Fix more formatting and schema issues

galaxyproject · Mar 27, 2024 · 87f5126 · 87f5126
1 parent 791348a
commit 87f5126
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Showing 6 changed files with 30 additions and 19 deletions.
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
@@ -8071,7 +8071,7 @@ export interface components {
              * Job State
              * @description The current job's state
              */
-            state?: string;
+            state?: components["schemas"]["JobState"] | null;
             /**
              * STDERR
              * @description Job STDERR text

diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
@@ -23,13 +23,13 @@ const props = defineProps({
     includeTimes: {
         type: Boolean,
         default: false,
-    }
+    },
 });
 
 const stdout_length = ref(50000);
 const stdout_text = ref("");
 const stderr_length = ref(50000);
-const stderr_text =  ref("");
+const stderr_text = ref("");
 
 const stdout_position = computed(() => stdout_text.value.length);
 const stderr_position = computed(() => stderr_text.value.length);
@@ -97,15 +97,15 @@ async function fetchInvocation(jobId) {
 
 <template>
     <div>
-        <JobDetailsProvider auto-refresh :job-id="props.job_id" @update:result="updateJob"/>
+        <JobDetailsProvider auto-refresh :job-id="props.job_id" @update:result="updateJob" />
         <JobConsoleOutputProvider
             auto-refresh
             :job-id="props.job_id"
             :stdout_position="stdout_position"
             :stdout_length="stdout_length"
             :stderr_position="stderr_position"
             :stderr_length="stderr_length"
-            @update:result="updateConsoleOutputs"/>
+            @update:result="updateConsoleOutputs" />
         <h2 class="h-md">Job Information</h2>
         <table id="job-information" class="tabletip info_data_table">
             <tbody>

diff --git a/client/src/components/providers/JobProvider.js b/client/src/components/providers/JobProvider.js
@@ -6,8 +6,7 @@ import { rethrowSimple } from "utils/simple-error";
 import { cleanPaginationParameters, stateIsTerminal } from "./utils";
 
 async function jobDetails({ jobId }) {
-    const url =
-        `${getAppRoot()}api/jobs/${jobId}?full=True`;
+    const url = `${getAppRoot()}api/jobs/${jobId}?full=True`;
     try {
         const { data } = await axios.get(url);
         return data;
@@ -16,9 +15,16 @@ async function jobDetails({ jobId }) {
     }
 }
 
-async function jobConsoleOutput({ jobId, stdout_position = 0, stdout_length = 0, stderr_position = 0, stderr_length = 0 }) {
-    const url = `${getAppRoot()}api/jobs/${jobId}/console_output?stdout_position=${stdout_position}&stdout_length=${stdout_length}` + 
-                                `&stderr_position=${stderr_position}&stderr_length=${stderr_length}`;
+async function jobConsoleOutput({
+    jobId,
+    stdout_position = 0,
+    stdout_length = 0,
+    stderr_position = 0,
+    stderr_length = 0,
+}) {
+    const url =
+        `${getAppRoot()}api/jobs/${jobId}/console_output?stdout_position=${stdout_position}&stdout_length=${stdout_length}` +
+        `&stderr_position=${stderr_position}&stderr_length=${stderr_length}`;
     try {
         const { data } = await axios.get(url);
         return data;

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
@@ -277,7 +277,9 @@ def get_accessible_job(self, trans, decoded_job_id) -> Job:
         trans.sa_session.refresh(job)
         return job
 
-    def get_job_console_output(self, trans, job, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0):
+    def get_job_console_output(
+        self, trans, job, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0
+    ):
         if job is None:
             raise ObjectNotFound()
 

diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -375,13 +375,13 @@ def outputs(
         summary="Returns STDOUT and STDERR from job.",
     )
     def console_output(
-            self,
-            job_id: Annotated[DecodedDatabaseIdField, JobIdPathParam],
-            stdout_position: int,
-            stdout_length: int,
-            stderr_position: int,
-            stderr_length: int,
-            trans: ProvidesUserContext = DependsOnTrans,
+        self,
+        job_id: Annotated[DecodedDatabaseIdField, JobIdPathParam],
+        stdout_position: int,
+        stdout_length: int,
+        stderr_position: int,
+        stderr_length: int,
+        trans: ProvidesUserContext = DependsOnTrans,
     ) -> JobConsoleOutput:
         """
         Get the stdout and/or stderr of a job. The position parameters are the index

diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -58,7 +58,10 @@ def show(
         id: DecodedDatabaseIdField,
         full: bool = False,
     ) -> Dict[str, Any]:
-        job = self.job_manager.get_accessible_job(trans, id,)
+        job = self.job_manager.get_accessible_job(
+            trans,
+            id,
+        )
         return view_show_job(trans, job, bool(full))
 
     def index(