From 78198c1152fe3897d4a6736699add7d35835801d Mon Sep 17 00:00:00 2001
From: Alexander Schlemmer <alexander@mail-schlemmer.de>
Date: Thu, 28 Oct 2021 15:12:24 +0200
Subject: [PATCH] WIP: created draft for generic analysis method
---
.../serverside/generic_analysis.py | 58 +++++++++++++++++++
src/caosadvancedtools/serverside/model.yml | 15 +++++
src/caosadvancedtools/serverside/sync.py | 7 +++
3 files changed, 80 insertions(+)
create mode 100644 src/caosadvancedtools/serverside/generic_analysis.py
create mode 100644 src/caosadvancedtools/serverside/model.yml
create mode 100755 src/caosadvancedtools/serverside/sync.py
diff --git a/src/caosadvancedtools/serverside/generic_analysis.py b/src/caosadvancedtools/serverside/generic_analysis.py
new file mode 100644
index 00000000..8b02326e
--- /dev/null
+++ b/src/caosadvancedtools/serverside/generic_analysis.py
@@ -0,0 +1,58 @@
+# 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)
diff --git a/src/caosadvancedtools/serverside/model.yml b/src/caosadvancedtools/serverside/model.yml
new file mode 100644
index 00000000..2f5a9634
--- /dev/null
+++ b/src/caosadvancedtools/serverside/model.yml
@@ -0,0 +1,15 @@
+# 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
diff --git a/src/caosadvancedtools/serverside/sync.py b/src/caosadvancedtools/serverside/sync.py
new file mode 100755
index 00000000..04283a15
--- /dev/null
+++ b/src/caosadvancedtools/serverside/sync.py
@@ -0,0 +1,7 @@
+#!/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()
--
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