Merge branch 'master' of github.com:elabftw/elabapi-python

* 'master' of github.com:elabftw/elabapi-python:
  chore: examples: update using local client module & fix some examples (#43)

Author: NicolasCARPi

examples/00-getting-started.py

@@ -5,45 +5,14 @@
 # This file is heavily commented and will show you various examples of using the API library #
 ##############################################################################################
 
-# We will use the standard "os" module to read values from environment
-import os
-
-# and this one to pretty print python object
-from pprint import pprint
-
-# You must have elabapi-python installed so it can be imported
-# This line will make the library available in our script
-# Install it with: pip install elabapi-python
 import elabapi_python
 
-# START CONFIG
-# Basic configuration: Api Key and Host URL
-# Get the Api Key from the environment or use the default development value
-API_KEY = os.getenv('API_KEY') or 'apiKey4Test'
-# Get the server address from the environment or use the default development value
-API_HOST = os.getenv('API_HOST') or 'https://elab.local:3148/api/v2'
-
-# Initialize a configuration object from the library
-configuration = elabapi_python.Configuration()
+# first, use the locally defined client.py module to get the api_client object. (see /examples/client.py)
+# it is fully configured and ready to be used to instantiate api objects
+from client import api_client
 
-# Set the host
-configuration.host = API_HOST
-# Verify the TLS certificate validity: should be set to True in production
-configuration.verify_ssl = False
-# For convenience, mask the warnings about skipping TLS verification
-if not configuration.verify_ssl:
-    import urllib3
-    urllib3.disable_warnings(category=urllib3.exceptions.InsecureRequestWarning)
-
-# Set this flag to True to get more verbose output
-configuration.debug = False
-
-# Create an API client object with our configuration
-api_client = elabapi_python.ApiClient(configuration)
-
-# Set the Api Key in Authorization header
-api_client.set_default_header(header_name='Authorization', header_value=API_KEY)
-# END CONFIG
+# add pprint to pretty print python objects
+from pprint import pprint
 
 # Note:
 # In order to make it easier to run only specific parts, the parts are grouped in functions that are called at the end of the script
@@ -64,7 +33,7 @@ def part1():
     pprint(api_response)
     print("")
     # Example usage
-    print(f"[*] The instance at {API_HOST} has {api_response.teams_count} teams and {api_response.all_users_count} users.")
+    print(f"[*] The instance at {api_client.configuration.host} has {api_response.teams_count} teams and {api_response.all_users_count} users.")
     print(f"[*] Total size of uploaded files: {api_response.uploads_filesize_sum_formatted}")
     print("\n------------------------ END PART 1 ------------------------\n")
 

examples/001-manipulating-metadata.py

@@ -5,16 +5,11 @@
 ###################################################################################################
 
 import elabapi_python
-
-# use the locally defined client.py module to get the api_client object, fully configured and ready to be used to instantiate api objects
 from client import api_client
 
-# Note:
-# In order to make it easier to run only specific parts, the parts are grouped in functions that are called at the end of the script
-
-######################################################
-# Part 1: creating a Resource with specific metadata #
-######################################################
+##############################################
+# Creating a Resource with specific metadata #
+##############################################
 # Doc: https://doc.elabftw.net/api/v2/#/Items/post-item
 # Start by creating our api object to interact with /items endpoint
 items_client = elabapi_python.ItemsApi(api_client)

examples/002-extra-field-to-column.py

@@ -6,15 +6,13 @@
 
 import elabapi_python
 import json
-
-# use the locally defined client.py module to get the api_client object, fully configured and ready to be used to instantiate api objects
 from client import api_client
 
 # Start by creating our api object to interact with /items endpoint
 items_client = elabapi_python.ItemsApi(api_client)
 
-# In this example, this corresponds to "Chemicals". Adapt to your instance.
-RESOURCE_CATEGORY_ID = 5
+# In this example, this corresponds to "Antibody". Adapt to your instance.
+RESOURCE_CATEGORY_ID = 3
 # this value is the same for all eLabFTW instances
 CURRENCY_EUROS = 4
 

examples/01-download-timestamp-archive.py

@@ -1,31 +1,14 @@
 #!/usr/bin/env python
 import datetime
 import elabapi_python
+from client import api_client
 
-#########################
-#         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
+##################################################################################
+# In this example script, we will download timestamps archives from experiments. #
+##################################################################################
 
-# 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)
+# define number of days to look back
+PERIOD_IN_DAYS = 7
 
 # create an instance of Experiments and another for Uploads
 experimentsApi = elabapi_python.ExperimentsApi(api_client)

examples/02-patch-metadata-per-category.py

@@ -1,28 +1,9 @@
 #!/usr/bin/env python
 import elabapi_python
+from client import api_client
 
-#########################
-#         CONFIG        #
-#########################
-API_HOST_URL = 'https://elab.local:3148/api/v2'
-# replace with your api key
-API_KEY = 'apiKey4Test'
-#########################
-#      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)
+# define which category's items are patched
+RESOURCE_CATEGORY_ID = 3
 
 # Synchronize metadata of the item_type with existing items
 # See: https://github.com/elabftw/elabftw/issues/3524
@@ -32,9 +13,8 @@
 
 metadata = '{"elabftw": {"extra_fields_groups": [{"id": 1,"name": "Drug settings"},{"id": 2,"name": "Mice info"}]},"extra_fields": {"Drug addition": {"type": "datetime-local","value": "","group_id": 1,"required": true,"description": "Time when drug is added"},"Drug concentration": {"type": "number","unit": "mM","units": ["mM","μM","nM"],"value": "","group_id": 1,"required": true},"Mouse sex": {"type": "select","value": "Male","options": ["Male","Female"],"group_id": 2}}}'
 
-for item in itemsApi.read_items(cat=1, limit=9999):
+for item in itemsApi.read_items(cat=RESOURCE_CATEGORY_ID, limit=9999):
     # skip items with metadata already
     if not item.metadata:
         print(f'Patching item {item.id}')
         itemsApi.patch_item(item.id, body={'metadata': metadata})
-

examples/03-experiment-file-handling.py

@@ -1,48 +1,58 @@
 #!/usr/bin/env python
+
+#################################################################################
+# In this example script, we will upload a file to an experiment and delete it. #
+# You can comment the 'delete' part to see results in your experiment.          #
+#################################################################################
+
+# Doc: https://doc.elabftw.net/api/v2/#/Uploads
+
+# part 1 (upload_file_to_experiment) will upload a file to a target experiment.
+# part 2 (download_matching_uploads_locally) will download locally a file from an eLabFTW experiment.
+# part 3 (cleanup) will remove the files from both the experiment and locally.
 import os
 import elabapi_python
-
-#########################
-#         CONFIG        #
-#########################
-API_HOST_URL = 'https://elab.local:3148/api/v2'
-# replace with your api key
-API_KEY = 'apiKey4Test'
-#########################
-#      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)
+from client import api_client
 
 # create an instance of Experiments and another for Uploads
 experimentsApi = elabapi_python.ExperimentsApi(api_client)
 uploadsApi = elabapi_python.UploadsApi(api_client)
 
-# get experiment with ID 256
-exp = experimentsApi.get_experiment(256)
-# upload the file 'README.md' present in the current folder
-uploadsApi.post_upload('experiments', 256, file='README.md', comment='Uploaded with APIv2')
-# display id, name and comment of the uploaded files
-for upload in uploadsApi.read_uploads('experiments', exp.id):
-    print(upload.id, upload.real_name, upload.comment)
-    # get and save file
-    with open('README.downloaded_with_api.md', 'wb') as file:
-        # the _preload_content flag is necessary so the api_client doesn't try and deserialize the response
-        file.write(uploadsApi.read_upload('experiments', 256, upload.id, format='binary', _preload_content=False).data)
+# define the target experiment
+EXPERIMENT_ID = 210
+# prepare the file. We'll use the 'README.md' present in current folder
+SOURCE_FILE = "README.md"
+# local downloads for the script
+DOWNLOADED_FILENAME = "README.downloaded_with_api.md"
+
+exp = experimentsApi.get_experiment(EXPERIMENT_ID)
+
+# --- part 1: Upload file to experiment ---
+def upload_file_to_experiment():
+    uploadsApi.post_upload('experiments', EXPERIMENT_ID, file=SOURCE_FILE, comment='Uploaded with APIv2')
+
+# --- part 2: Download uploads locally ---
+def download_matching_uploads_locally():
+    # display id, name and comment of the uploaded files and download them locally
+    for upload in uploadsApi.read_uploads('experiments', exp.id):
+        print(upload.id, upload.real_name, upload.comment, upload.state)
+        # get and save file
+        with open(DOWNLOADED_FILENAME, 'wb') as file:
+            # the _preload_content flag is necessary so the api_client doesn't try and deserialize the response
+            file.write(uploadsApi.read_upload('experiments', EXPERIMENT_ID, upload.id, format='binary', _preload_content=False).data)
+
+# --- part 3: delete the downloaded file ---
+def cleanup():
     # delete all the files where the name is 'README.md'
-    if upload.real_name == 'README.md':
-        uploadsApi.delete_upload('experiments', 256, upload.id)
+    for upload in uploadsApi.read_uploads('experiments', exp.id):
+        if upload.real_name == SOURCE_FILE:
+            uploadsApi.delete_upload('experiments', EXPERIMENT_ID, upload.id)
+    # cleanup: delete the downloaded file
+    try:
+        os.remove(DOWNLOADED_FILENAME)
+    except FileNotFoundError:
+        pass
 
-# cleanup: delete the downloaded file
-os.remove('README.downloaded_with_api.md')
+upload_file_to_experiment()
+download_matching_uploads_locally()
+cleanup()

examples/04-create-teamgroup-add-user.py

@@ -1,28 +1,6 @@
 #!/usr/bin/env python
 import elabapi_python
-
-#########################
-#         CONFIG        #
-#########################
-API_HOST_URL = 'https://elab.local:3148/api/v2'
-# replace with your api key
-API_KEY = 'apiKey4Test'
-#########################
-#      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)
+from client import api_client
 
 # Load teamgroup api
 teamgroupsApi = elabapi_python.TeamgroupsApi(api_client)

examples/05-create-modify-item.py

@@ -1,35 +1,13 @@
 #!/usr/bin/env python
 import elabapi_python
-
-#########################
-#         CONFIG        #
-#########################
-API_HOST_URL = 'https://elab.local:3148/api/v2'
-# replace with your api key
-API_KEY = 'apiKey4Test'
-#########################
-#      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)
+from client import api_client
 
 # Load items api
 itemsApi = elabapi_python.ItemsApi(api_client)
 
 # Create an item with the category_id 1 (items_types ID = 1)
 targetCategory = 1
-response = itemsApi.post_item_with_http_info(body={'category_id': targetCategory, 'tags': ['some tag', 'another tag']})
+response = itemsApi.post_item_with_http_info(body={'category': targetCategory, 'tags': ['some tag', 'another tag']})
 locationHeaderInResponse = response[2].get('Location')
 print(f'The newly created item is here: {locationHeaderInResponse}')
 itemId = int(locationHeaderInResponse.split('/').pop())

examples/06-create-users.py

@@ -1,28 +1,7 @@
 #!/usr/bin/env python
 import elabapi_python
 
-#########################
-#         CONFIG        #
-#########################
-API_HOST_URL = 'https://elab.local:3148/api/v2'
-# replace with your api key
-API_KEY = 'apiKey4Test'
-#########################
-#      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)
+from client import api_client
 
 #### SCRIPT START #####
 # Description: create users in batch