From ddb4e7b65e68b5a60d3f9d6c91c853d8d95b56b3 Mon Sep 17 00:00:00 2001
From: Henry Luetcke <hluetcke@ethz.ch>
Date: Wed, 24 Oct 2018 16:31:09 +0200
Subject: [PATCH] connection to openBIS, Masterdata methods
---
df_to_cell.m | 6 ------
df_to_table.m | 10 ++++++++++
get_dataset_types.m | 14 ++++++++++++++
get_datasets.m | 2 +-
get_experiment_types.m | 7 +++----
get_material_types.m | 14 ++++++++++++++
get_sample_types.m | 14 ++++++++++++++
get_terms.m | 15 +++++++++++++++
login.m | 23 ++++++++++++++++++++++-
logout.m | 13 +++++++++++++
pybis_example.ipynb | 20 ++++++++++----------
11 files changed, 116 insertions(+), 22 deletions(-)
delete mode 100644 df_to_cell.m
create mode 100644 df_to_table.m
create mode 100644 get_dataset_types.m
create mode 100644 get_material_types.m
create mode 100644 get_sample_types.m
create mode 100644 get_terms.m
create mode 100644 logout.m
diff --git a/df_to_cell.m b/df_to_cell.m
deleted file mode 100644
index c2ce512553e..00000000000
--- a/df_to_cell.m
+++ /dev/null
@@ -1,6 +0,0 @@
-function [matlab_cell] = df_to_cell(df)
-csv_temp = sprintf('%s.csv', tempname);
-df.to_csv(csv_temp);
-matlab_cell = readtable(csv_temp);
-delete(csv_temp);
-end
\ No newline at end of file
diff --git a/df_to_table.m b/df_to_table.m
new file mode 100644
index 00000000000..7135acb2bc9
--- /dev/null
+++ b/df_to_table.m
@@ -0,0 +1,10 @@
+function [matlab_table] = df_to_table(df)
+%df_to_table
+% Returns a Matlab table for a Python dataframe
+
+csv_temp = sprintf('%s.csv', tempname);
+df.to_csv(csv_temp);
+matlab_table = readtable(csv_temp);
+delete(csv_temp);
+
+end
\ No newline at end of file
diff --git a/get_dataset_types.m b/get_dataset_types.m
new file mode 100644
index 00000000000..e11aaddee27
--- /dev/null
+++ b/get_dataset_types.m
@@ -0,0 +1,14 @@
+function dataset_types = get_dataset_types
+%get_dataset_types
+% Returns a table of all available dataset types
+
+global obi
+
+% test connection
+test_connection(obi)
+
+dataset_types = obi.get_dataset_types();
+
+dataset_types = df_to_table(dataset_types.df);
+
+end
diff --git a/get_datasets.m b/get_datasets.m
index cc1e71fa94c..67688f26240 100644
--- a/get_datasets.m
+++ b/get_datasets.m
@@ -5,5 +5,5 @@ function [datasets] = get_datasets(ds_type)
global obi
datasets = obi.get_datasets(pyargs('type',ds_type));
-datasets = df_to_cell(datasets.df);
+datasets = df_to_table(datasets.df);
end
diff --git a/get_experiment_types.m b/get_experiment_types.m
index befeaeccbe9..a2d70f0286f 100644
--- a/get_experiment_types.m
+++ b/get_experiment_types.m
@@ -1,6 +1,6 @@
function experiment_types = get_experiment_types
-%UNTITLED2 Summary of this function goes here
-% Detailed explanation goes here
+%get_experiment_types
+% Returns a table of all available experiment types
global obi
@@ -8,8 +8,7 @@ global obi
test_connection(obi)
experiment_types = obi.get_experiment_types();
-experiment_types = df_to_cell(experiment_types.df);
+experiment_types = df_to_table(experiment_types.df);
end
-
diff --git a/get_material_types.m b/get_material_types.m
new file mode 100644
index 00000000000..ab92d06d5bc
--- /dev/null
+++ b/get_material_types.m
@@ -0,0 +1,14 @@
+function material_types = get_material_types
+%get_material_types
+% Returns a table of all available material types
+
+global obi
+
+% test connection
+test_connection(obi)
+
+material_types = obi.get_material_types();
+
+material_types = df_to_table(material_types.df);
+
+end
diff --git a/get_sample_types.m b/get_sample_types.m
new file mode 100644
index 00000000000..65f5435dfc9
--- /dev/null
+++ b/get_sample_types.m
@@ -0,0 +1,14 @@
+function sample_types = get_sample_types
+%get_sample_types
+% Returns a table of all available sample types
+
+global obi
+
+% test connection
+test_connection(obi)
+
+sample_types = obi.get_sample_types();
+
+sample_types = df_to_table(sample_types.df);
+
+end
diff --git a/get_terms.m b/get_terms.m
new file mode 100644
index 00000000000..3114cc7dec6
--- /dev/null
+++ b/get_terms.m
@@ -0,0 +1,15 @@
+function terms = get_terms
+%get_sample_types
+%Returns information about existing vocabulary terms.
+%If a vocabulary code is provided, it only returns the terms of that vocabulary
+
+global obi
+
+% test connection
+test_connection(obi)
+
+terms = obi.get_terms();
+
+terms = df_to_table(terms.df);
+
+end
diff --git a/login.m b/login.m
index f49d23f2419..441a746f49e 100644
--- a/login.m
+++ b/login.m
@@ -1,11 +1,32 @@
-function login(url, user, pw)
+function login(varargin)
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
global obi
+if nargin
+ url = varargin{1};
+ user = varargin{2};
+ pw = varargin{3};
+else
+ [url, user, pw] = user_url_pw_inputdlg;
+end
+
obi = py.pybis.Openbis(url, pyargs('verify_certificates', 0));
obi.login(user, pw, pyargs('save_token', 1));
end
+function [url, user, pw] = user_url_pw_inputdlg
+
+prompt = {'openBIS URL:', 'openBIS user:'};
+title = 'openBIS connection details';
+definput = {'https://XYZ.ethz.ch/openbis:8443', ''};
+answer = inputdlg(prompt, title, 1, definput);
+
+url = answer{1};
+user = answer{2};
+
+pw = passwordEntryDialog('CheckPasswordLength',0);
+
+end
\ No newline at end of file
diff --git a/logout.m b/logout.m
new file mode 100644
index 00000000000..9942dc2aed4
--- /dev/null
+++ b/logout.m
@@ -0,0 +1,13 @@
+function logout
+%LOGOUT
+% Log out of openBIS. After logout, the session token is no longer valid.
+
+global obi
+
+% test connection
+test_connection(obi)
+
+obi.logout;
+
+end
+
diff --git a/pybis_example.ipynb b/pybis_example.ipynb
index 4008e1d7517..ad001d3d1a8 100644
--- a/pybis_example.ipynb
+++ b/pybis_example.ipynb
@@ -30,7 +30,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 5,
"metadata": {},
"outputs": [
{
@@ -48,7 +48,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
@@ -58,16 +58,16 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "'hluetcke-181024130359554x90E8C39FF84921ECC3D5436AE2ECFD05'"
+ "'hluetcke-181024154540290xCA25DBE8ED8C9FB138503F6C3F0C8D69'"
]
},
- "execution_count": 5,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
@@ -78,7 +78,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
@@ -87,7 +87,7 @@
"True"
]
},
- "execution_count": 6,
+ "execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
@@ -98,7 +98,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
@@ -143,7 +143,7 @@
"0 DSS1 https://limb.ethz.ch:443/datastore_server https://limb.ethz.ch:443"
]
},
- "execution_count": 7,
+ "execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
@@ -441,7 +441,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.5"
}
},
"nbformat": 4,
--
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