feat: support string entity ids, upgrade to SDK v3

examples/download_as_tsv.py

@@ -2,7 +2,7 @@
 from pipebio.pipebio_client import PipebioClient
 from pipebio.util import Util
 
-document_id = int(os.environ['TARGET_DOCUMENT_ID'])
+document_id = os.environ['TARGET_DOCUMENT_ID']
 
 client = PipebioClient(url='https://app.pipebio.com')
 

examples/download_original_file.py

@@ -2,7 +2,7 @@
 from pipebio.pipebio_client import PipebioClient
 from pipebio.util import Util
 
-document_id = int(os.environ['TARGET_DOCUMENT_ID'])
+document_id = os.environ['TARGET_DOCUMENT_ID']
 
 client = PipebioClient(url='https://app.pipebio.com')
 

examples/download_to_genbank.py

@@ -4,7 +4,7 @@
 from pipebio.pipebio_client import PipebioClient
 from pipebio.util import Util
 
-document_id = int(os.environ['TARGET_DOCUMENT_ID'])
+document_id = os.environ['TARGET_DOCUMENT_ID']
 
 client = PipebioClient(url='https://app.pipebio.com')
 

examples/download_to_memory.py

@@ -1,7 +1,7 @@
 import os
 from pipebio.pipebio_client import PipebioClient
 
-document_id = int(os.environ['TARGET_DOCUMENT_ID'])
+document_id = os.environ['TARGET_DOCUMENT_ID']
 
 client = PipebioClient(url='https://app.pipebio.com')
 

examples/upload_fasta.py

@@ -4,7 +4,7 @@
 from pipebio.pipebio_client import PipebioClient
 
 
-folder_id = int(os.environ['TARGET_FOLDER_ID'])
+folder_id = os.environ['TARGET_FOLDER_ID']
 shareable_id = os.environ['TARGET_SHAREABLE_ID']
 
 client = PipebioClient(url='https://app.pipebio.com')

examples/upload_tsv.py

@@ -10,7 +10,7 @@
 from pipebio.pipebio_client import PipebioClient
 from pipebio.uploader import Uploader
 
-folder_id = int(os.environ['TARGET_FOLDER_ID'])
+folder_id = os.environ['TARGET_FOLDER_ID']
 shareable_id = os.environ['TARGET_SHAREABLE_ID']
 sequence_document_kind = SequenceDocumentKind.DNA
 

examples/workflows_example.py

@@ -19,7 +19,7 @@
 
 upload_jobs = client.upload_files(
     absolute_folder_path=os.path.join(dirname(getsourcefile(lambda: 0)), f'../sample_data/adimab/'),
-    parent_id=int(target_folder_id),
+    parent_id=target_folder_id,
     project_id=current_project_id,
     filename_pattern='.*\.fsa',
     poll_jobs=True
@@ -32,12 +32,11 @@
 
 # Create a folder to store the results of this workflow.
 workflow_folder = client.entities.create_folder(
-    current_project_id,
-    # NOTE: The parameters name & id are back to front. We'll fix that in an upcoming version.
+    project_id=current_project_id,
     name='Trial WF',
     parent_id=target_folder_id,
     # Optionally hide the workflow results until the Workflow is done.
-    # While you're working on the workflow maybe it's best to show the folder.
+    # While you're working on the workflow you may like to hide hide the folder and set it visible afterwards.
     visible=True,
 )
 workflow_folder_id = workflow_folder['id']

examples_test.py

@@ -70,7 +70,6 @@ def clean_up():
         folder_id = os.environ['TARGET_FOLDER_ID']
         entities = client.shareables.list_entities(shareable_id)
         target_folder = client.entities.get(folder_id)
-        entity_ids = list(
-            int(e['id']) for e in entities if e['path'].startswith(target_folder['path']) and e['id'] != folder_id)
+        entity_ids = list(e['id'] for e in entities if e['path'].startswith(target_folder['path']) and e['id'] != folder_id)
         if len(entity_ids):
             client.entities.delete(entity_ids)

requirements.txt

@@ -1,2 +1,2 @@
-pipebio~=2.3.10
+pipebio~=3.0.0
 pytest~=6.2.5