='__doc__')
+    parser.add_argument("--entity", help="An id an input dataset.")
+    parser.add_argument("--entity", help="An id of a parameter record.")
+    parser.add_argument(
+        '-a', '--auth-token', required=False,
+        help="An authentication token (not needed, only for compatibility).")
+
+    return parser.parse_args()
+
+
+def run(plugin: str):
+    """
+    Generically run a data analysis script.
+    This script should be installed as a pip package.
+    It should be located in package plugin and implement at least
+    a main function that takes a DataAnalysisRecord as a single argument.
+    """
+    m = importlib.import_module(plugin)
+    args = _parse_arguments()
+    input_dataset = db.Record(id=args.entity)
+    parameters = db.Record(id=args.parameter)
+
+    dataAnalysisRecord = db.Record()
+    dataAnalysisRecord.add_property(input_dataset)
+    dataAnalysisRecord.add_property(parameters)
+
+    m.main(dataAnalysisRecord) 

src/caosadvancedtools/serverside/model.yml

+# Parent of all datasets which are used as input to or output from
+# analysis scripts
+Dataset:
+
+# Parent of all parametersets which are used as input for analysis scripts
+ParameterSet:
+
+DataAnalysis:
+  recommended_properties:
+    InputDataset:
+      datatype: Dataset
+    OutputDataset:
+      datatype: Dataset
+    ParameterSet:
+    date:
\ No newline at end of file

src/caosadvancedtools/serverside/sync.py

+#!/usr/bin/env python3
+# Sync data model for generic data analysis method
+# A. Schlemmer, 09/2021
+
+from caosadvancedtools.models import parser
+model = parser.parse_model_from_yaml("model.yml")
+model.sync_data_model()