Merge pull request #41 from Aratz/refactor_rebased

Remove support for mover

alembic/versions/74b309c44134_drop_ddsproject_table.py

@@ -0,0 +1,33 @@
+"""Drop DDSProject table
+
+Revision ID: 74b309c44134
+Revises: 8a4cc1553379
+Create Date: 2022-06-16 15:37:24.124003
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '74b309c44134'
+down_revision = '8a4cc1553379'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.drop_table('dds_projects')
+    op.add_column(
+            'delivery_orders',
+            sa.Column('ngi_project_name', sa.String(), nullable=True))
+
+
+def downgrade():
+    op.drop_column('delivery_orders', 'ngi_project_name')
+    op.create_table(
+        'dds_projects',
+        sa.Column('dds_project_id', sa.String(), nullable=False),
+        sa.Column('project_name', sa.String(), nullable=True),
+        sa.PrimaryKeyConstraint('dds_project_id')
+    )

alembic/versions/85082f64ccd0_add_dds_project_table.py

@@ -15,9 +15,12 @@
 branch_labels = None
 depends_on = None
 
+
 def upgrade():
-    op.create_table('dds_projects',
-            sa.Column('dds_project_id', sa.String, nullable=False, primary_key=True),
+    op.create_table(
+            'dds_projects',
+            sa.Column(
+                'dds_project_id', sa.String, nullable=False, primary_key=True),
             sa.Column('project_name', sa.String),
             )
 

alembic/versions/8a4cc1553379_decommission_mover.py

@@ -0,0 +1,30 @@
+"""decommission mover
+
+Revision ID: 8a4cc1553379
+Revises: 85082f64ccd0
+Create Date: 2022-06-02 10:35:30.789457
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '8a4cc1553379'
+down_revision = '85082f64ccd0'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    with op.batch_alter_table('delivery_orders') as batch_op:
+        batch_op.drop_column('mover_delivery_id')
+        batch_op.drop_column('md5sum_file')
+        batch_op.alter_column('mover_pid', new_column_name='dds_pid')
+
+
+def downgrade():
+    with op.batch_alter_table('delivery_orders') as batch_op:
+        batch_op.alter_column('dds_pid', new_column_name='mover_pid')
+    op.add_column('delivery_orders', sa.Column('md5sum_file', sa.String(), nullable=True))
+    op.add_column('delivery_orders', sa.Column('mover_delivery_id', sa.String(), nullable=True))

config/app.config

@@ -8,7 +8,6 @@ runfolder_directory: tests/resources/runfolders
 general_project_directory: tests/resources/projects
 staging_directory: /tmp/
 project_links_directory: /tmp/
-path_to_mover: '/usr/local/mover/1.0.0/'
 dds_conf:
   log_path: dds.log
 port: 9999

delivery/app.py

@@ -25,12 +25,11 @@
     FileSystemBasedUnorganisedRunfolderRepository
 from delivery.repositories.staging_repository import DatabaseBasedStagingRepository
 from delivery.repositories.deliveries_repository import DatabaseBasedDeliveriesRepository
-from delivery.repositories.project_repository import GeneralProjectRepository, UnorganisedRunfolderProjectRepository, DDSProjectRepository
+from delivery.repositories.project_repository import GeneralProjectRepository, UnorganisedRunfolderProjectRepository
 from delivery.repositories.delivery_sources_repository import DatabaseBasedDeliverySourcesRepository
 from delivery.repositories.sample_repository import RunfolderProjectBasedSampleRepository
 
 
-from delivery.services.mover_service import MoverDeliveryService
 from delivery.services.dds_service import DDSService
 from delivery.services.external_program_service import ExternalProgramService
 from delivery.services.staging_service import StagingService
@@ -100,16 +99,17 @@ def create_and_migrate_db(db_engine, alembic_path, db_connection_string):
 
 def compose_application(config):
     """
-    Instantiates all service, repos, etc which are then used by the application.
-    The resulting dictionary can then be passed on to routes which instantiates the
-    http handlers.
+    Instantiates all service, repos, etc which are then used by the
+    application.  The resulting dictionary can then be passed on to routes
+    which instantiates the http handlers.
     :param config: a configuration instance
     :return: a dictionary with references to any relevant resources
     """
 
     def _assert_is_dir(directory):
         if not FileSystemService.isdir(directory):
-            raise AssertionError("{} is not a directory".format(os.path.abspath(directory)))
+            raise AssertionError(
+                    "{} is not a directory".format(os.path.abspath(directory)))
 
     staging_dir = config['staging_directory']
     _assert_is_dir(staging_dir)
@@ -132,7 +132,8 @@ def _assert_is_dir(directory):
     general_project_dir = config['general_project_directory']
     _assert_is_dir(general_project_dir)
 
-    general_project_repo = GeneralProjectRepository(root_directory=general_project_dir)
+    general_project_repo = GeneralProjectRepository(
+            root_directory=general_project_dir)
     external_program_service = ExternalProgramService()
 
     db_connection_string = config["db_connection_string"]
@@ -144,46 +145,45 @@ def _assert_is_dir(directory):
     session_factory = scoped_session(sessionmaker())
     session_factory.configure(bind=engine)
 
-    staging_repo = DatabaseBasedStagingRepository(session_factory=session_factory)
+    staging_repo = DatabaseBasedStagingRepository(
+            session_factory=session_factory)
 
-    staging_service = StagingService(external_program_service=external_program_service,
-                                     runfolder_repo=runfolder_repo,
-                                     project_dir_repo=general_project_repo,
-                                     staging_repo=staging_repo,
-                                     staging_dir=staging_dir,
-                                     project_links_directory=project_links_directory,
-                                     session_factory=session_factory)
+    staging_service = StagingService(
+            external_program_service=external_program_service,
+            runfolder_repo=runfolder_repo,
+            project_dir_repo=general_project_repo,
+            staging_repo=staging_repo,
+            staging_dir=staging_dir,
+            project_links_directory=project_links_directory,
+            session_factory=session_factory)
 
-    delivery_repo = DatabaseBasedDeliveriesRepository(session_factory=session_factory)
-
-    path_to_mover = config['path_to_mover']
-    mover_delivery_service = MoverDeliveryService(external_program_service=external_program_service,
-                                                  staging_service=staging_service,
-                                                  delivery_repo=delivery_repo,
-                                                  session_factory=session_factory,
-                                                  path_to_mover=path_to_mover)
+    delivery_repo = DatabaseBasedDeliveriesRepository(
+            session_factory=session_factory)
 
     dds_conf = config['dds_conf']
-    dds_project_repo = DDSProjectRepository(session_factory=session_factory)
-    dds_service = DDSService(external_program_service=external_program_service,
-                                                  staging_service=staging_service,
-                                                  staging_dir=staging_dir,
-                                                  delivery_repo=delivery_repo,
-                                                  dds_project_repo=dds_project_repo,
-                                                  session_factory=session_factory,
-                                                  dds_conf=dds_conf)
-
-    delivery_sources_repo = DatabaseBasedDeliverySourcesRepository(session_factory=session_factory)
+    dds_service = DDSService(
+            external_program_service=external_program_service,
+            staging_service=staging_service,
+            staging_dir=staging_dir,
+            delivery_repo=delivery_repo,
+            session_factory=session_factory,
+            dds_conf=dds_conf)
+
+    delivery_sources_repo = DatabaseBasedDeliverySourcesRepository(
+            session_factory=session_factory)
+
     runfolder_service = RunfolderService(runfolder_repo)
 
-    delivery_service = DeliveryService(mover_service=mover_delivery_service,
-                                       staging_service=staging_service,
-                                       delivery_sources_repo=delivery_sources_repo,
-                                       general_project_repo=general_project_repo,
-                                       runfolder_service=runfolder_service,
-                                       project_links_directory=project_links_directory)
+    delivery_service = DeliveryService(
+            dds_service=dds_service,
+            staging_service=staging_service,
+            delivery_sources_repo=delivery_sources_repo,
+            general_project_repo=general_project_repo,
+            runfolder_service=runfolder_service,
+            project_links_directory=project_links_directory)
 
-    best_practice_analysis_service = BestPracticeAnalysisService(general_project_repo)
+    best_practice_analysis_service = BestPracticeAnalysisService(
+            general_project_repo)
 
     organise_service = OrganiseService(
         runfolder_service=RunfolderService(unorganised_runfolder_repo))
@@ -192,7 +192,6 @@ def _assert_is_dir(directory):
                 runfolder_repo=runfolder_repo,
                 external_program_service=external_program_service,
                 staging_service=staging_service,
-                mover_delivery_service=mover_delivery_service,
                 dds_service=dds_service,
                 delivery_service=delivery_service,
                 general_project_repo=general_project_repo,

delivery/exceptions.py

@@ -2,21 +2,22 @@
 
 class RunfolderNotFoundException(Exception):
     """
-    Should be raised when a runfolder is not found
+    Should be raised when a runfolder is not found.
     """
     pass
 
 
 class ChecksumNotFoundException(Exception):
     """
-    Should be raised when a file checksum could not be found in the list of checksums
+    Should be raised when a file checksum could not be found in the list of
+    checksums.
     """
     pass
 
 
 class ChecksumFileNotFoundException(Exception):
     """
-    Should be raised when an expected checksum file could not be found
+    Should be raised when an expected checksum file could not be found.
     """
     pass
 
@@ -37,22 +38,16 @@ class ProjectReportNotFoundException(Exception):
 
 class TooManyProjectsFound(Exception):
     """
-    Should be raise when to many projects match some specific criteria
+    Should be raise when to many projects match some specific criteria.
     """
     pass
 
 
 class InvalidStatusException(Exception):
     """
-    Should be raised when an object is found to be in a invalid state, e.g. if the program tries to start staging
-    on a StagingOrder which is already `in_progress`
-    """
-    pass
-
-
-class CannotParseMoverOutputException(Exception):
-    """
-    Should be raised when movers output cannot be parsed for e.g. a mover delivery id.
+    Should be raised when an object is found to be in a invalid state, e.g. if
+    the program tries to start staging on a StagingOrder which is already
+    `in_progress`.
     """
     pass
 
@@ -81,12 +76,14 @@ class SamplesheetNotFoundException(Exception):
 
 class ProjectsDirNotfoundException(Exception):
     """
-    Should be raised when a directory containing projects could not be found
+    Should be raised when a directory containing projects could not be found.
     """
     pass
 
+
 class CannotParseDDSOutputException(Exception):
     """
-    Should be raised when DDS's output cannot be parsed for e.g. creating a project.
+    Should be raised when DDS's output cannot be parsed for e.g. creating a
+    project.
     """
     pass

delivery/handlers/dds_handlers.py

@@ -2,6 +2,7 @@
 
 from delivery.handlers import *
 from delivery.handlers.utility_handlers import ArteriaDeliveryBaseHandler
+from delivery.models.project import DDSProject
 
 import os
 import tempfile
@@ -50,20 +51,11 @@ async def post(self, project_name):
         project_metadata = self.body_as_object(
                 required_members=required_members)
 
-        with tempfile.NamedTemporaryFile(mode='w', delete=True) as token_file:
-            if os.path.exists(project_metadata["auth_token"]):
-                token_path = project_metadata["auth_token"]
-            else:
-                token_file.write(project_metadata["auth_token"])
-                token_file.flush()
-
-                token_path = token_file.name
-
-            dds_project_id = await self.dds_service.create_dds_project(
-                    project_name,
-                    project_metadata,
-                    token_path,
-                    )
+        dds_project = await DDSProject.new(
+                project_name,
+                project_metadata,
+                project_metadata["auth_token"],
+                self.dds_service)
 
         self.set_status(ACCEPTED)
-        self.write_json({'dds_project_id': dds_project_id})
+        self.write_json({'dds_project_id': dds_project.project_id})