From f1dddfb4b1377566746764ce33a8a6d31b524739 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 30 Aug 2024 18:43:54 +0200
Subject: [PATCH] Fix job summary for optional unset job data inputs

Fixes https://sentry.galaxyproject.org/share/issue/31c83cea41a94a7c9c367a66d89fae37/:
```
AttributeError: 'NoneType' object has no attribute 'id'
  File "starlette/applications.py", line 123, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 186, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 164, in __call__
    await self.app(scope, receive, _send)
  File "starlette_context/middleware/raw_middleware.py", line 92, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 189, in __call__
    with collapse_excgroups():
  File "contextlib.py", line 155, in __exit__
    self.gen.throw(typ, value, traceback)
  File "starlette/_utils.py", line 93, in collapse_excgroups
    raise exc
  File "starlette/middleware/base.py", line 191, in __call__
    response = await self.dispatch_func(request, call_next)
  File "galaxy/webapps/galaxy/fast_app.py", line 109, in add_x_frame_options
    response = await call_next(request)
  File "starlette/middleware/base.py", line 165, in call_next
    raise app_exc
  File "starlette/middleware/base.py", line 151, in coro
    await self.app(scope, receive_or_disconnect, send_no_error)
  File "starlette/middleware/exceptions.py", line 65, in __call__
    await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
  File "starlette/_exception_handler.py", line 64, in wrapped_app
    raise exc
  File "starlette/_exception_handler.py", line 53, in wrapped_app
    await app(scope, receive, sender)
  File "starlette/routing.py", line 756, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/routing.py", line 776, in app
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 297, in handle
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 77, in app
    await wrap_app_handling_exceptions(app, request)(scope, receive, send)
  File "starlette/_exception_handler.py", line 64, in wrapped_app
    raise exc
  File "starlette/_exception_handler.py", line 53, in wrapped_app
    await app(scope, receive, sender)
  File "starlette/routing.py", line 72, in app
    response = await func(request)
  File "fastapi/routing.py", line 278, in app
    raw_response = await run_endpoint_function(
  File "fastapi/routing.py", line 193, in run_endpoint_function
    return await run_in_threadpool(dependant.call, **values)
  File "starlette/concurrency.py", line 42, in run_in_threadpool
    return await anyio.to_thread.run_sync(func, *args)
  File "anyio/to_thread.py", line 56, in run_sync
    return await get_async_backend().run_sync_in_worker_thread(
  File "anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread
    return await future
  File "anyio/_backends/_asyncio.py", line 851, in run
    result = context.run(func, *args)
  File "galaxy/webapps/galaxy/api/jobs.py", line 410, in parameters_display_by_dataset
    return summarize_job_parameters(trans, job)
  File "galaxy/managers/jobs.py", line 1055, in summarize_job_parameters
    parameters = inputs_recursive(tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages)
  File "galaxy/managers/jobs.py", line 994, in inputs_recursive
    element_id = element.id
```
which you can reproduce by connecting an optional dataset and a required
dataset to a multiple="true" data parameter and then looking at the tool
input parameters.
---
 client/src/api/schema/schema.ts                     |  2 +-
 .../JobParameters/JobParametersArrayValue.vue       |  3 ++-
 lib/galaxy/managers/jobs.py                         | 13 ++++++++-----
 lib/galaxy/schema/jobs.py                           |  2 +-
 4 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index f878a162098a..9abd677c7b27 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -9132,7 +9132,7 @@ export interface components {
              * @description The values of the job parameter
              */
             value?:
-                | components["schemas"]["EncodedJobParameterHistoryItem"][]
+                | (components["schemas"]["EncodedJobParameterHistoryItem"] | null)[]
                 | number
                 | number
                 | boolean
diff --git a/client/src/components/JobParameters/JobParametersArrayValue.vue b/client/src/components/JobParameters/JobParametersArrayValue.vue
index 31be3694434a..014d0e6d12de 100644
--- a/client/src/components/JobParameters/JobParametersArrayValue.vue
+++ b/client/src/components/JobParameters/JobParametersArrayValue.vue
@@ -1,8 +1,9 @@
 <template>
     <div>
         <div v-for="(elVal, pvIndex) in parameter_value" :key="pvIndex">
+            <span v-if="elVal === null">No input provided</span>
             <GenericHistoryItem
-                v-if="['hda', 'hdca', 'dce'].includes(elVal.src)"
+                v-else-if="['hda', 'hdca', 'dce'].includes(elVal.src)"
                 :item-id="elVal.id"
                 :item-src="elVal.src" />
             <span v-else> {{ elVal.hid }}: {{ elVal.name }} </span>
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 546085b26a2e..98cdf2408cb6 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -5,10 +5,12 @@
     datetime,
 )
 from typing import (
+    Any,
     cast,
     Dict,
     List,
     Optional,
+    Union,
 )
 
 import sqlalchemy
@@ -989,16 +991,17 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
                     or input.type == "data_collection"
                     or isinstance(input_value, model.HistoryDatasetAssociation)
                 ):
-                    value = []
+                    value: List[Union[Dict[str, Any], None]] = []
                     for element in listify(input_value):
-                        element_id = element.id
                         if isinstance(element, model.HistoryDatasetAssociation):
                             hda = element
-                            value.append({"src": "hda", "id": element_id, "hid": hda.hid, "name": hda.name})
+                            value.append({"src": "hda", "id": element.id, "hid": hda.hid, "name": hda.name})
                         elif isinstance(element, model.DatasetCollectionElement):
-                            value.append({"src": "dce", "id": element_id, "name": element.element_identifier})
+                            value.append({"src": "dce", "id": element.id, "name": element.element_identifier})
                         elif isinstance(element, model.HistoryDatasetCollectionAssociation):
-                            value.append({"src": "hdca", "id": element_id, "hid": element.hid, "name": element.name})
+                            value.append({"src": "hdca", "id": element.id, "hid": element.hid, "name": element.name})
+                        elif element is None:
+                            value.append(None)
                         else:
                             raise Exception(
                                 f"Unhandled data input parameter type encountered {element.__class__.__name__}"
diff --git a/lib/galaxy/schema/jobs.py b/lib/galaxy/schema/jobs.py
index fe6316262983..ec7a971a3614 100644
--- a/lib/galaxy/schema/jobs.py
+++ b/lib/galaxy/schema/jobs.py
@@ -223,7 +223,7 @@ class JobParameter(Model):
         title="Depth",
         description="The depth of the job parameter.",
     )
-    value: Optional[Union[List[EncodedJobParameterHistoryItem], float, int, bool, str]] = Field(
+    value: Optional[Union[List[Optional[EncodedJobParameterHistoryItem]], float, int, bool, str]] = Field(
         default=None, title="Value", description="The values of the job parameter", union_mode="left_to_right"
     )
     notes: Optional[str] = Field(default=None, title="Notes", description="Notes associated with the job parameter.")