manage spaces

ed6b642a · Henry Luetcke · Adam Laskowski · ddb4e7b6 · ed6b642a · ed6b642a
Commit ed6b642a authored 6 years ago by Henry Luetcke Committed by Adam Laskowski 2 years ago
--- a/delete_space.m
+++ b/delete_space.m
+function delete_space(code, reason)
+% DELETE_SPACE
+% Delete space in the openBIS instance. A reason has to be specified.
+
+global obi
+
+% test connection
+test_connection(obi)
+
+space = obi.get_space(code);
+space.delete(reason);
+
+end
\ No newline at end of file
--- a/get_spaces.m
+++ b/get_spaces.m
+function spaces = get_spaces
+% GET_SPACES
+% Get a list of all available spaces (DataFrame object). To create a sample or a 
+% dataset, you need to specify in which space it should live.
+
+global obi
+
+% test connection
+test_connection(obi)
+
+spaces = obi.get_spaces();
+
+spaces = df_to_table(spaces.df);
+
+end
--- a/new_space.m
+++ b/new_space.m
+function new_space(code, description)
+% NEW_SPACE
+% Creates a new space in the openBIS instance.
+
+global obi
+
+% test connection
+test_connection(obi)
+
+space = obi.new_space(pyargs('code',  code, 'description', description));
+space.save;
+
+end
\ No newline at end of file
--- a/pybis_example.ipynb
+++ b/pybis_example.ipynb
@@ -372,6 +372,57 @@
    "ds.get_files(start_folder='original')"
   ]
  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "space = o.get_space('MATLAB_TEST')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "            <table border=\"1\" class=\"dataframe\">\n",
+       "            <thead>\n",
+       "                <tr style=\"text-align: right;\">\n",
+       "                <th>attribute</th>\n",
+       "                <th>value</th>\n",
+       "                </tr>\n",
+       "            </thead>\n",
+       "            <tbody>\n",
+       "        <tr> <td>code</td> <td>MATLAB_TEST</td> </tr><tr> <td>permId</td> <td>MATLAB_TEST</td> </tr><tr> <td>description</td> <td>test space for Matlab access to openBIS</td> </tr><tr> <td>registrator</td> <td>hluetcke</td> </tr><tr> <td>registrationDate</td> <td>2018-08-17 10:39:05</td> </tr><tr> <td>modificationDate</td> <td>2018-08-17 10:39:05</td> </tr>\n",
+       "            </tbody>\n",
+       "            </table>\n",
+       "        "
+      ],
+      "text/plain": [
+       "attribute         value\n",
+       "----------------  ---------------------------------------\n",
+       "code              MATLAB_TEST\n",
+       "permId            MATLAB_TEST\n",
+       "description       test space for Matlab access to openBIS\n",
+       "registrator       hluetcke\n",
+       "registrationDate  2018-08-17 10:39:05\n",
+       "modificationDate  2018-08-17 10:39:05"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "space.delete"
+   ]
+  },
  {
   "cell_type": "markdown",
   "metadata": {},

 %% Cell type:code id: tags:

 ``` python
 from pybis import Openbis
 import getpass
 import matplotlib.pyplot as plt
 %matplotlib inline
 ```

 %% Cell type:markdown id: tags:

 ### Connecting to openBIS

 %% Cell type:code id: tags:

 ``` python
 o = Openbis('https://limb.ethz.ch/openbis:8443', verify_certificates=False)
 ```

 %% Cell type:code id: tags:

 ``` python
 username = 'hluetcke'
 pw = getpass.getpass()
 ```

 %% Output

     ·····················

 %% Cell type:code id: tags:

 ``` python
 o.login(username, pw, save_token=True)   # saves the session token in ~/.pybis/example.com.token
 del pw
 ```

 %% Cell type:code id: tags:

 ``` python
 o.token
 ```

 %% Output

    'hluetcke-181024154540290xCA25DBE8ED8C9FB138503F6C3F0C8D69'

 %% Cell type:code id: tags:

 ``` python
 o.is_session_active()
 ```

 %% Output

    True

 %% Cell type:code id: tags:

 ``` python
 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:

 ### Masterdata

 %% Cell type:code id: tags:

 ``` python
 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:

 ``` python
 o.get_sample_types()
 ```

 %% Cell type:code id: tags:

 ``` python
 o.get_sample_type('PLATE')
 ```

 %% Cell type:code id: tags:

 ``` python
 o.get_material_types()
 ```

 %% Cell type:code id: tags:

 ``` python
 o.get_dataset_types()
 ```

 %% Cell type:code id: tags:

 ``` python
 o.get_terms()
 ```

 %% Cell type:markdown id: tags:

 ### List and get datasets

 %% Cell type:code id: tags:

 ``` python
 datasets = o.get_datasets(type='HISTOLOGY')
 ```

 %% Cell type:code id: tags:

 ``` python
 counter = 0
 for ds in datasets:
    print(ds)
    counter += 1
    if counter > 10:
        break
 ```

 %% Cell type:code id: tags:

 ``` python
 ds = o.get_dataset('20101105142920015-6525')
 ```

 %% Cell type:code id: tags:

 ``` python
 ds.get_files(start_folder='original')
 ```

+%% Cell type:code id: tags:
+
+``` python
+space = o.get_space('MATLAB_TEST')
+```
+
+%% Cell type:code id: tags:
+
+``` python
+space.delete
+```
+
+%% Output
+
+    attribute         value
+    ----------------  ---------------------------------------
+    code              MATLAB_TEST
+    permId            MATLAB_TEST
+    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:

 ### Download and import files

 %% Cell type:code id: tags:

 ``` python
 ds.download(files='original/441_x40001.tif', destination='data', wait_until_finished=True)
 ```

 %% Cell type:code id: tags:

 ``` python
 plt.imshow(plt.imread('data/20101105142920015-6525/original/441_x40001.tif'))
 ```

 %% Cell type:code id: tags:

 ``` python
 o.logout()
 ```

 %% Cell type:code id: tags:

 ``` python
 o.get_experiment_types()
 ```

 %% Cell type:code id: tags:

 ``` python
 o.get_dataset_types()
 ```