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Commit ed30a77b authored by Henry Luetcke's avatar Henry Luetcke Committed by Adam Laskowski
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implement dataset methods

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1 merge request!40SSDM-13578 : 2PT : Database and V3 Implementation - include the new AFS "free"...
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object/OpenBis.m
+ 93
− 3
View file @ ed30a77b
...@@ -4,10 +4,10 @@ classdef OpenBis ...@@ -4,10 +4,10 @@ classdef OpenBis
% and provides methods for interacting with the Python (pyBIS) Openbis object. % and provides methods for interacting with the Python (pyBIS) Openbis object.
% %
% Usage: % Usage:
% Construct the MATLAB OpenBis object like this: % Construct the MATLAB OpenBis object like this:
% obi = OpenBis() % obi = OpenBis()
% This will ask for URL, user name and password to connect to openBIS server. % This will ask for URL, user name and password to connect to openBIS server.
% These can also be provided as optional input arguments. % These can also be provided as optional input arguments.
% %
% Methods are generally called like this: % Methods are generally called like this:
% spaces = obi.get_spaces() % spaces = obi.get_spaces()
...@@ -186,6 +186,96 @@ classdef OpenBis ...@@ -186,6 +186,96 @@ classdef OpenBis
project.save(); project.save();
end end
%% Dataset methods
% this section defines following Matlab methods:
% get_datasets
% get_dataset
% get_dataset_files
% dataset_download
function datasets = get_datasets(obj, varargin)
% Return table of matching datasets.
% Optional input arguments:
% code, type, experiment, project, tags
defaultCode = '';
defaultType = '';
defaultExp = '';
defaultProj = '';
defaultTags = '';
p = inputParser;
addRequired(p, 'obj');
addParameter(p, 'code', defaultCode, @ischar);
addParameter(p, 'type', defaultType, @ischar);
addParameter(p, 'experiment', defaultExp, @ischar);
addParameter(p, 'project', defaultProj, @ischar);
addParameter(p, 'tags', defaultTags, @ischar);
parse(p, obj, varargin{:});
a = p.Results;
datasets = obj.pybis.get_datasets(pyargs('code', a.code, 'type', a.type, 'experiment', a.experiment, ...
'project', a.project, 'tags', a.tags));
datasets = df_to_table(datasets.df);
end
function dataset = get_dataset(obj, permid, varargin)
only_data = false;
p = inputParser;
addRequired(p, 'obj');
addRequired(p, 'permid', @ischar);
addOptional(p, 'only_data', only_data, @islogical);
parse(p, obj, permid, varargin{:});
a = p.Results;
dataset = obj.pybis.get_dataset(pyargs('permid', a.permid, 'only_data', a.only_data));
end
function files = get_dataset_files(obj, dataset, varargin)
start_folder = '/';
p = inputParser;
addRequired(p, 'obj');
addRequired(p, 'dataset');
addOptional(p, 'start_folder', start_folder, @ischar);
parse(p, obj, dataset, varargin{:});
a = p.Results;
files = dataset.get_files(pyargs('start_folder', a.start_folder));
files = df_to_table(files);
end
function path_to_file = dataset_download(obj, dataset, files, varargin)
% provide files as cell array of files
destination = 'data';
wait_until_finished = true;
workers = 10;
p = inputParser;
addRequired(p, 'obj');
addRequired(p, 'dataset');
addRequired(p, 'files', @iscellstr);
addParameter(p, 'destination', destination, @ischar);
addParameter(p, 'wait_until_finished', wait_until_finished, @islogical);
addParameter(p, 'workers', workers, @isscalar);
parse(p, obj, dataset, files, varargin{:});
a = p.Results;
dataset.download(pyargs('files', a.files, 'destination', a.destination, 'wait_until_finished', a.wait_until_finished, 'workers', int16(a.workers)));
path_to_file = fullfile(a.destination, dataset.char, a.files);
end
end end
......
pybis_example.ipynb
+ 69
− 375
View file @ ed30a77b
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
from pybis import Openbis from pybis import Openbis
import getpass import getpass
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
%matplotlib inline %matplotlib inline
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Connecting to openBIS ### Connecting to openBIS
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o = Openbis('https://limb.ethz.ch/openbis:8443', verify_certificates=False) o = Openbis('https://limb.ethz.ch/openbis:8443', verify_certificates=False)
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
username = 'hluetcke' username = 'hluetcke'
pw = getpass.getpass() pw = getpass.getpass()
``` ```
%% Output
·····················
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.login(username, pw, save_token=True) # saves the session token in ~/.pybis/example.com.token o.login(username, pw, save_token=True) # saves the session token in ~/.pybis/example.com.token
del pw del pw
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.token o.token
``` ```
%% Output
'hluetcke-181026151925182x3063F8B1C01218403A7F2B2FFC989331'
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.is_session_active() o.is_session_active()
``` ```
%% Output
True
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_datastores() o.get_datastores()
``` ```
%% Output
code downloadUrl hostUrl
0 DSS1 https://limb.ethz.ch:443/datastore_server https://limb.ethz.ch:443
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Masterdata ### Masterdata
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_experiment_types() o.get_experiment_types()
``` ```
%% Output
code description modificationDate
-- ---------- ----------------------------------------------- -------------------
0 IHC Immunohistochemistry 2010-10-01 15:27:15
1 LACZ Experiments with lacZ staining. 2010-10-06 16:24:22
2 CULTURE Culture 2010-08-19 08:49:11
3 ISH in situ hybridization 2010-08-19 08:49:25
4 SKELETAL Skeletal 2010-08-19 08:49:34
5 METHODS Folder to store protocols 2016-05-24 16:36:12
6 PAPER Experiments from a paper. 2010-11-12 12:08:37
7 LIGHTSHEET Lightsheet imaging 2018-05-31 13:29:04
8 SAMPLE For Sample registration. 2010-11-22 10:28:53
9 MATERIALS Folder to store biological and chemical samples 2016-05-24 16:35:51
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_sample_types() o.get_sample_types()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_sample_type('PLATE') o.get_sample_type('PLATE')
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_material_types() o.get_material_types()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_dataset_types() o.get_dataset_types()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_terms() o.get_terms()
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### List and get datasets ### Samples / objects
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
datasets = o.get_datasets(type='HISTOLOGY') o.get_sample_types()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
counter = 0 obj = o.new_object(type='UNKNOWN', space='MATLAB_TEST', code='12345')
for ds in datasets:
print(ds)
counter += 1
if counter > 10:
break
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
ds = o.get_dataset('20101105142920015-6525') obj.save()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
ds.get_files(start_folder='original')
``` ```
%% Cell type:markdown id: tags:
### List and get datasets
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
space = o.get_space('MATLAB_TEST') datasets = o.get_datasets(type='HISTOLOGY')
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
space.delete counter = 0
for ds in datasets:
print(ds)
counter += 1
if counter > 10:
break
``` ```
%% Output %% Cell type:code id: tags:
``` python
ds = o.get_dataset('20101105142049776-6512')
```
attribute value %% Cell type:code id: tags:
---------------- ---------------------------------------
code MATLAB_TEST ``` python
permId MATLAB_TEST ds.get_files(start_folder='original')
description test space for Matlab access to openBIS ```
registrator hluetcke
registrationDate 2018-08-17 10:39:05
modificationDate 2018-08-17 10:39:05
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Download and import files ### Download and import files
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
ds.download(files='original/441_x40001.tif', destination='data', wait_until_finished=True) ds.download(files='', destination='data', wait_until_finished=True)
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
plt.imshow(plt.imread('data/20101105142920015-6525/original/441_x40001.tif')) plt.imshow(plt.imread('data/20101105142920015-6525/original/441_x40001.tif'))
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.logout() o.logout()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_experiment_types() o.get_experiment_types()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_dataset_types() o.get_dataset_types()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
o.get_projects(space='MATLAB_TEST', code=None) o.get_projects(space='MATLAB_TEST', code=None)
``` ```
%% Output
identifier permId leader registrator registrationDate modifier modificationDate
-- ------------------------- ---------------------- -------- ------------- ------------------- ---------- -------------------
0 /MATLAB_TEST/TEST_PROJECT 20180817104532621-9268 None hluetcke 2018-08-17 10:45:33 hluetcke 2018-08-17 10:45:33
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
project = o.new_project(space='MATLAB_TEST', code='ANOTHER_TEST', description='TGIF') project = o.new_project(space='MATLAB_TEST', code='ANOTHER_TEST', description='TGIF')
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
project.save() project.save()
``` ```
%% Output
Project successfully created.
attribute value
---------------- -------------------------
code ANOTHER_TEST
description TGIF
permId 20181026152148956-9272
identifier /MATLAB_TEST/ANOTHER_TEST
space MATLAB_TEST
leader
registrator hluetcke
registrationDate 2018-10-26 15:21:49
modifier
modificationDate 2018-10-26 15:21:49
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
project.delete('just a test') project.delete('just a test')
``` ```
%% Output
Project 20181026152148956-9272 successfully deleted.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
``` ```
......
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