add example with creating items with metadata/tag/link from CSV

Author: NicolasCARPi

examples/08.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+import time
+import datetime
+import elabapi_python
+from elabapi_python.rest import ApiException
+
+# necessary imports for this example
+import csv
+import json
+
+#########################
+#         CONFIG        #
+#########################
+# replace with the URL of your instance
+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)
+
+#### SCRIPT START ##################
+# Description: read a csv file
+# and create an item for each row, linked to a project
+####################################
+
+# Load the items api
+itemsApi = elabapi_python.ItemsApi(api_client)
+# and the links too
+linksApi = elabapi_python.LinksToItemsApi(api_client)
+
+# this is the path to the CSV file that we will read
+csv_path = 'data/samples.csv'
+
+# in which category (items_types) our samples will be created
+# this corresponds to the previously created "Samples" category in our database
+category_id = 1
+
+# project map (see comment below when linking to a project)
+project_map = {'Changes in a child’s subgingival microbiome following prophylaxis': 17, 'Another project': 16}
+
+# this is our metadata json, with an empty value for now, as it will change for every row
+# here the main body is hidden with display_main_text: false
+base_json='{"extra_fields":{"Sample type":{"type":"select","value":"","options":["Saliva","Tongue","Nose"],"group_id":null,"description":"The type of the sample"}},"elabftw":{"display_main_text": false}}'
+# we load it as an object
+metadata_as_json = json.loads(base_json)
+# read the csv and loop over rows
+with open(csv_path, newline='') as csvfile:
+    csvreader = csv.DictReader(csvfile, delimiter=',', quotechar='"')
+    for row in csvreader:
+        # create an item in the correct category, we also add a tag with the sample_type here
+        response = itemsApi.post_item_with_http_info(body={'category_id': category_id, 'tags': [row['sample_type']]})
+        # the previous request gives us the ID of the newly created item, so look into the Location header to get it
+        locationHeaderInResponse = response[2].get('Location')
+        print(f'The newly created item is here: {locationHeaderInResponse}')
+        itemId = int(locationHeaderInResponse.split('/').pop())
+        # replace the value of the Sample type in metadata with the sample_type of the row
+        metadata_as_json['extra_fields']['Sample type']['value'] = row['sample_type']
+        # and now we modify the item with the correct title/metadata
+        itemsApi.patch_item(itemId, body={'title': row['sample_name'], 'body': '', 'metadata': json.dumps(metadata_as_json)})
+
+        # now we want to link our entry to the project
+        # one option would be to GET all items of a particular category and look for the title of our project to get its ID
+        # but we will instead use a map because we don't have too many projects and they will never change their ID
+        project_id = project_map[row['project_name']]
+        linksApi.post_entity_items_links('items', itemId, project_id)

examples/README.md

@@ -33,3 +33,7 @@ Create users in batch.
 # 07.py
 
 Patch instance config: modify the settings of the Sysadmin Panel.
+
+# 08.py
+
+Read a CSV file for samples, create them in the database with metadata, tags and links.

examples/data/samples.csv

@@ -0,0 +1,6 @@
+sample_name,project_name,sample_type
+Sample 1,Changes in a child’s subgingival microbiome following prophylaxis,Saliva
+Sample 2,Changes in a child’s subgingival microbiome following prophylaxis,Saliva
+Sample 3,Changes in a child’s subgingival microbiome following prophylaxis,Tongue
+Sample 4,Another project,Nose
+Sample 5,Another project,Saliva