From 8f04e9b0384322b685176fb82d0883aeff8c5a74 Mon Sep 17 00:00:00 2001
From: nkongenely <nkongenely94@gmil.com>
Date: Mon, 16 Sep 2024 09:52:52 +0300
Subject: [PATCH 01/12] Testing

---
 .python-version                                |   1 +
 delivery/handlers/staging_handlers.py          |   2 +-
 delivery/services/delivery_service.py          |   4 ++++
 delivery/services/organise_service.py          |   8 ++++++--
 delivery/services/staging_service.py           |  11 +++++++++--
 tests/integration_tests/base.py                |   4 +++-
 tests/integration_tests/test_integration.py    |   1 +
 .../integration_tests/test_integration_dds.py  |  12 ++++++------
 tests/resources/readme/README.md               | Bin 985 -> 1024 bytes
 .../MD5/checksums.md5                          |   0
 .../Projects/XYZ_123/test_file                 | Bin 0 -> 1024 bytes
 .../ABC_123/test_file                          | Bin 0 -> 1024 bytes
 .../ABC_123/test_file                          | Bin 0 -> 1024 bytes
 .../test_file                                  | Bin 0 -> 1024 bytes
 14 files changed, 31 insertions(+), 12 deletions(-)
 create mode 100644 .python-version
 create mode 100644 tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/MD5/checksums.md5
 create mode 100644 tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/Projects/XYZ_123/test_file
 create mode 100644 tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/Projects/ABC_123/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/ABC_123/test_file
 create mode 100644 tests/resources/runfolders/160930_ST-E00216_0556_BH37CWALXX_be6y0p1m/Projects/ABC_123/160930_ST-E00216_0556_BH37CWALXX_be6y0p1m/ABC_123/test_file
 create mode 100644 tests/resources/runfolders/160930_ST-E00216_0556_BH37CWALXX_jugr4wkp/Projects/XYZ_123/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/test_file

diff --git a/.python-version b/.python-version
new file mode 100644
index 0000000..66fa45e
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+arteria_delivery
diff --git a/delivery/handlers/staging_handlers.py b/delivery/handlers/staging_handlers.py
index 877d4a2..efada52 100644
--- a/delivery/handlers/staging_handlers.py
+++ b/delivery/handlers/staging_handlers.py
@@ -30,7 +30,7 @@ def _construct_response_from_project_and_status(self, staging_order_projects_and
 
         return link_results, id_results
 
-
+ 
 class StagingProjectRunfoldersHandler(BaseStagingHandler):
     """
     Handler class for handling how to start staging of runfolders belonging to a project. Polling for status,
diff --git a/delivery/services/delivery_service.py b/delivery/services/delivery_service.py
index d09c968..9a398d4 100644
--- a/delivery/services/delivery_service.py
+++ b/delivery/services/delivery_service.py
@@ -71,6 +71,9 @@ def _create_links_area_for_project_runfolders(self, project_name, projects, batc
         :param batch_nbr: which batch of deliveries of this project this corresponds to
         :return: the path to the dir created
         """
+        path = os.path.join(self.project_links_directory, project_name)
+        list_dir = [(x[0], os.listdir(x[0])) for x in os.walk(path)]
+        print(f"logging... delivery_service _create_links_area_for_project_runfolders path = {path}...list= {list_dir} ")
 
         project_dir = os.path.join(self.project_links_directory, project_name, str(batch_nbr))
         try:
@@ -184,6 +187,7 @@ def deliver_all_runfolders_for_project(self, project_name, mode):
                                                           batch_nbr=batch_nbr)
 
         self.delivery_sources_repo.add_source(source)
+        print(f"logging... delivery_service deliver_all_runfolders_for_project path = {source}...project_name= {project_name},.. source_name= {project_name}/batch{batch_nbr}, links_directory= {links_directory} ")
 
         stage_order = self.staging_service.create_new_stage_order(path=source.path, project_name=project_name)
         self.staging_service.stage_order(stage_order)
diff --git a/delivery/services/organise_service.py b/delivery/services/organise_service.py
index 49f927b..b39a951 100644
--- a/delivery/services/organise_service.py
+++ b/delivery/services/organise_service.py
@@ -29,7 +29,7 @@ def __init__(self, runfolder_service, file_system_service=FileSystemService()):
         """
         self.runfolder_service = runfolder_service
         self.file_system_service = file_system_service
-
+ 
     def organise_runfolder(self, runfolder_id, lanes, projects, force):
         """
         Organise a runfolder in preparation for delivery. This will create separate subdirectories for each of the
@@ -116,6 +116,7 @@ def organise_project(
                     organised_project_runfolder_path,
                     lanes))
         # symlink the project files
+        
         organised_project_files = []
         if project.project_files:
             for project_file in project.project_files:
@@ -147,7 +148,7 @@ def organise_project_file(self, project_file, organised_project_path):
         before organisation
         :param organised_project_path: path where the project will be organised
         """
-
+        
         # the relative path from the project file base to the project file (e.g. plots/filename.png)
         relpath = self.file_system_service.relpath(
             project_file.file_path,
@@ -162,6 +163,9 @@ def organise_project_file(self, project_file, organised_project_path):
 
         # copy the source file to the organised file destination
         self.file_system_service.copy(project_file.file_path, destination)
+        print(f"logging... organise_project_file destination = {destination}")
+        log.info(f"logging... organise_project_file destination = {destination}")
+        breakpoint()
 
         # return a new RunFolder file object representing the organised file at its new location
         return RunfolderFile(
diff --git a/delivery/services/staging_service.py b/delivery/services/staging_service.py
index 0052487..848a3ef 100644
--- a/delivery/services/staging_service.py
+++ b/delivery/services/staging_service.py
@@ -88,6 +88,8 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
         staging_order = staging_repo.get_staging_order_by_id(staging_order_id, session)
         try:
             staging_source_with_trailing_slash = staging_order.source + "/"
+            # runfolders_for_projects = 
+            # print(f"logging... _copy_dir os.readlink = {os.readlink(staging_source_with_trailing_slash)}")
             cmd = ['rsync', '--stats', '-r', '--copy-links', '--times',
                    staging_source_with_trailing_slash, staging_order.staging_target]
             log.debug("Running rsync with command: {}".format(" ".join(cmd)))
@@ -99,6 +101,10 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
 
             execution_result = yield external_program_service.wait_for_execution(execution)
             log.debug("Execution result: {}".format(execution_result))
+            staging_target = [(x[0], os.listdir(x[0])) for x in os.walk(staging_order.staging_target)]
+            print(f"logging... _copy_dir os.walk staging_order.staging_source_with_trailing_slash = {staging_source_with_trailing_slash}")
+            log.info(f"logging... _copy_dir os.walk staging_order.staging_target = {staging_target}")
+            breakpoint()
             if execution_result.status_code == 0:
 
                 # Parse the file size from the output of rsync stats:
@@ -149,10 +155,10 @@ def stage_order(self, stage_order):
                                  "external_program_service": self.external_program_service,
                                  "staging_repo": self.staging_repo,
                                  "session_factory": self.session_factory}
-
+            print(f"logging... staging_service stage_order stage_order.staging_target before = {stage_order.staging_target}")
             if not self.file_system_service.exists(stage_order.staging_target):
                 self.file_system_service.makedirs(stage_order.staging_target)
-
+            print(f"logging... staging_service stage_order stage_order.staging_target after = {stage_order.staging_target}")
             yield StagingService._copy_dir(**args_for_copy_dir)
 
         # TODO Better error handling
@@ -162,6 +168,7 @@ def stage_order(self, stage_order):
             raise e
 
     def create_new_stage_order(self, path, project_name):
+        print(f"logging... staging_service create_new_stage_order path = {path}......staging_dir = {self.staging_dir}")
         staging_order = self.staging_repo.create_staging_order(source=path,
                                                                status=StagingStatus.pending,
                                                                staging_target_dir=self.staging_dir,
diff --git a/tests/integration_tests/base.py b/tests/integration_tests/base.py
index 13cbbcf..835469d 100644
--- a/tests/integration_tests/base.py
+++ b/tests/integration_tests/base.py
@@ -30,8 +30,10 @@ def __init__(self, *args):
         # Default duration of mock delivery
         self.mock_duration = 0.1
 
-    def _create_projects_dir_with_random_data(self, base_dir, proj_name='ABC_123'):
+    def _create_projects_dir_with_random_data(self, base_dir, proj_name='ABC_123', runfolder_name=None):
         tmp_proj_dir = os.path.join(base_dir, 'Projects', proj_name)
+        if runfolder_name:
+            tmp_proj_dir = os.path.join(tmp_proj_dir, runfolder_name, proj_name)
         os.makedirs(tmp_proj_dir)
         with open(os.path.join(tmp_proj_dir, 'test_file'), 'wb') as f:
             f.write(os.urandom(1024))
diff --git a/tests/integration_tests/test_integration.py b/tests/integration_tests/test_integration.py
index a5ec4d9..4b5ed3a 100644
--- a/tests/integration_tests/test_integration.py
+++ b/tests/integration_tests/test_integration.py
@@ -52,6 +52,7 @@ def test_can_return_projects(self):
 
     def test_can_organise_project(self):
         runfolder = unorganised_runfolder()
+        breakpoint()
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                          prefix="{}_".format(runfolder.name)) as runfolder_path:
             runfolder = unorganised_runfolder(
diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 7234440..bcd3952 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -174,14 +174,14 @@ def test_can_stage_and_deliver_batch_flowcells(self):
     @gen_test
     def test_can_stage_and_deliver_force_flowcells(self):
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
-                                         prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
+                                       prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
                 tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                             prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
-            self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123')
-            self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123')
-
+            self._create_projects_dir_with_random_data(tmpdir1, 'ABC_123', ("").join(tmpdir1.split("/")[-1]))
+            self._create_projects_dir_with_random_data(tmpdir2, 'ABC_123', ("").join(tmpdir2.split("/")[-1]))
+            # breakpoint()
             # First just stage it
-            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'XYZ_123'])
+            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'ABC_123'])
             payload = {'delivery_mode': 'BATCH'}
             response = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
             self.assertEqual(response.code, 202)
@@ -204,7 +204,7 @@ def test_can_stage_and_deliver_force_flowcells(self):
             time.sleep(1)
 
             for project, link in staging_status_links.items():
-                self.assertEqual(project, 'XYZ_123')
+                self.assertEqual(project, 'ABC_123')
 
                 status_response = yield self.http_client.fetch(link)
                 self.assertEqual(json.loads(status_response.body)["status"], StagingStatus.staging_successful.name)
diff --git a/tests/resources/readme/README.md b/tests/resources/readme/README.md
index a31412e28f296002568453f83f42b4041a83042a..646621891922500045bce0033f520e09700230f5 100644
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diff --git a/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/MD5/checksums.md5 b/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/MD5/checksums.md5
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diff --git a/tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/Projects/ABC_123/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/ABC_123/test_file b/tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/Projects/ABC_123/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/ABC_123/test_file
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diff --git a/tests/resources/runfolders/160930_ST-E00216_0556_BH37CWALXX_jugr4wkp/Projects/XYZ_123/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/test_file b/tests/resources/runfolders/160930_ST-E00216_0556_BH37CWALXX_jugr4wkp/Projects/XYZ_123/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/test_file
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literal 0
HcmV?d00001


From 6c1d85c997c7736e3e2d72831244b04f0175dd4b Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Mon, 16 Sep 2024 14:25:27 +0200
Subject: [PATCH 02/12] DATAOPS-467:Removed_extra_runfolder

---
 .python-version                               |   1 -
 delivery/services/delivery_service.py         |  15 +++++++------
 delivery/services/organise_service.py         |   3 ---
 delivery/services/staging_service.py          |  20 +++++-------------
 tests/integration_tests/base.py               |   2 +-
 tests/integration_tests/test_integration.py   |   2 +-
 .../integration_tests/test_integration_dds.py |  12 ++++++-----
 .../MD5/checksums.md5                         |   0
 .../Projects/ABC_123/test_file                |   1 -
 .../Projects/XYZ_123/test_file                | Bin 1024 -> 0 bytes
 .../ABC_123/test_file                         | Bin 1024 -> 0 bytes
 .../ABC_123/test_file                         | Bin 1024 -> 0 bytes
 .../test_file                                 | Bin 1024 -> 0 bytes
 13 files changed, 22 insertions(+), 34 deletions(-)
 delete mode 100644 .python-version
 delete mode 100644 tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/MD5/checksums.md5
 delete mode 100644 tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
 delete mode 100644 tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/Projects/XYZ_123/test_file
 delete mode 100644 tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/Projects/ABC_123/160930_ST-E00216_0555_BH37CWALXX_z2l4kn_0/ABC_123/test_file
 delete mode 100644 tests/resources/runfolders/160930_ST-E00216_0556_BH37CWALXX_be6y0p1m/Projects/ABC_123/160930_ST-E00216_0556_BH37CWALXX_be6y0p1m/ABC_123/test_file
 delete mode 100644 tests/resources/runfolders/160930_ST-E00216_0556_BH37CWALXX_jugr4wkp/Projects/XYZ_123/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/test_file

diff --git a/.python-version b/.python-version
deleted file mode 100644
index 66fa45e..0000000
--- a/.python-version
+++ /dev/null
@@ -1 +0,0 @@
-arteria_delivery
diff --git a/delivery/services/delivery_service.py b/delivery/services/delivery_service.py
index 9a398d4..f720878 100644
--- a/delivery/services/delivery_service.py
+++ b/delivery/services/delivery_service.py
@@ -71,9 +71,6 @@ def _create_links_area_for_project_runfolders(self, project_name, projects, batc
         :param batch_nbr: which batch of deliveries of this project this corresponds to
         :return: the path to the dir created
         """
-        path = os.path.join(self.project_links_directory, project_name)
-        list_dir = [(x[0], os.listdir(x[0])) for x in os.walk(path)]
-        print(f"logging... delivery_service _create_links_area_for_project_runfolders path = {path}...list= {list_dir} ")
 
         project_dir = os.path.join(self.project_links_directory, project_name, str(batch_nbr))
         try:
@@ -85,7 +82,13 @@ def _create_links_area_for_project_runfolders(self, project_name, projects, batc
         for project in projects:
             try:
                 link_name = os.path.join(project_dir, project.runfolder_name)
-                self.file_system_service.symlink(project.path, link_name)
+                project_path = project.path
+                if (
+                    os.path.exists(runfolder_path := os.path.join(project.path, project.runfolder_name)) and 
+                    len(os.listdir(project_path)) == 1
+                ):
+                    project_path = runfolder_path
+                self.file_system_service.symlink(project_path, link_name)
             except FileExistsError as e:
                 log.error("Project link: {} already exists".format(project_dir))
                 raise e
@@ -132,7 +135,7 @@ def _get_projects_to_deliver(self, projects, mode, batch_nbr):
                     raise NotImplementedError("This is not a valid state, delivery mode needs to be CLEAN/"
                                               "BATCH/FORCE.")
 
-    def deliver_all_runfolders_for_project(self, project_name, mode):
+    def deliver_all_runfolders_for_project(self, project_name, mode, request_url=None):
         """
         This method will attempt to deliver all runfolders for the specified
         project.
@@ -187,8 +190,6 @@ def deliver_all_runfolders_for_project(self, project_name, mode):
                                                           batch_nbr=batch_nbr)
 
         self.delivery_sources_repo.add_source(source)
-        print(f"logging... delivery_service deliver_all_runfolders_for_project path = {source}...project_name= {project_name},.. source_name= {project_name}/batch{batch_nbr}, links_directory= {links_directory} ")
-
         stage_order = self.staging_service.create_new_stage_order(path=source.path, project_name=project_name)
         self.staging_service.stage_order(stage_order)
         return {source.project_name: stage_order.id}, projects_to_deliver
diff --git a/delivery/services/organise_service.py b/delivery/services/organise_service.py
index b39a951..7754e0a 100644
--- a/delivery/services/organise_service.py
+++ b/delivery/services/organise_service.py
@@ -163,9 +163,6 @@ def organise_project_file(self, project_file, organised_project_path):
 
         # copy the source file to the organised file destination
         self.file_system_service.copy(project_file.file_path, destination)
-        print(f"logging... organise_project_file destination = {destination}")
-        log.info(f"logging... organise_project_file destination = {destination}")
-        breakpoint()
 
         # return a new RunFolder file object representing the organised file at its new location
         return RunfolderFile(
diff --git a/delivery/services/staging_service.py b/delivery/services/staging_service.py
index 848a3ef..bd5ebfd 100644
--- a/delivery/services/staging_service.py
+++ b/delivery/services/staging_service.py
@@ -88,30 +88,22 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
         staging_order = staging_repo.get_staging_order_by_id(staging_order_id, session)
         try:
             staging_source_with_trailing_slash = staging_order.source + "/"
-            # runfolders_for_projects = 
-            # print(f"logging... _copy_dir os.readlink = {os.readlink(staging_source_with_trailing_slash)}")
             cmd = ['rsync', '--stats', '-r', '--copy-links', '--times',
                    staging_source_with_trailing_slash, staging_order.staging_target]
-            log.debug("Running rsync with command: {}".format(" ".join(cmd)))
-
             execution = external_program_service.run(cmd)
 
             staging_order.pid = execution.pid
             session.commit()
 
             execution_result = yield external_program_service.wait_for_execution(execution)
-            log.debug("Execution result: {}".format(execution_result))
-            staging_target = [(x[0], os.listdir(x[0])) for x in os.walk(staging_order.staging_target)]
-            print(f"logging... _copy_dir os.walk staging_order.staging_source_with_trailing_slash = {staging_source_with_trailing_slash}")
-            log.info(f"logging... _copy_dir os.walk staging_order.staging_target = {staging_target}")
-            breakpoint()
+
             if execution_result.status_code == 0:
 
                 # Parse the file size from the output of rsync stats:
                 # Total file size: 207,707,566 bytes
                 match = re.search(r'Total file size: ([\d,]+) bytes',
-                                  execution_result.stdout,
-                                  re.MULTILINE)
+                                execution_result.stdout,
+                                re.MULTILINE)
                 size_of_transfer = match.group(1)
                 size_of_transfer = int(size_of_transfer.replace(",", ""))
                 staging_order.size = size_of_transfer
@@ -121,7 +113,7 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
             else:
                 staging_order.status = StagingStatus.staging_failed
                 log.error("Failed in staging: {} because rsync returned exit code: {}".
-                         format(staging_order, execution_result.status_code))
+                        format(staging_order, execution_result.status_code))
 
         # TODO Better exception handling here...
         except Exception as e:
@@ -155,10 +147,9 @@ def stage_order(self, stage_order):
                                  "external_program_service": self.external_program_service,
                                  "staging_repo": self.staging_repo,
                                  "session_factory": self.session_factory}
-            print(f"logging... staging_service stage_order stage_order.staging_target before = {stage_order.staging_target}")
             if not self.file_system_service.exists(stage_order.staging_target):
                 self.file_system_service.makedirs(stage_order.staging_target)
-            print(f"logging... staging_service stage_order stage_order.staging_target after = {stage_order.staging_target}")
+            
             yield StagingService._copy_dir(**args_for_copy_dir)
 
         # TODO Better error handling
@@ -168,7 +159,6 @@ def stage_order(self, stage_order):
             raise e
 
     def create_new_stage_order(self, path, project_name):
-        print(f"logging... staging_service create_new_stage_order path = {path}......staging_dir = {self.staging_dir}")
         staging_order = self.staging_repo.create_staging_order(source=path,
                                                                status=StagingStatus.pending,
                                                                staging_target_dir=self.staging_dir,
diff --git a/tests/integration_tests/base.py b/tests/integration_tests/base.py
index 835469d..f2942f2 100644
--- a/tests/integration_tests/base.py
+++ b/tests/integration_tests/base.py
@@ -33,7 +33,7 @@ def __init__(self, *args):
     def _create_projects_dir_with_random_data(self, base_dir, proj_name='ABC_123', runfolder_name=None):
         tmp_proj_dir = os.path.join(base_dir, 'Projects', proj_name)
         if runfolder_name:
-            tmp_proj_dir = os.path.join(tmp_proj_dir, runfolder_name, proj_name)
+            tmp_proj_dir = os.path.join(tmp_proj_dir, runfolder_name)
         os.makedirs(tmp_proj_dir)
         with open(os.path.join(tmp_proj_dir, 'test_file'), 'wb') as f:
             f.write(os.urandom(1024))
diff --git a/tests/integration_tests/test_integration.py b/tests/integration_tests/test_integration.py
index 4b5ed3a..277fb0a 100644
--- a/tests/integration_tests/test_integration.py
+++ b/tests/integration_tests/test_integration.py
@@ -52,7 +52,7 @@ def test_can_return_projects(self):
 
     def test_can_organise_project(self):
         runfolder = unorganised_runfolder()
-        breakpoint()
+
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                          prefix="{}_".format(runfolder.name)) as runfolder_path:
             runfolder = unorganised_runfolder(
diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index bcd3952..033d24c 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -1,3 +1,4 @@
+import os
 import json
 import time
 import tempfile
@@ -177,11 +178,12 @@ def test_can_stage_and_deliver_force_flowcells(self):
                                        prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
                 tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                             prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
-            self._create_projects_dir_with_random_data(tmpdir1, 'ABC_123', ("").join(tmpdir1.split("/")[-1]))
-            self._create_projects_dir_with_random_data(tmpdir2, 'ABC_123', ("").join(tmpdir2.split("/")[-1]))
-            # breakpoint()
+
+            self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123', os.path.basename(tmpdir1))
+            self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123', os.path.basename(tmpdir2))
+
             # First just stage it
-            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'ABC_123'])
+            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'XYZ_123'])
             payload = {'delivery_mode': 'BATCH'}
             response = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
             self.assertEqual(response.code, 202)
@@ -204,7 +206,7 @@ def test_can_stage_and_deliver_force_flowcells(self):
             time.sleep(1)
 
             for project, link in staging_status_links.items():
-                self.assertEqual(project, 'ABC_123')
+                self.assertEqual(project, 'XYZ_123')
 
                 status_response = yield self.http_client.fetch(link)
                 self.assertEqual(json.loads(status_response.body)["status"], StagingStatus.staging_successful.name)
diff --git a/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/MD5/checksums.md5 b/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/MD5/checksums.md5
deleted file mode 100644
index e69de29..0000000
diff --git a/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file b/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
deleted file mode 100644
index db11c83..0000000
--- a/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
+++ /dev/null
@@ -1 +0,0 @@
-Test content...
\ No newline at end of file
diff --git a/tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/Projects/XYZ_123/test_file b/tests/resources/runfolders/160930_ST-E00216_0555_BH37CWALXX_tfez43vf/Projects/XYZ_123/test_file
deleted file mode 100644
index 465c233907d512cafc0f023dbbb5f7d0eec7cc2f..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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deleted file mode 100644
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From 5693bf14656f5d50a05899c013abd06595499a7c Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Mon, 16 Sep 2024 14:34:46 +0200
Subject: [PATCH 03/12] Removed unwanted code and cleaned u files

---
 delivery/handlers/staging_handlers.py           |   1 -
 delivery/services/delivery_service.py           |   2 +-
 delivery/services/organise_service.py           |   2 --
 delivery/services/staging_service.py            |  10 +++++-----
 tests/integration_tests/test_integration.py     |   1 -
 tests/integration_tests/test_integration_dds.py |   3 +--
 tests/resources/readme/README.md                | Bin 1024 -> 0 bytes
 7 files changed, 7 insertions(+), 12 deletions(-)
 delete mode 100644 tests/resources/readme/README.md

diff --git a/delivery/handlers/staging_handlers.py b/delivery/handlers/staging_handlers.py
index efada52..7c5529c 100644
--- a/delivery/handlers/staging_handlers.py
+++ b/delivery/handlers/staging_handlers.py
@@ -30,7 +30,6 @@ def _construct_response_from_project_and_status(self, staging_order_projects_and
 
         return link_results, id_results
 
- 
 class StagingProjectRunfoldersHandler(BaseStagingHandler):
     """
     Handler class for handling how to start staging of runfolders belonging to a project. Polling for status,
diff --git a/delivery/services/delivery_service.py b/delivery/services/delivery_service.py
index f720878..5a8f72c 100644
--- a/delivery/services/delivery_service.py
+++ b/delivery/services/delivery_service.py
@@ -135,7 +135,7 @@ def _get_projects_to_deliver(self, projects, mode, batch_nbr):
                     raise NotImplementedError("This is not a valid state, delivery mode needs to be CLEAN/"
                                               "BATCH/FORCE.")
 
-    def deliver_all_runfolders_for_project(self, project_name, mode, request_url=None):
+    def deliver_all_runfolders_for_project(self, project_name, mode):
         """
         This method will attempt to deliver all runfolders for the specified
         project.
diff --git a/delivery/services/organise_service.py b/delivery/services/organise_service.py
index 7754e0a..71ebd66 100644
--- a/delivery/services/organise_service.py
+++ b/delivery/services/organise_service.py
@@ -29,7 +29,6 @@ def __init__(self, runfolder_service, file_system_service=FileSystemService()):
         """
         self.runfolder_service = runfolder_service
         self.file_system_service = file_system_service
- 
     def organise_runfolder(self, runfolder_id, lanes, projects, force):
         """
         Organise a runfolder in preparation for delivery. This will create separate subdirectories for each of the
@@ -148,7 +147,6 @@ def organise_project_file(self, project_file, organised_project_path):
         before organisation
         :param organised_project_path: path where the project will be organised
         """
-        
         # the relative path from the project file base to the project file (e.g. plots/filename.png)
         relpath = self.file_system_service.relpath(
             project_file.file_path,
diff --git a/delivery/services/staging_service.py b/delivery/services/staging_service.py
index bd5ebfd..cc1a1d2 100644
--- a/delivery/services/staging_service.py
+++ b/delivery/services/staging_service.py
@@ -96,14 +96,14 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
             session.commit()
 
             execution_result = yield external_program_service.wait_for_execution(execution)
-
+            log.debug("Execution result: {}".format(execution_result))
             if execution_result.status_code == 0:
 
                 # Parse the file size from the output of rsync stats:
                 # Total file size: 207,707,566 bytes
                 match = re.search(r'Total file size: ([\d,]+) bytes',
-                                execution_result.stdout,
-                                re.MULTILINE)
+                                 execution_result.stdout,
+                                 re.MULTILINE)
                 size_of_transfer = match.group(1)
                 size_of_transfer = int(size_of_transfer.replace(",", ""))
                 staging_order.size = size_of_transfer
@@ -113,7 +113,7 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
             else:
                 staging_order.status = StagingStatus.staging_failed
                 log.error("Failed in staging: {} because rsync returned exit code: {}".
-                        format(staging_order, execution_result.status_code))
+                         format(staging_order, execution_result.status_code))
 
         # TODO Better exception handling here...
         except Exception as e:
@@ -149,7 +149,7 @@ def stage_order(self, stage_order):
                                  "session_factory": self.session_factory}
             if not self.file_system_service.exists(stage_order.staging_target):
                 self.file_system_service.makedirs(stage_order.staging_target)
-            
+
             yield StagingService._copy_dir(**args_for_copy_dir)
 
         # TODO Better error handling
diff --git a/tests/integration_tests/test_integration.py b/tests/integration_tests/test_integration.py
index 277fb0a..a5ec4d9 100644
--- a/tests/integration_tests/test_integration.py
+++ b/tests/integration_tests/test_integration.py
@@ -52,7 +52,6 @@ def test_can_return_projects(self):
 
     def test_can_organise_project(self):
         runfolder = unorganised_runfolder()
-
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                          prefix="{}_".format(runfolder.name)) as runfolder_path:
             runfolder = unorganised_runfolder(
diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 033d24c..6ffb6ff 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -175,10 +175,9 @@ def test_can_stage_and_deliver_batch_flowcells(self):
     @gen_test
     def test_can_stage_and_deliver_force_flowcells(self):
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
-                                       prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
+                                        prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
                 tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                             prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
-
             self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123', os.path.basename(tmpdir1))
             self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123', os.path.basename(tmpdir2))
 
diff --git a/tests/resources/readme/README.md b/tests/resources/readme/README.md
deleted file mode 100644
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GIT binary patch
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ze<LmAly1XD{)(mnP+Tq)5ppF3mORYu{Gk`^maecA{tune3iy~^d87!YVm2QmB4MAM
uFiV-r#Pyfk+a3Exi+2)H>;&9H>yoSO#vHMFxlqb}?1L)cr%eGRWPoSfQwX#G


From 6a033a736ab613b5cd5e1644106251175ab2616b Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Tue, 17 Sep 2024 13:39:02 +0200
Subject: [PATCH 04/12] Code formatting and changes after PR review

---
 .github/workflows/tests.yml                   |  2 +-
 delivery/handlers/staging_handlers.py         |  1 +
 delivery/services/delivery_service.py         |  1 +
 delivery/services/organise_service.py         |  4 +--
 delivery/services/staging_service.py          |  6 +++--
 .../Projects/ABC_123/test_file                |  1 +
 tests/resources/README.md                     | 25 +++++++++++++++++++
 7 files changed, 35 insertions(+), 5 deletions(-)
 create mode 100644 tests/resources/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
 create mode 100644 tests/resources/README.md

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 4bb7172..8fceb34 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,6 +1,6 @@
 name: Run Unit Tests
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build:
diff --git a/delivery/handlers/staging_handlers.py b/delivery/handlers/staging_handlers.py
index 7c5529c..877d4a2 100644
--- a/delivery/handlers/staging_handlers.py
+++ b/delivery/handlers/staging_handlers.py
@@ -30,6 +30,7 @@ def _construct_response_from_project_and_status(self, staging_order_projects_and
 
         return link_results, id_results
 
+
 class StagingProjectRunfoldersHandler(BaseStagingHandler):
     """
     Handler class for handling how to start staging of runfolders belonging to a project. Polling for status,
diff --git a/delivery/services/delivery_service.py b/delivery/services/delivery_service.py
index 5a8f72c..3a5e224 100644
--- a/delivery/services/delivery_service.py
+++ b/delivery/services/delivery_service.py
@@ -190,6 +190,7 @@ def deliver_all_runfolders_for_project(self, project_name, mode):
                                                           batch_nbr=batch_nbr)
 
         self.delivery_sources_repo.add_source(source)
+
         stage_order = self.staging_service.create_new_stage_order(path=source.path, project_name=project_name)
         self.staging_service.stage_order(stage_order)
         return {source.project_name: stage_order.id}, projects_to_deliver
diff --git a/delivery/services/organise_service.py b/delivery/services/organise_service.py
index 71ebd66..25b70af 100644
--- a/delivery/services/organise_service.py
+++ b/delivery/services/organise_service.py
@@ -29,6 +29,7 @@ def __init__(self, runfolder_service, file_system_service=FileSystemService()):
         """
         self.runfolder_service = runfolder_service
         self.file_system_service = file_system_service
+
     def organise_runfolder(self, runfolder_id, lanes, projects, force):
         """
         Organise a runfolder in preparation for delivery. This will create separate subdirectories for each of the
@@ -114,8 +115,7 @@ def organise_project(
                     sample,
                     organised_project_runfolder_path,
                     lanes))
-        # symlink the project files
-        
+        # symlink the project files    
         organised_project_files = []
         if project.project_files:
             for project_file in project.project_files:
diff --git a/delivery/services/staging_service.py b/delivery/services/staging_service.py
index cc1a1d2..7737e4a 100644
--- a/delivery/services/staging_service.py
+++ b/delivery/services/staging_service.py
@@ -90,6 +90,7 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
             staging_source_with_trailing_slash = staging_order.source + "/"
             cmd = ['rsync', '--stats', '-r', '--copy-links', '--times',
                    staging_source_with_trailing_slash, staging_order.staging_target]
+            log.debug("Running rsync with command: {}".format(" ".join(cmd)))
             execution = external_program_service.run(cmd)
 
             staging_order.pid = execution.pid
@@ -102,8 +103,8 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
                 # Parse the file size from the output of rsync stats:
                 # Total file size: 207,707,566 bytes
                 match = re.search(r'Total file size: ([\d,]+) bytes',
-                                 execution_result.stdout,
-                                 re.MULTILINE)
+                                  execution_result.stdout,
+                                  re.MULTILINE)
                 size_of_transfer = match.group(1)
                 size_of_transfer = int(size_of_transfer.replace(",", ""))
                 staging_order.size = size_of_transfer
@@ -147,6 +148,7 @@ def stage_order(self, stage_order):
                                  "external_program_service": self.external_program_service,
                                  "staging_repo": self.staging_repo,
                                  "session_factory": self.session_factory}
+            
             if not self.file_system_service.exists(stage_order.staging_target):
                 self.file_system_service.makedirs(stage_order.staging_target)
 
diff --git a/tests/resources/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file b/tests/resources/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
new file mode 100644
index 0000000..db11c83
--- /dev/null
+++ b/tests/resources/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
@@ -0,0 +1 @@
+Test content...
\ No newline at end of file
diff --git a/tests/resources/README.md b/tests/resources/README.md
new file mode 100644
index 0000000..16318a0
--- /dev/null
+++ b/tests/resources/README.md
@@ -0,0 +1,25 @@
+# DELIVERY OF FASTQ FILES FROM NGI-UPPSALA,THE SNP&SEQ TECHNOLOGY PLATFORM
+
+This delivery includes sequencing data in FASTQ format, a summary report created with MultiQC, checksums and a copy of the sample sheet used for demultiplexing. 
+
+## Delivery structure
+```
+<project>
+└── <runfolder>
+    ├── README.md
+    ├── checksums.md5
+    ├── SampleSheet.csv
+    ├── <runfolder>_<project>_multiqc_report_data.zip
+    ├── <runfolder>_<project>_multiqc_report.html
+    ├── <Sample1 id>
+        ├── <sample1 name>_<sample number>_R1_001.fastq.gz
+        └── <sample1 name>_<sample number>_R2_001.fastq.gz 
+    ├── <Sample2 id>
+        ├── <sample2 name>_<sample number>_R1_001.fastq.gz
+        └── <sample2 name>_<sample number>_R2_001.fastq.gz
+     :
+     :
+    └── <SampleN id>
+        ├── <sampleN name>_<sample number>_R1_001.fastq.gz
+        └── <sampleN name>_<sample number>_R2_001.fastq.gz
+```
\ No newline at end of file

From b59ee2b00ce1817be16e90146fc6f420e28a8690 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Tue, 17 Sep 2024 13:49:44 +0200
Subject: [PATCH 05/12] Refactored code

---
 delivery/services/staging_service.py                            | 2 +-
 .../160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename tests/resources/{ => runfolders}/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file (100%)

diff --git a/delivery/services/staging_service.py b/delivery/services/staging_service.py
index 7737e4a..debfe5f 100644
--- a/delivery/services/staging_service.py
+++ b/delivery/services/staging_service.py
@@ -148,7 +148,7 @@ def stage_order(self, stage_order):
                                  "external_program_service": self.external_program_service,
                                  "staging_repo": self.staging_repo,
                                  "session_factory": self.session_factory}
-            
+
             if not self.file_system_service.exists(stage_order.staging_target):
                 self.file_system_service.makedirs(stage_order.staging_target)
 
diff --git a/tests/resources/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file b/tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
similarity index 100%
rename from tests/resources/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file
rename to tests/resources/runfolders/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123/test_file

From 4ef760350ba287d8d526ea9292f8a2953597d645 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Thu, 19 Sep 2024 15:27:15 +0200
Subject: [PATCH 06/12] Adding integration tests between organise and staging
 serveice

---
 delivery/services/delivery_service.py         | 10 ++----
 .../integration_tests/test_integration_dds.py | 35 +++++++++++++++----
 2 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/delivery/services/delivery_service.py b/delivery/services/delivery_service.py
index 3a5e224..d6d2991 100644
--- a/delivery/services/delivery_service.py
+++ b/delivery/services/delivery_service.py
@@ -82,13 +82,9 @@ def _create_links_area_for_project_runfolders(self, project_name, projects, batc
         for project in projects:
             try:
                 link_name = os.path.join(project_dir, project.runfolder_name)
-                project_path = project.path
-                if (
-                    os.path.exists(runfolder_path := os.path.join(project.path, project.runfolder_name)) and 
-                    len(os.listdir(project_path)) == 1
-                ):
-                    project_path = runfolder_path
-                self.file_system_service.symlink(project_path, link_name)
+                self.file_system_service.symlink(
+                    os.path.join(project.path, project.runfolder_name), link_name
+                )
             except FileExistsError as e:
                 log.error("Project link: {} already exists".format(project_dir))
                 raise e
diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 6ffb6ff..b449831 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -8,7 +8,7 @@
 from delivery.models.db_models import StagingStatus, DeliveryStatus
 
 from tests.integration_tests.base import BaseIntegration
-
+from tests.test_utils import unorganised_runfolder
 
 class TestIntegrationDDS(BaseIntegration):
     @gen_test
@@ -178,11 +178,32 @@ def test_can_stage_and_deliver_force_flowcells(self):
                                         prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
                 tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                             prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
-            self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123', os.path.basename(tmpdir1))
-            self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123', os.path.basename(tmpdir2))
+            # First organise
+            unorganised_runfolder1 = unorganised_runfolder(
+                name=os.path.basename(tmpdir1),
+                root_path=os.path.dirname(tmpdir1))
+            unorganised_runfolder2 = unorganised_runfolder(
+                name=os.path.basename(tmpdir2),
+                root_path=os.path.dirname(tmpdir2))
+            
+            self._create_runfolder_structure_on_disk(unorganised_runfolder1)
+            self._create_runfolder_structure_on_disk(unorganised_runfolder2)
 
-            # First just stage it
-            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'XYZ_123'])
+            url = "/".join([self.API_BASE, "organise", "runfolder", unorganised_runfolder1.name])
+            response1 = yield self.http_client.fetch(self.get_url(url), method='POST', body='')
+
+            self.assertEqual(response1.code, 200)
+
+            response_json1 = json.loads(response1.body)
+
+            url = "/".join([self.API_BASE, "organise", "runfolder", unorganised_runfolder2.name])
+            response2 = yield self.http_client.fetch(self.get_url(url), method='POST', body='')
+            self.assertEqual(response2.code, 200)
+
+            response_json2 = json.loads(response2.body)
+
+            # Then just stage it
+            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'JKL_123'])
             payload = {'delivery_mode': 'BATCH'}
             response = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
             self.assertEqual(response.code, 202)
@@ -200,12 +221,14 @@ def test_can_stage_and_deliver_force_flowcells(self):
             response_json = json.loads(response_forced.body)
 
             staging_status_links = response_json.get("staging_order_links")
+            #TODO: Assert the staged folder structure has only one runfolder folder 
+            print(f"staging_status_links......{staging_status_links}")
 
             # Insert a pause to allow staging to complete
             time.sleep(1)
 
             for project, link in staging_status_links.items():
-                self.assertEqual(project, 'XYZ_123')
+                self.assertEqual(project, 'JKL_123')
 
                 status_response = yield self.http_client.fetch(link)
                 self.assertEqual(json.loads(status_response.body)["status"], StagingStatus.staging_successful.name)

From 6286d01003c798f8ca71491de2448e7ad47b4302 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Fri, 20 Sep 2024 10:41:58 +0200
Subject: [PATCH 07/12] Added test to check runfolders are not duplicated

---
 tests/integration_tests/test_integration_dds.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index b449831..11c652c 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -221,9 +221,13 @@ def test_can_stage_and_deliver_force_flowcells(self):
             response_json = json.loads(response_forced.body)
 
             staging_status_links = response_json.get("staging_order_links")
-            #TODO: Assert the staged folder structure has only one runfolder folder 
-            print(f"staging_status_links......{staging_status_links}")
+            staging_order_ids = response_json.get("staging_order_ids")
 
+            # Assert the staged folder structure has only one runfolder folder
+            temp_staging_dir = f"/tmp/{staging_order_ids.get('JKL_123')}/JKL_123"
+            for runfolder in os.listdir(temp_staging_dir):
+                self.assertFalse(set(runfolder).issuperset(set(os.listdir(f"{temp_staging_dir}/{runfolder}"))))
+            
             # Insert a pause to allow staging to complete
             time.sleep(1)
 

From b3d437cdb355d44088438daefead761b293d08a0 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Fri, 20 Sep 2024 12:30:38 +0200
Subject: [PATCH 08/12] Refactored code

---
 .../integration_tests/test_integration_dds.py | 23 ++++++++-----------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 11c652c..47cf616 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -172,6 +172,12 @@ def test_can_stage_and_deliver_batch_flowcells(self):
                 status_response = yield self.http_client.fetch(link)
                 self.assertEqual(json.loads(status_response.body)["status"], StagingStatus.staging_successful.name)
 
+    def create_unorganised_test_runfolders(self, tmpdir):
+            return(
+                unorganised_runfolder(
+                name=os.path.basename(tmpdir),
+                root_path=os.path.dirname(tmpdir))
+                                                 )
     @gen_test
     def test_can_stage_and_deliver_force_flowcells(self):
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
@@ -179,29 +185,20 @@ def test_can_stage_and_deliver_force_flowcells(self):
                 tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                             prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
             # First organise
-            unorganised_runfolder1 = unorganised_runfolder(
-                name=os.path.basename(tmpdir1),
-                root_path=os.path.dirname(tmpdir1))
-            unorganised_runfolder2 = unorganised_runfolder(
-                name=os.path.basename(tmpdir2),
-                root_path=os.path.dirname(tmpdir2))
+            unorganised_runfolder1 = self.create_unorganised_test_runfolders(tmpdir1)
+            unorganised_runfolder2 = self.create_unorganised_test_runfolders(tmpdir2)
             
             self._create_runfolder_structure_on_disk(unorganised_runfolder1)
             self._create_runfolder_structure_on_disk(unorganised_runfolder2)
 
             url = "/".join([self.API_BASE, "organise", "runfolder", unorganised_runfolder1.name])
             response1 = yield self.http_client.fetch(self.get_url(url), method='POST', body='')
-
             self.assertEqual(response1.code, 200)
-
-            response_json1 = json.loads(response1.body)
-
+           
             url = "/".join([self.API_BASE, "organise", "runfolder", unorganised_runfolder2.name])
             response2 = yield self.http_client.fetch(self.get_url(url), method='POST', body='')
             self.assertEqual(response2.code, 200)
-
-            response_json2 = json.loads(response2.body)
-
+ 
             # Then just stage it
             url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'JKL_123'])
             payload = {'delivery_mode': 'BATCH'}

From 0d26c3ef2e0ab94b020f8baa2e45816be171c460 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Mon, 23 Sep 2024 11:29:35 +0200
Subject: [PATCH 09/12] Correcting integration tests

---
 delivery/services/staging_service.py            |  9 +++++----
 tests/integration_tests/test_integration_dds.py | 13 +++++++------
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/delivery/services/staging_service.py b/delivery/services/staging_service.py
index debfe5f..fb23639 100644
--- a/delivery/services/staging_service.py
+++ b/delivery/services/staging_service.py
@@ -102,11 +102,12 @@ def _copy_dir(staging_order_id, external_program_service, session_factory, stagi
 
                 # Parse the file size from the output of rsync stats:
                 # Total file size: 207,707,566 bytes
-                match = re.search(r'Total file size: ([\d,]+) bytes',
-                                  execution_result.stdout,
-                                  re.MULTILINE)
+
+                match = re.search(r'Total file size: ([\d,.]+) bytes',
+                                execution_result.stdout,
+                                re.MULTILINE)
                 size_of_transfer = match.group(1)
-                size_of_transfer = int(size_of_transfer.replace(",", ""))
+                size_of_transfer = int(size_of_transfer.replace(",", "").replace(".", ""))
                 staging_order.size = size_of_transfer
 
                 staging_order.status = StagingStatus.staging_successful
diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 47cf616..74d51b5 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -119,8 +119,8 @@ def test_can_stage_and_deliver_clean_flowcells(self):
                                          prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1,\
              tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                          prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
-                self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123')
-                self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123')
+                self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123', os.path.basename(tmpdir1))
+                self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123', os.path.basename(tmpdir2))
 
                 url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'XYZ_123'])
                 payload = {'delivery_mode': 'CLEAN'}
@@ -147,12 +147,13 @@ def test_can_stage_and_deliver_batch_flowcells(self):
                                          prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
                 tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                             prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
-            self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123')
-            self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123')
+            self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123', os.path.basename(tmpdir1))
+            self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123', os.path.basename(tmpdir2))
 
             url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'XYZ_123'])
             payload = {'delivery_mode': 'BATCH'}
             response = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
+
             self.assertEqual(response.code, 202)
 
             payload = {'delivery_mode': 'BATCH'}
@@ -177,7 +178,7 @@ def create_unorganised_test_runfolders(self, tmpdir):
                 unorganised_runfolder(
                 name=os.path.basename(tmpdir),
                 root_path=os.path.dirname(tmpdir))
-                                                 )
+             )
     @gen_test
     def test_can_stage_and_deliver_force_flowcells(self):
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
@@ -199,7 +200,7 @@ def test_can_stage_and_deliver_force_flowcells(self):
             response2 = yield self.http_client.fetch(self.get_url(url), method='POST', body='')
             self.assertEqual(response2.code, 200)
  
-            # Then just stage it
+            # Then stage it
             url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'JKL_123'])
             payload = {'delivery_mode': 'BATCH'}
             response = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))

From 91fc8cff8b1da38168a5b356d479c265229320e6 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Fri, 27 Sep 2024 15:17:06 +0200
Subject: [PATCH 10/12] Testing reformatting changes

---
 .../integration_tests/test_integration_dds.py | 59 ++++++++++++++-----
 1 file changed, 43 insertions(+), 16 deletions(-)

diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 74d51b5..4b18d1d 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -174,15 +174,53 @@ def test_can_stage_and_deliver_batch_flowcells(self):
                 self.assertEqual(json.loads(status_response.body)["status"], StagingStatus.staging_successful.name)
 
     def create_unorganised_test_runfolders(self, tmpdir):
-            return(
-                unorganised_runfolder(
+            return unorganised_runfolder(
                 name=os.path.basename(tmpdir),
-                root_path=os.path.dirname(tmpdir))
-             )
+                root_path=os.path.dirname(tmpdir)
+            )
+    
     @gen_test
     def test_can_stage_and_deliver_force_flowcells(self):
         with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
-                                        prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
+                                         prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
+                tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
+                                            prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
+            self._create_projects_dir_with_random_data(tmpdir1, 'XYZ_123', os.path.basename(tmpdir1))
+            self._create_projects_dir_with_random_data(tmpdir2, 'XYZ_123', os.path.basename(tmpdir2))
+
+            # First just stage it
+            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'XYZ_123'])
+            payload = {'delivery_mode': 'BATCH'}
+            response = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
+            self.assertEqual(response.code, 202)
+
+            # The it should be denied (since if has already been staged)
+            payload = {'delivery_mode': 'BATCH'}
+            response_failed = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload), raise_error=False)
+            self.assertEqual(response_failed.code, 403)
+
+            # Then it should work once force is specified.
+            payload = {'delivery_mode': 'FORCE'}
+            response_forced = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
+            self.assertEqual(response_forced.code, 202)
+
+            response_json = json.loads(response_forced.body)
+
+            staging_status_links = response_json.get("staging_order_links")
+
+            # Insert a pause to allow staging to complete
+            time.sleep(1)
+
+            for project, link in staging_status_links.items():
+                self.assertEqual(project, 'XYZ_123')
+
+                status_response = yield self.http_client.fetch(link)
+                self.assertEqual(json.loads(status_response.body)["status"], StagingStatus.staging_successful.name)
+
+    @gen_test
+    def test_can_organise_stage_and_deliver_force_flowcells(self):
+        with tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
+                                         prefix='160930_ST-E00216_0555_BH37CWALXX_') as tmpdir1, \
                 tempfile.TemporaryDirectory(dir='./tests/resources/runfolders/',
                                             prefix='160930_ST-E00216_0556_BH37CWALXX_') as tmpdir2:
             # First organise
@@ -201,17 +239,6 @@ def test_can_stage_and_deliver_force_flowcells(self):
             self.assertEqual(response2.code, 200)
  
             # Then stage it
-            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'JKL_123'])
-            payload = {'delivery_mode': 'BATCH'}
-            response = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
-            self.assertEqual(response.code, 202)
-
-            # The it should be denied (since if has already been staged)
-            payload = {'delivery_mode': 'BATCH'}
-            response_failed = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload), raise_error=False)
-            self.assertEqual(response_failed.code, 403)
-
-            # Then it should work once force is specified.
             payload = {'delivery_mode': 'FORCE'}
             response_forced = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
             self.assertEqual(response_forced.code, 202)

From 36614d72bd5e3fa20feaf0cb32e53099d10e98d6 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Fri, 27 Sep 2024 17:45:11 +0200
Subject: [PATCH 11/12] Testing reformatting changes

---
 tests/integration_tests/test_integration_dds.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 4b18d1d..2fe08f1 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -239,6 +239,7 @@ def test_can_organise_stage_and_deliver_force_flowcells(self):
             self.assertEqual(response2.code, 200)
  
             # Then stage it
+            url = "/".join([self.API_BASE, "stage", "project", 'runfolders', 'JKL_123'])
             payload = {'delivery_mode': 'FORCE'}
             response_forced = yield self.http_client.fetch(self.get_url(url), method='POST', body=json.dumps(payload))
             self.assertEqual(response_forced.code, 202)

From c5e980da1c73998d7a220681ae1ddd0c03c5b0d0 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Fri, 11 Oct 2024 13:53:49 +0200
Subject: [PATCH 12/12] Reformatting anf changed how to assert a folder is not
 in directory

---
 tests/integration_tests/test_integration_dds.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/integration_tests/test_integration_dds.py b/tests/integration_tests/test_integration_dds.py
index 2fe08f1..8fa7947 100644
--- a/tests/integration_tests/test_integration_dds.py
+++ b/tests/integration_tests/test_integration_dds.py
@@ -249,11 +249,6 @@ def test_can_organise_stage_and_deliver_force_flowcells(self):
             staging_status_links = response_json.get("staging_order_links")
             staging_order_ids = response_json.get("staging_order_ids")
 
-            # Assert the staged folder structure has only one runfolder folder
-            temp_staging_dir = f"/tmp/{staging_order_ids.get('JKL_123')}/JKL_123"
-            for runfolder in os.listdir(temp_staging_dir):
-                self.assertFalse(set(runfolder).issuperset(set(os.listdir(f"{temp_staging_dir}/{runfolder}"))))
-            
             # Insert a pause to allow staging to complete
             time.sleep(1)
 
@@ -263,6 +258,11 @@ def test_can_organise_stage_and_deliver_force_flowcells(self):
                 status_response = yield self.http_client.fetch(link)
                 self.assertEqual(json.loads(status_response.body)["status"], StagingStatus.staging_successful.name)
 
+            # Assert the staged folder structure has only one runfolder folder
+            temp_staging_dir = f"/tmp/{staging_order_ids.get('JKL_123')}/JKL_123"
+            for runfolder in os.listdir(temp_staging_dir):
+                self.assertFalse(runfolder in os.listdir(f"{temp_staging_dir}/{runfolder}"))
+
     @gen_test
     def test_can_create_project(self):
         project_name = "CD-1234"