Feature/renaming

README.md

@@ -27,6 +27,6 @@ containers or as virtual machines.
 | ingesters   | Split the Crypt4GH header and move the remainder to the storage backend. No cryptographic task, nor connection to the keyserver. |
 | verifiers   | Connect to the keyserver (via SSL) and decrypt the stored files and checksum them against their embedded checksum. |
 | vault       | Storage backend: as a regular file system or as a S3 object store. |
-| ID mapper   | Handles the so-called _Stable ID_ filename mappings from CentralEGA. |
+| Finalize    | Handles the so-called _Stable ID_ filename mappings from CentralEGA. |
 
 Find the [LocalEGA documentation](http://localega.readthedocs.io) hosted on [ReadTheDocs.org](https://readthedocs.org/).

deploy/bootstrap/lega.sh

@@ -84,7 +84,7 @@ chroot_sessions = True
 
 [vault]
 driver = S3Storage
-url = http://s3:9000
+url = http://vault:9000
 access_key = ${S3_ACCESS_KEY}
 secret_key = ${S3_SECRET_KEY}
 #region = lega
@@ -235,20 +235,20 @@ fi
 
 cat >> ${PRIVATE}/lega.yml <<EOF
   # Stable ID mapper
-  id-mapper:
+  finalize:
     depends_on:
       - db
       - mq
     image: nbisweden/ega-base:dev
-    container_name: id-mapper
+    container_name: finalize
     labels:
-        lega_label: "id-mapper"
+        lega_label: "finalize"
     volumes:
        - ./lega/conf.ini:/etc/ega/conf.ini:ro
     restart: on-failure:3
     networks:
       - lega
-    entrypoint: ["gosu", "lega", "ega-id-mapper"]
+    entrypoint: ["gosu", "lega", "ega-finalize"]
 
   # Ingestion Workers
   ingest:
@@ -358,7 +358,7 @@ cat >> ${PRIVATE}/lega.yml <<EOF
   # Data Out re-encryption service
   res:
     depends_on:
-      - s3
+      - vault
       - keys
     hostname: res
     container_name: res
@@ -379,26 +379,26 @@ cat >> ${PRIVATE}/lega.yml <<EOF
       - EGA_SHAREDPASS_PATH=/etc/ega/pgp/ega.shared.pass
       - EGA_EBI_AWS_ACCESS_KEY=${S3_ACCESS_KEY}
       - EGA_EBI_AWS_ACCESS_SECRET=${S3_SECRET_KEY}
-      - EGA_EBI_AWS_ENDPOINT_URL=http://s3:${DOCKER_PORT_s3}
+      - EGA_EBI_AWS_ENDPOINT_URL=http://vault:${DOCKER_PORT_s3}
       - EGA_EBI_AWS_ENDPOINT_REGION=
     volumes:
       - ./lega/pgp/ega.shared.pass:/etc/ega/pgp/ega.shared.pass:ro
     restart: on-failure:3
     networks:
       - lega
 
-  # S3
-  s3:
-    hostname: s3
-    container_name: s3
+  # Storage backend: S3
+  vault:
+    hostname: vault
+    container_name: vault
     labels:
-        lega_label: "s3"
+        lega_label: "vault"
     image: minio/minio
     environment:
       - MINIO_ACCESS_KEY=${S3_ACCESS_KEY}
       - MINIO_SECRET_KEY=${S3_SECRET_KEY}
     volumes:
-      - s3:/data
+      - vault:/data
     restart: on-failure:3
     networks:
       - lega
@@ -410,7 +410,7 @@ cat >> ${PRIVATE}/lega.yml <<EOF
 volumes:
   db:
   inbox:
-  s3:
+  vault:
 EOF
 
 #########################################################################

deploy/tests/src/test/resources/config.properties

@@ -11,5 +11,5 @@ container.label.inbox = inbox
 container.label.ingest = ingest
 container.label.keys = keys
 container.label.mq = mq
-container.label.s3 = s3
+container.label.s3 = vault
 container.label.verify = verify

docs/code.rst

@@ -14,7 +14,7 @@ Python Modules
     lega.ingest
     lega.verify
     lega.keyserver
-    lega.mapper
+    lega.finalize
 
 *******************
 Inbox notifications
@@ -31,7 +31,7 @@ Ingestion Worker
    :members:
 .. automodule:: lega.verify
    :members:
-.. automodule:: lega.mapper
+.. automodule:: lega.finalize
    :members:
 
 

setup.py

@@ -26,7 +26,7 @@
               'ega-verify = lega.verify:main',
               'ega-keyserver = lega.keyserver:main',
               'ega-notifications = lega.notifications:main',
-              'ega-id-mapper = lega.mapper:main',
+              'ega-finalize = lega.finalize:main',
               'ega-conf = lega.conf.__main__:main',
           ]
       },

tests/test_mapper.py → tests/test_finalize.py

@@ -1,12 +1,12 @@
 import unittest
-from lega.mapper import main, work
+from lega.finalize import main, work
 from unittest import mock
 
 
-class testMapper(unittest.TestCase):
-    """Mapper.
+class testFinalize(unittest.TestCase):
+    """Finalize.
 
-    Testing mapper functionalities.
+    Testing Finalizer functionalities.
     """
 
     def setUp(self):
@@ -17,18 +17,18 @@ def tearDown(self):
         """Remove anything that was setup."""
         pass
 
-    @mock.patch('lega.mapper.db')
+    @mock.patch('lega.finalize.db')
     def test_work(self, mock_db):
-        """Test mapper worker, should insert into database."""
+        """Test finalize worker, should insert into database."""
         # mock_db.set_stable_id.return_value = mock.Mock()
         data = {'stable_id': '1', 'file_id': '123'}
         work(data)
         mock_db.set_stable_id.assert_called_with('123', '1')
 
-    @mock.patch('lega.mapper.get_connection')
-    @mock.patch('lega.mapper.consume')
+    @mock.patch('lega.finalize.get_connection')
+    @mock.patch('lega.finalize.consume')
     def test_main(self, mock_consume, mock_connection):
-        """Test main mapper, by mocking cosume call."""
+        """Test main finalize, by mocking cosume call."""
         mock_consume.return_value = mock.MagicMock()
         main()
         mock_consume.assert_called()