manage stale db status and version bump

FNNDSC · Mar 5, 2024 · cc7d807 · cc7d807
1 parent 8e77410
commit cc7d807
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Showing 5 changed files with 54 additions and 10 deletions.
diff --git a/app/config.py b/app/config.py
@@ -3,7 +3,7 @@
 
 class Settings(BaseSettings):
     pflink_mongodb: MongoDsn = 'mongodb://localhost:27017'
-    version: str = "3.8.7"
+    version: str = "3.8.8"
     mongo_username: str = "admin"
     mongo_password: str = "admin"
     log_level: str = "DEBUG"

diff --git a/app/controllers/subprocesses/status.py b/app/controllers/subprocesses/status.py
@@ -232,7 +232,6 @@ def get_analysis_status(response: dict) -> dict:
     """
     Get details about an analysis running on the given feed
     """
-    MAX_JOBS = 12
     analysis_details = {}
 
     created = response['created_jobs']

diff --git a/app/controllers/subprocesses/wf_manager.py b/app/controllers/subprocesses/wf_manager.py
@@ -149,7 +149,7 @@ def analysis_retry(workflow: WorkflowDBSchema):
     """
     # Reset workflow status if max service_retry is not reached
     if workflow.service_retry < 5 and not workflow.response.status and workflow.response.workflow_state == State.ANALYZING:
-        logger.warning(f"Retrying request.{workflow.service_retry}/5 retries left.", extra=d)
+        logger.warning(f"Retrying request.{5 - workflow.service_retry}/5 retries left.", extra=d)
         workflow.service_retry += 1
         workflow.response.feed_id = ""
         workflow.response.feed_name = ""
@@ -161,7 +161,7 @@ def analysis_retry(workflow: WorkflowDBSchema):
         update_workflow(key, workflow)
         if workflow.service_retry >= 5: logger.warning("All retries exhausted. Giving up on this workflow request.",
                                                        extra=d)
-    return workflow
+    return retrieve_workflow(key)
 
 def update_status(request: WorkflowRequestSchema):
     """
@@ -272,11 +272,11 @@ def do_cube_create_feed(request: WorkflowRequestSchema, cube_url: str, retries:
     """
     Create a new feed in `CUBE` if not already present
     """
-    logger.info(f"Creating Chris client with {cube_url, request.cube_user_info.username, request.cube_user_info.password}", extra=d)
+    logger.debug(f"Creating Chris client with {cube_url, request.cube_user_info.username, request.cube_user_info.password}", extra=d)
     client = do_cube_create_user(cube_url, request.cube_user_info.username, request.cube_user_info.password)
-    logger.info(f"Created client details {client}", extra=d)
+    logger.debug(f"Created client details {client}", extra=d)
 
-    logger.info(f"Fetching PACS details for {request.PACS_directive.__dict__}", extra=d)
+    logger.debug(f"Fetching PACS details for {request.PACS_directive.__dict__}", extra=d)
     pacs_details = {}
     try:
         pacs_details = client.getPACSdetails(request.PACS_directive.__dict__)
@@ -285,7 +285,7 @@ def do_cube_create_feed(request: WorkflowRequestSchema, cube_url: str, retries:
     feed_name = substitute_dicom_tags(request.workflow_info.feed_name, pacs_details)
     logger.info(f"Fetching data path..", extra=d)
     data_path = client.getSwiftPath(pacs_details)
-    logger.info(f"Received data path: {data_path}", extra=d)
+    logger.debug(f"Received data path: {data_path}", extra=d)
     if retries > 0:
         feed_name = feed_name + f"-retry#{retries}"
 
@@ -317,12 +317,13 @@ def __run_plugin_instance(previous_id: str, request: WorkflowRequestSchema, clie
     """
     # search for plugin
     plugin_search_params = {"name": request.workflow_info.plugin_name, "version": request.workflow_info.plugin_version}
+    logger.info(f"Adding plugin: {plugin_search_params} to pl_inst: {previous_id}", extra=d)
     plugin_id = client.getPluginId(plugin_search_params)
 
     # convert CLI params from string to a JSON dictionary
     feed_params = str_to_param_dict(request.workflow_info.plugin_params)
     feed_params["previous_id"] = previous_id
-    logger.info(f"Creating new analysis with plugin: {plugin_search_params}  and parameters: {feed_params}",
+    logger.debug(f"Creating new analysis with plugin: {plugin_search_params}  and parameters: {feed_params}",
                  extra=d)
     feed_resp = client.createFeed(plugin_id, feed_params)
 
@@ -333,9 +334,10 @@ def __run_pipeline_instance(previous_id: str, request: WorkflowRequestSchema, cl
     """
     # search for pipeline
     pipeline_search_params = {"name": request.workflow_info.pipeline_name}
+    logger.info(f"Adding pipeline: {pipeline_search_params} to pl_inst: {previous_id}", extra=d)
     pipeline_id = client.getPipelineId(pipeline_search_params)
     pipeline_params = {"previous_plugin_inst_id": previous_id, "name": request.workflow_info.pipeline_name}
-    logger.info(f"Creating new analysis with pipeline: {pipeline_search_params}.",
+    logger.debug(f"Creating new analysis with pipeline: {pipeline_search_params}.",
                 extra=d)
     feed_resp = client.createWorkflow(str(pipeline_id), pipeline_params)
 

diff --git a/cmd.sh b/cmd.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+docker run --rm fnndsc/pl-dicom_filter:1.1.2 chris_plugin_info
diff --git a/run-MainThread.log b/run-MainThread.log
@@ -0,0 +1,41 @@
+2024-03-05T10:57:27.162733-05:00	START
+2024-03-05T10:57:48.036372-05:00	
+{
+    "status": true,
+    "obj": {
+        "run": {
+            "status": true,
+            "stdout": {
+                "id": 145,
+                "creation_date": "2024-03-05T10:57:47.956671-05:00",
+                "name": "pl-dicom_filter",
+                "version": "1.1.2",
+                "dock_image": "fnndsc/pl-dicom_filter:1.1.2",
+                "public_repo": "https://github.com/FNNDSC/pl-dicom_filter",
+                "icon": "",
+                "type": "ds",
+                "stars": 0,
+                "authors": "FNNDSC <[email protected]>",
+                "title": "A ChRIS plugin to filter dicom files using dicom tags",
+                "category": "",
+                "description": "A ChRIS DS plugin template",
+                "documentation": "https://github.com/FNNDSC/python-chrisapp-template",
+                "license": "MIT",
+                "execshell": "/usr/local/bin/python",
+                "selfpath": "/usr/local/bin",
+                "selfexec": "dicom_filter",
+                "min_number_of_workers": 1,
+                "max_number_of_workers": 1,
+                "min_cpu_limit": 1000,
+                "max_cpu_limit": 2147483647,
+                "min_memory_limit": 2048,
+                "max_memory_limit": 2147483647,
+                "min_gpu_limit": 0,
+                "max_gpu_limit": 0
+            },
+            "stderr": "",
+            "returncode": 0
+        }
+    }
+}
+2024-03-05T10:57:48.036535-05:00	END