From 86c33475de2845a7672950bdeb87b58587695e49 Mon Sep 17 00:00:00 2001
From: Henry Luetcke <hluetcke@ethz.ch>
Date: Tue, 6 Jul 2021 15:11:40 +0200
Subject: [PATCH] fix bug in new_experiment function
---
OpenBis.m | 21 +++++++++++++++------
obi_test.m | 1 +
pybis_example.ipynb | 16 +++++++---------
3 files changed, 23 insertions(+), 15 deletions(-)
diff --git a/OpenBis.m b/OpenBis.m
index 51f0100451c..c1c37e89f2c 100644
--- a/OpenBis.m
+++ b/OpenBis.m
@@ -312,18 +312,27 @@ classdef OpenBis
experiment = obj.pybis.get_experiment(id);
end
- function experiment = new_experiment(obj, type, code, project)
+ function exp = new_experiment(obj, type, code, project)
%new_experiment
% Create a new experiment of specific type in a defined project
% Required input arguments:
- % type ... new experiment type
+ % type ... new experiment type - see: obi.get_experiment_types()
% code ... new experiment code
- % project ... project for new experiment ('SPACE/Project')
+ % project ... project for new experiment ('/SPACE/Project')
% Usage:
- % experiment = obi.new_experiment('type', 'space', 'Space/Project')
+ % exp = obi.new_experiment('type', 'EXP1234', '/SPACE/Project')
- experiment = obj.pybis.new_experiment(pyargs('type', type, 'code', code, 'project', project));
- experiment.save();
+ % determine type object
+ t = obj.pybis.get_experiment_type(type);
+
+ % determine project type
+ p = obj.get_project(project);
+
+ % instantiate a new experiment object
+ exp = py.pybis.pybis.Experiment(obj.pybis, pyargs('type', t, 'code', code, 'project', p));
+
+ % save experiment
+ exp.save();
end
diff --git a/obi_test.m b/obi_test.m
index b60c1391cf8..9e2afd791dc 100644
--- a/obi_test.m
+++ b/obi_test.m
@@ -41,6 +41,7 @@ projects = obi.get_projects(space_name, project_name);
assert(any(ismember(projects.identifier, sprintf('/%s/%s', space_name, project_name))), 'Project has not been created');
%% 4. Create experiment for test
+experiment_name = 'TESTING_EXPERIMENT';
%% 5. Create dataset with dummy files
diff --git a/pybis_example.ipynb b/pybis_example.ipynb
index 04e58a250de..ddc3b291ca8 100644
--- a/pybis_example.ipynb
+++ b/pybis_example.ipynb
@@ -7,9 +7,7 @@
"outputs": [],
"source": [
"from pybis import Openbis\n",
- "import getpass\n",
- "import matplotlib.pyplot as plt\n",
- "%matplotlib inline"
+ "import getpass"
]
},
{
@@ -25,7 +23,7 @@
"metadata": {},
"outputs": [],
"source": [
- "o = Openbis('https://openbis-tst.ethz.ch/openbis:8443', verify_certificates=False)"
+ "o = Openbis('https://127.0.0.1/openbis:8443', verify_certificates=False)"
]
},
{
@@ -34,7 +32,7 @@
"metadata": {},
"outputs": [],
"source": [
- "username = 'h'\n",
+ "username = 'hluetcke'\n",
"pw = getpass.getpass()"
]
},
@@ -280,7 +278,7 @@
"metadata": {},
"outputs": [],
"source": [
- "experiment = o.new_experiment(type='UNKNOWN', code='EXP123456', project='/SIS_HLUETCKE/DEMO')"
+ "experiment = o.new_experiment(type='UNKNOWN', code='EXP123456789', project='/HLUETCKE/PLAYGROUND')"
]
},
{
@@ -463,7 +461,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python [default]",
+ "display_name": "Python 3",
"language": "python",
"name": "python3"
},
@@ -477,9 +475,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.7"
+ "version": "3.9.1"
}
},
"nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
}
--
GitLab