move final few terrain methods to PyCyAPI (#299)

docker-compose.dev.yml

@@ -247,10 +247,4 @@ services:
       interval: 60s
       timeout: 60s
       retries: 2
-      start_period: 20s
-  # TODO: singularity-in-docker and docker-in-docker containers as test agents
-  # sind:
-  #   image: computationalplantscience/sind
-  #   command: ["/usr/sbin/sshd", "-D"]
-  #   working_dir: /opt/work
-  #   privileged: true
+      start_period: 20s

plantit/plantit/datasets/views.py

@@ -16,7 +16,6 @@
 from pycyapi.clients import TerrainClient, AsyncTerrainClient
 
 import plantit.queries as q
-import plantit.terrain as terrain
 from plantit.datasets.models import DatasetAccessPolicy, DatasetRole
 from plantit.miappe.models import Investigation, Study
 from plantit.notifications.models import Notification
@@ -56,7 +55,8 @@ async def shared(request):
 
     policies = await sync_to_async(list)(DatasetAccessPolicy.objects.filter(guest=request.user))
     paths = [policy.path for policy in policies]
-    dirs = await terrain.get_dirs_async(paths, request.user.profile.cyverse_access_token, int(settings.HTTP_TIMEOUT))
+    client = AsyncTerrainClient(request.user.profile.cyverse_access_token, int(settings.HTTP_TIMEOUT))
+    dirs = await client.get_dirs_async(paths)
     return JsonResponse({'datasets': [dir for dir in dirs]})
 
 

plantit/plantit/queries.py

@@ -20,7 +20,7 @@
 from django.utils import timezone
 
 from pycyapi.clients import TerrainClient
-import plantit.terrain as terrain
+from pycyapi.exceptions import Unauthorized
 import plantit.mapbox as mapbox
 from plantit import github as github
 from plantit import loess as loess
@@ -526,8 +526,14 @@ def refresh_user_cyverse_tokens(user: User):
         return
 
     try:
-        access_token, refresh_token = terrain.refresh_tokens(username=user.username, refresh_token=user.profile.cyverse_refresh_token)
-    except terrain.Unauthorized as e:
+        client = TerrainClient(user.profile.cyverse_access_token)
+        access_token, refresh_token = client.refresh_tokens(
+            username=user.username,
+            client_id=settings.CYVERSE_CLIENT_ID,
+            client_secret=settings.CYVERSE_CLIENT_SECRET,
+            refresh_token=user.profile.cyverse_refresh_token,
+            redirect_uri=settings.CYVERSE_REDIRECT_URL)
+    except Unauthorized as e:
         decoded = jwt.decode(user.profile.cyverse_refresh_token, options={
             'verify_signature': False,
             'verify_aud': False,