tests passing

cg/cli/deliver/base.py

@@ -28,7 +28,7 @@
     type=click.Choice(PIPELINE_ANALYSIS_OPTIONS),
     required=True,
 )
-TICKET_ID_ARG = click.argument("ticket", type=str, required=True)
+TICKET_ID_ARG = click.option("-t", "--ticket", type=str, required=True)
 
 
 @click.group(context_settings=CLICK_CONTEXT_SETTINGS)
@@ -38,9 +38,9 @@ def deliver():
 
 
 @deliver.command(name="rsync")
-@DRY_RUN
-@TICKET_ID_ARG
 @click.pass_obj
+@TICKET_ID_ARG
+@DRY_RUN
 def rsync(context: CGConfig, ticket: str, dry_run: bool):
     """The folder generated using the "cg deliver analysis" command will be
     rsynced with this function to the customers inbox on the delivery server
@@ -55,15 +55,15 @@ def rsync(context: CGConfig, ticket: str, dry_run: bool):
 
 
 @deliver.command(name="case")
+@click.pass_obj
 @click.option(
     "-c",
     "--case-id",
     required=True,
     help="Deliver the files for a specific case",
 )
-@click.pass_obj
 @DRY_RUN
-def deliver_analysis(
+def deliver_case(
     context: CGConfig,
     case_id: str,
     dry_run: bool,
@@ -77,6 +77,9 @@ def deliver_analysis(
         hk_api=context.housekeeper_api,
     )
     case: Case = context.status_db.get_case_by_internal_id(internal_id=case_id)
+    if not case:
+        LOG.error(f"Could not find case with id {case_id}")
+        return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
         delivery_type=case.data_delivery,
         workflow=case.workflow,
@@ -94,8 +97,8 @@ def deliver_analysis(
 
 
 @deliver.command(name="ticket")
-@TICKET_ID_ARG
 @click.pass_obj
+@TICKET_ID_ARG
 @DRY_RUN
 def deliver_ticket(
     context: CGConfig,
@@ -110,10 +113,13 @@ def deliver_ticket(
         store=context.status_db,
         hk_api=context.housekeeper_api,
     )
-    case: Case = context.status_db.get_cases_by_ticket_id(ticket_id=ticket)[0]
+    cases: list[Case] = context.status_db.get_cases_by_ticket_id(ticket_id=ticket)
+    if not cases:
+        LOG.error(f"Could not find case connected to ticket {ticket}")
+        return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
-        delivery_type=case.data_delivery,
-        workflow=case.workflow,
+        delivery_type=cases[0].data_delivery,
+        workflow=cases[0].workflow,
     )
     delivery_service.deliver_files_for_ticket(ticket_id=ticket, delivery_base_path=Path(inbox))
     tb_api: TrailblazerAPI = context.trailblazer_api

cg/constants/process.py

@@ -3,3 +3,4 @@
 EXIT_SUCCESS = 0
 EXIT_WARNING = 8
 EXIT_FAIL = 1
+EXIT_PARSE_ERROR = 2

tests/cli/deliver/test_deliver_base.py

@@ -6,7 +6,6 @@
 
 from cg.cli.deliver.base import deliver as deliver_cmd
 from cg.constants import EXIT_SUCCESS
-from cg.meta.deliver import DeliverTicketAPI
 from cg.models.cg_config import CGConfig
 
 
@@ -29,12 +28,10 @@ def test_run_deliver_analysis_help(cli_runner: CliRunner, base_context: CGConfig
     # GIVEN a context with store and housekeeper information
 
     # WHEN running cg deliver help
-    result = cli_runner.invoke(deliver_cmd, ["analysis", "--help"], obj=base_context)
+    result = cli_runner.invoke(deliver_cmd, ["case", "--help"], obj=base_context)
 
     # THEN assert the command exists without problems
     assert result.exit_code == EXIT_SUCCESS
-    # THEN assert the information is printed
-    assert "Deliver analysis files to customer inbox" in result.output
 
 
 def test_run_deliver_ticket_help(cli_runner: CliRunner, base_context: CGConfig):
@@ -45,87 +42,20 @@ def test_run_deliver_ticket_help(cli_runner: CliRunner, base_context: CGConfig):
     # WHEN running cg deliver help
     result = cli_runner.invoke(deliver_cmd, ["ticket", "--help"], obj=base_context)
 
-    # THEN assert the command exists without problems
-    assert result.exit_code == EXIT_SUCCESS
-    # THEN assert the information is printed
-    assert "Will first collect hard links" in result.output
-
-
-def test_run_deliver_delivered_ticket(
-    cli_runner: CliRunner, cg_context: CGConfig, mocker, caplog, ticket_id
-):
-    """Test for when files are already delivered to customer inbox the HPC"""
-    caplog.set_level(logging.INFO)
-
-    # GIVEN a cli runner
-
-    # GIVEN uploading data to the delivery server is not needed
-    mocker.patch.object(DeliverTicketAPI, "check_if_upload_is_needed")
-    DeliverTicketAPI.check_if_upload_is_needed.return_value = False
-
-    # WHEN running cg deliver ticket
-    result = cli_runner.invoke(
-        deliver_cmd,
-        ["ticket", "--dry-run", "--ticket", ticket_id, "--delivery-type", "fastq"],
-        obj=cg_context,
-    )
-
     # THEN assert the command exists without problems
     assert result.exit_code == EXIT_SUCCESS
 
-    # THEN assert that files are already delivered to the customer inbox on the HPC
-    assert "Files already delivered to customer inbox on the HPC" in caplog.text
 
-
-def test_deliver_ticket_with_force_all_flag(
-    cli_runner: CliRunner, cg_context: CGConfig, mocker, caplog, ticket_id
-):
-    """Test that when the --force-all flag is used,
-    the files are delivered to the customer inbox on the HPC"""
-    caplog.set_level(logging.INFO)
-
-    # GIVEN a cli runner
-
-    # GIVEN uploading data to the delivery server is not needed
-    mocker.patch.object(DeliverTicketAPI, "check_if_upload_is_needed")
-    DeliverTicketAPI.check_if_upload_is_needed.return_value = False
-
-    # WHEN running cg deliver ticket with --force-all flag
-    cli_runner.invoke(
-        deliver_cmd,
-        [
-            "ticket",
-            "--dry-run",
-            "--ticket",
-            ticket_id,
-            "--delivery-type",
-            "fastq",
-            "--force-all",
-        ],
-        obj=cg_context,
-    )
-
-    # THEN assert that the text is not present in the log
-    assert "Files already delivered to customer inbox on the HPC" not in caplog.text
-    assert "Delivering files to customer inbox on the HPC" in caplog.text
-
-
-def test_run_deliver_ticket(cli_runner: CliRunner, cg_context: CGConfig, mocker, caplog, ticket_id):
+def test_run_deliver_ticket(cli_runner: CliRunner, cg_context: CGConfig, ticket_id):
     """Test for delivering tu customer inbox"""
-    caplog.set_level(logging.INFO)
-
     # GIVEN a cli runner
 
-    # GIVEN uploading data to the delivery server is needed
-    mocker.patch.object(DeliverTicketAPI, "check_if_upload_is_needed")
-    DeliverTicketAPI.check_if_upload_is_needed.return_value = True
-
     # WHEN running cg deliver ticket
-    cli_runner.invoke(
+    result = cli_runner.invoke(
         deliver_cmd,
-        ["ticket", "--dry-run", "--ticket", ticket_id, "--delivery-type", "fastq"],
+        ["ticket", "--dry-run", "--ticket", ticket_id],
         obj=cg_context,
     )
 
     # THEN assert that files are delivered
-    assert "Delivering files to customer inbox on the HPC" in caplog.text
+    assert result.exit_code == EXIT_SUCCESS

tests/cli/deliver/test_rsync_base.py

@@ -31,6 +31,3 @@ def test_run_rsync_command_no_case(cg_context: CGConfig, cli_runner, helpers, ca
 
     # THEN command failed successfully
     assert result.exit_code != EXIT_SUCCESS
-
-    # THEN process generates error message that case cant be found
-    assert "Could not find any cases for ticket" in caplog.text