remove signpost from sheepdog deps (#291)

* Remove backwards compatibility tests for signpost

* Remove if-else logic for signpost

* rename app.signpost to app.index_client

* rename transaction.signpost to transaction.index_client

* un-alias IndexClient from SignpostClient

* rename config vb SIGNPOST to INDEX_CLIENT

* rename signpost_obj to file_record

* miscellaneous signpost cleanup

requirements.txt

@@ -25,13 +25,11 @@ more-itertools==5.0.0
 cdispyutils==0.2.13
 datamodelutils==0.4.5
 psqlgraph==1.2.3
--e git+https://[email protected]/NCI-GDC/[email protected]#egg=signpost
 # required for gdcdatamodel, not required for sheepdog
 -e git+https://[email protected]/uc-cdis/[email protected]#egg=cdiserrors
 -e git+https://[email protected]/uc-cdis/cdislogging.git@master#egg=cdislogging
 -e git+https://[email protected]/NCI-GDC/cdisutils.git@f54e393c89939b2200dfae45c6235cbe2bae1206#egg=cdisutils
 gdcdictionary==1.2.0
 gdcdatamodel==1.3.12
 -e git+https://[email protected]/uc-cdis/[email protected]#egg=indexclient
--e git+https://[email protected]/NCI-GDC/python-signpostclient.git@ca686f55772e9a7f839b4506090e7d2bb0de5f15#egg=signpostclient
 -e git+https://[email protected]/uc-cdis/[email protected]#egg=storageclient

run.py

@@ -61,7 +61,7 @@ def fake_get_nodes(dids):
     return nodes
 
 
-def fake_urls_from_signpost(did):
+def fake_urls_from_index_client(did):
     return ["s3://fake-host/fake_bucket/{}".format(did)]
 
 
@@ -123,7 +123,7 @@ def run_with_fake_download():
             "sheepdog.download",
             key_for=fake_key_for,
             key_for_node=fake_key_for_node,
-            urls_from_signpost=fake_urls_from_signpost,
+            urls_from_index_client=fake_urls_from_index_client,
         ):
             if os.environ.get("GDC_FAKE_AUTH"):
                 run_with_fake_auth()

sheepdog/api.py

@@ -14,7 +14,7 @@
 from datamodelutils import models, validators, postgres_admin
 
 
-from indexclient.client import IndexClient as SignpostClient
+from indexclient.client import IndexClient
 
 import sheepdog
 from sheepdog.errors import (
@@ -78,11 +78,11 @@ def db_init(app):
 
     app.oauth_client = oauth2_client.OAuthClient(**app.config["OAUTH2"])
 
-    app.logger.info("Initializing Signpost driver")
-    app.signpost = SignpostClient(
-        app.config["SIGNPOST"]["host"],
-        version=app.config["SIGNPOST"]["version"],
-        auth=app.config["SIGNPOST"]["auth"],
+    app.logger.info("Initializing index client")
+    app.index_client = IndexClient(
+        app.config["INDEX_CLIENT"]["host"],
+        version=app.config["INDEX_CLIENT"]["version"],
+        auth=app.config["INDEX_CLIENT"]["auth"],
     )
 
 
@@ -124,7 +124,6 @@ def app_init(app):
     app.logger.info("Initializing app")
 
     # explicit options set for compatibility with gdc's api
-    app.config["USE_SIGNPOST"] = False
     app.config["AUTH_SUBMISSION_LIST"] = True
     app.config["USE_DBGAP"] = False
     app.config["IS_GDC"] = False

sheepdog/dev_settings.py

@@ -2,9 +2,9 @@
 from boto.s3.connection import OrdinaryCallingFormat
 from os import environ as env
 
-# Signpost
-SIGNPOST = {
-    "host": env.get("SIGNPOST_HOST", "http://localhost:8888"),
+# Index client
+INDEX_CLIENT = {
+    "host": env.get("INDEX_CLIENT_HOST", "http://localhost:8888"),
     "version": "v0",
     "auth": None,
 }

sheepdog/test_settings.py

@@ -1,7 +1,7 @@
 from collections import OrderedDict
 from .config import LEGACY_MODE
 
-SIGNPOST = {
+INDEX_CLIENT = {
     "host": "http://localhost:8000",
     "version": "v0",
     "auth": ("fake_user", "fake_password"),

sheepdog/transactions/deletion/__init__.py

@@ -61,7 +61,7 @@ def handle_deletion_request(program, project, ids, to_delete=None, **tx_kwargs):
         program=program,
         project=project,
         logger=flask.current_app.logger,
-        signpost=flask.current_app.signpost,
+        index_client=flask.current_app.index_client,
         to_delete=to_delete,
         db_driver=db_driver,
         **tx_kwargs

sheepdog/transactions/release/__init__.py

@@ -39,7 +39,7 @@ def handle_release_transaction(program, project, **tx_kwargs):
         program=program,
         project=project,
         logger=flask.current_app.logger,
-        signpost=flask.current_app.signpost,
+        index_client=flask.current_app.index_client,
         db_driver=db_driver,
         **tx_kwargs
     )

sheepdog/transactions/review/__init__.py

@@ -41,7 +41,7 @@ def _single_transaction(tx_cls, program, project, **tx_kwargs):
         program=program,
         project=project,
         logger=flask.current_app.logger,
-        signpost=flask.current_app.signpost,
+        index_client=flask.current_app.index_client,
         db_driver=db_driver,
         **tx_kwargs
     )

sheepdog/transactions/submission/__init__.py

@@ -25,7 +25,7 @@ def handle_submission_transaction(program, project, *doc_args, **tx_kwargs):
         program=program,
         project=project,
         logger=flask.current_app.logger,
-        signpost=flask.current_app.signpost,
+        index_client=flask.current_app.index_client,
         db_driver=db_driver,
         **tx_kwargs
     )

sheepdog/transactions/transaction_base.py

@@ -55,7 +55,7 @@ def __init__(self, program, project, **kwargs):
             dry_run: If True, the transaction will not be committed
             role: The role required to take this transaction
             user: The initializer of the transaction
-            signpost: Signpost driver (default: capp.signpost)
+            index_client: index client (default: capp.index_client)
             db_driver: PsqlGraph driver (default: capp.db)
             logger: Logging driver (default: capp.logger)
             transaction_id: Optionally inherit and write to an existing
@@ -70,7 +70,7 @@ def __init__(self, program, project, **kwargs):
         self.role = kwargs.pop("role", None)
         # To be pulled from flask request context if not provided
         self.logger = kwargs.pop("logger", None) or current_app.logger
-        self.signpost = kwargs.pop("signpost", None) or current_app.signpost
+        self.index_client = kwargs.pop("index_client", None) or current_app.index_client
         self.db_driver = kwargs.pop("db_driver", None) or current_app.db
         self.config = kwargs.pop("flask_config", None) or current_app.config
         #: Create a transaction log, this will be created and committed to the

sheepdog/transactions/upload/__init__.py

@@ -69,7 +69,7 @@ def _single_transaction(role, program, project, *doc_args, **tx_kwargs):
         project=project,
         role=role,
         logger=flask.current_app.logger,
-        signpost=flask.current_app.signpost,
+        index_client=flask.current_app.index_client,
         flask_config=flask.current_app.config,
         db_driver=db_driver,
         external_proxies=utils.get_external_proxies(),
@@ -123,7 +123,7 @@ def handle_single_transaction(role, program, project, **tx_kwargs):
         role=role,
         logger=flask.current_app.logger,
         flask_config=flask.current_app.config,
-        signpost=flask.current_app.signpost,
+        index_client=flask.current_app.index_client,
         external_proxies=utils.get_external_proxies(),
         db_driver=db_driver,
         **tx_kwargs
@@ -246,7 +246,7 @@ def handle_bulk_transaction(role, program, project, **tx_kwargs):
         project=project,
         role=role,
         logger=flask.current_app.logger,
-        signpost=flask.current_app.signpost,
+        index_client=flask.current_app.index_client,
         db_driver=flask.current_app.db,
         external_proxies=utils.get_external_proxies(),
         **tx_kwargs