add more examples

Author: NicolasCARPi

.gitignore

@@ -1 +1,2 @@
 generated/
+openapi.yaml

README.md

@@ -12,17 +12,27 @@ pip install --user elabapi-python
 
 See the [examples folder](./examples).
 
+# Dev
+
 ## Using the helper script
 
 ~~~bash
 # generate the library
 ./helper.sh generate
+# generate from local file: openapi.yaml must be in current dir
+./helper.sh generate-from-local
 # build packages
 ./helper.sh build
 # publish new version (after editing config.json, with twine installed)
 ./helper.sh publish
 ~~~
 
-## License
+## Installing the library for dev
+
+~~~bash
+cd generated && python setup.py develop --user
+~~~
+
+# License
 
 MIT, see [license file](./LICENSE).

examples/01.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+import time
+import datetime
+import elabapi_python
+from elabapi_python.rest import ApiException
+
+#########################
+#         CONFIG        #
+#########################
+API_HOST_URL = 'https://elab.local:3148/api/v2'
+# replace with your api key
+API_KEY = 'apiKey4Test'
+# number of days to look back
+PERIOD_IN_DAYS = 7
+#########################
+#      END CONFIG       #
+#########################
+
+# Configure the api client
+configuration = elabapi_python.Configuration()
+configuration.api_key['api_key'] = API_KEY
+configuration.api_key_prefix['api_key'] = 'Authorization'
+configuration.host = API_HOST_URL
+configuration.debug = False
+configuration.verify_ssl = False
+
+# create an instance of the API class
+api_client = elabapi_python.ApiClient(configuration)
+# fix issue with Authorization header not being properly set by the generated lib
+api_client.set_default_header(header_name='Authorization', header_value=API_KEY)
+
+# create an instance of Experiments and another for Uploads
+experimentsApi = elabapi_python.ExperimentsApi(api_client)
+uploadsApi = elabapi_python.UploadsApi(api_client)
+
+# calculate the date
+today = datetime.date.today()
+date_from = today - datetime.timedelta(days = PERIOD_IN_DAYS)
+
+# look for experiments that are timestamped
+for exp in experimentsApi.read_experiments(extended=f'timestamped:yes timestamped_at:>{date_from}'):
+    for upload in uploadsApi.read_uploads('experiments', exp.id):
+        # get and save binary file
+        now = datetime.datetime.now()
+        with open(f'{exp.id}-{exp.elabid}-{now.strftime("%Y-%m-%d_%H-%M-%S")}-timestamp-archive.zip', 'wb') as zipfile:
+            # the _preload_content flag is necessary so the api_client doesn't try and deserialize the response
+            zipfile.write(uploadsApi.read_upload('experiments', exp.id, upload.id, format='binary', _preload_content=False).data)
+

examples/02.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+import time
+import datetime
+import elabapi_python
+from elabapi_python.rest import ApiException
+
+#########################
+#         CONFIG        #
+#########################
+API_HOST_URL = 'https://elab.local:3148/api/v2'
+# replace with your api key
+API_KEY = 'apiKey4Test'
+# number of days to look back
+PERIOD_IN_DAYS = 7
+#########################
+#      END CONFIG       #
+#########################
+
+# Configure the api client
+configuration = elabapi_python.Configuration()
+configuration.api_key['api_key'] = API_KEY
+configuration.api_key_prefix['api_key'] = 'Authorization'
+configuration.host = API_HOST_URL
+configuration.debug = False
+configuration.verify_ssl = False
+
+# create an instance of the API class
+api_client = elabapi_python.ApiClient(configuration)
+# fix issue with Authorization header not being properly set by the generated lib
+api_client.set_default_header(header_name='Authorization', header_value=API_KEY)
+
+# Synchronize metadata of the item_type with existing items
+# See: https://github.com/elabftw/elabftw/issues/3524
+
+# create an instance of Items api
+itemsApi = elabapi_python.ItemsApi(api_client)
+
+for item in itemsApi.read_items(cat=9):
+    # skip items with metadata already
+    if not item.metadata:
+        print(f'Patching item {item.id}')
+        itemsApi.patch_item(item.id, body={'metadata': '{"new":"metadata"}'})
+

examples/README.md

@@ -0,0 +1,15 @@
+# Examples for using this library
+
+Work in progress!
+
+# 00.py
+
+Read all items.
+
+# 01.py
+
+Download all the timestamp archive zip created in the past 7 days.
+
+# 02.py
+
+Look for all items of a particular category and patch the metadata if it is empty.

helper.sh

@@ -8,13 +8,22 @@ openapi_yaml_url="https://raw.githubusercontent.com/elabftw/elabftw/hypernext/ap
 # folder with the generated python code
 lib="generated"
 
-function generate {
-    # clean up first
+function cleanup {
     rm -rfv "$lib"
-    # now generate the lib
+}
+
+# generate the lib from remote hypernext spec
+function generate {
+    cleanup
     docker run --user "$(id -u)":"$(id -gn)" --rm -v "${PWD}":/local "$docker_image" generate -i "$openapi_yaml_url" -l python -o /local/"$lib" -c /local/config.json --git-user-id elabftw --git-repo-id elabapi-python
 }
 
+# generate the lib from a local file in current directory
+function generate-from-local {
+    cleanup
+    docker run --user "$(id -u)":"$(id -gn)" --rm -v "${PWD}":/local "$docker_image" generate -i /local/openapi.yaml -l python -o /local/"$lib" -c /local/config.json --git-user-id elabftw --git-repo-id elabapi-python
+}
+
 function build {
     cd "$lib" || exit 1
     python setup.py sdist bdist_egg bdist_wheel