From 7d895edf28e28c070f4b80ca48d9e48bbcacfbdc Mon Sep 17 00:00:00 2001
From: Alexander Schlemmer <alexander@mail-schlemmer.de>
Date: Mon, 2 May 2022 12:14:44 +0200
Subject: [PATCH] TST: created pytest file
---
integrationtests/.pycaosdb.ini | 13 +++
integrationtests/test-profile/profile.yml | 5 +-
.../test_use_case_cardiac_simulations.py | 89 +++++++++++++++++++
.../use_case_cardiac_simulation/crawl_data.sh | 2 +-
.../insert_data_model.py | 4 -
5 files changed, 105 insertions(+), 8 deletions(-)
create mode 100644 integrationtests/.pycaosdb.ini
create mode 100644 integrationtests/test_use_case_cardiac_simulations.py
diff --git a/integrationtests/.pycaosdb.ini b/integrationtests/.pycaosdb.ini
new file mode 100644
index 00000000..4958eb59
--- /dev/null
+++ b/integrationtests/.pycaosdb.ini
@@ -0,0 +1,13 @@
+[Connection]
+ssl_insecure=false
+url=https://localhost:10443/
+password=caosdb
+username=admin
+password_method=plain
+cacert=/home/salexan/Projekte/2022/220309_DPGErlangenHackathon/live/live-profile/custom/other/cert/caosdb.cert.pem
+
+timeout=10000
+debug=0
+
+[Container]
+debug=0
diff --git a/integrationtests/test-profile/profile.yml b/integrationtests/test-profile/profile.yml
index 4cbbe28c..cafe041c 100644
--- a/integrationtests/test-profile/profile.yml
+++ b/integrationtests/test-profile/profile.yml
@@ -21,9 +21,8 @@ default:
# extroot: From where files are copied/symlinked. This is a
# list of `NAME: PATH` pairs or a single path.
extroot:
- "": "paths/extroot"
- #
- # "base": "/path/to/base/dir"
+ # "": "paths/extroot"
+ "base": "../use_case_cardiac_simulation/extroot"
# "other": "/path/to/other"
#
# dropoffbox: (Soon to be deprecated.) Files can be written here, but note that you may need to
diff --git a/integrationtests/test_use_case_cardiac_simulations.py b/integrationtests/test_use_case_cardiac_simulations.py
new file mode 100644
index 00000000..a15b06c1
--- /dev/null
+++ b/integrationtests/test_use_case_cardiac_simulations.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
+# 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+# 2021 Alexander Schlemmer
+#
+# 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/>.
+#
+# ** end header
+#
+
+"""
+module description
+"""
+
+from caosdb import EmptyUniqueQueryError
+import argparse
+import sys
+from argparse import RawTextHelpFormatter
+from newcrawler import Crawler
+import caosdb as db
+from newcrawler.identifiable_adapters import CaosDBIdentifiableAdapter
+import pytest
+from caosadvancedtools.models.parser import parse_model_from_yaml
+from caosadvancedtools.models import parser as parser
+import yaml
+
+from caosadvancedtools.loadFiles import loadpath
+
+from subprocess import run
+
+from caosadvancedtools.testutils import clear_database, set_test_key
+set_test_key("10b128cf8a1372f30aa3697466bb55e76974e0c16a599bb44ace88f19c8f61e2")
+
+import os
+
+def rfp(*pathcomponents):
+ """
+ Return full path.
+ Shorthand convenience function.
+ """
+ return os.path.join(os.path.dirname(__file__), *pathcomponents)
+
+
+def test_complete_crawler(clear_database):
+ # Setup the data model:
+ model = parser.parse_model_from_yaml("use_case_cardiac_simulation/model.yml")
+ model.sync_data_model(noquestion=True, verbose=False)
+
+ # Insert the data:
+ for path in [
+ "/opt/caosdb/mnt/extroot/base/SimulationData",
+ "/opt/caosdb/mnt/extroot/base/DataAnalysis"]:
+ loadpath(
+ path=path,
+ include=None,
+ exclude=None,
+ prefix="/",
+ dryrun=False,
+ forceAllowSymlinks=False)
+
+ # Run the crawler:
+ run([
+ "crawler2.0",
+ "--debug",
+ '--load-identifiables=identifiables.yml',
+ "-s",
+ "--provenance=provenance.yml",
+ "simulation_cfood_baltasar.yml",
+ "extroot/"], cwd="use_case_cardiac_simulation",
+ check=True)
+
+ res = db.execute_query("FIND Record MonodomainTissueSimulationRun")
+ assert len(res) > 0
diff --git a/integrationtests/use_case_cardiac_simulation/crawl_data.sh b/integrationtests/use_case_cardiac_simulation/crawl_data.sh
index 01e28a09..af2e8f92 100755
--- a/integrationtests/use_case_cardiac_simulation/crawl_data.sh
+++ b/integrationtests/use_case_cardiac_simulation/crawl_data.sh
@@ -2,4 +2,4 @@
# Run the crawler2.0 to test the data structure
# A. Schlemmer, 03/2022
-crawler2.0 --debug --load-identifiables="identifiables.yml" -s --provenance=provenance.yml simulation_cfood_baltasar.yml ../../extroot/
+crawler2.0 --debug --load-identifiables="identifiables.yml" -s --provenance=provenance.yml simulation_cfood_baltasar.yml extroot/
diff --git a/integrationtests/use_case_cardiac_simulation/insert_data_model.py b/integrationtests/use_case_cardiac_simulation/insert_data_model.py
index 13382999..e3302073 100755
--- a/integrationtests/use_case_cardiac_simulation/insert_data_model.py
+++ b/integrationtests/use_case_cardiac_simulation/insert_data_model.py
@@ -2,7 +2,3 @@
# Insert the data model using the yaml interface
# A. Schlemmer, 02/2022
-from caosadvancedtools.models import parser as parser
-
-model = parser.parse_model_from_yaml("model.yml")
-model.sync_data_model()
--
GitLab