From 58d24dc6e438bc6d9383a5c0c0a0478a951eca3e Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Tue, 17 Oct 2023 14:55:36 -0400
Subject: [PATCH 01/24] Add option to load stdout and stderr when requesting
 job status

---
 lib/galaxy/managers/jobs.py                | 26 +++++++++++++++++++++-
 lib/galaxy/webapps/galaxy/api/job_files.py |  6 ++++-
 lib/galaxy/webapps/galaxy/api/jobs.py      | 14 +++++++++++-
 lib/galaxy/webapps/galaxy/services/jobs.py | 13 ++++++++++-
 4 files changed, 55 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 8b3d0a37024e..2f6225bd851d 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -231,7 +231,7 @@ def update_job_lock(self, job_lock: JobLock):
         )
         return self.job_lock()
 
-    def get_accessible_job(self, trans, decoded_job_id):
+    def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0):
         job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
         if job is None:
             raise ObjectNotFound()
@@ -248,6 +248,30 @@ def get_accessible_job(self, trans, decoded_job_id):
                 if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user):
                     raise ItemAccessibilityException("You are not allowed to rerun this job.")
         trans.sa_session.refresh(job)
+
+        # If stdout_length and stdout_position are legitimate values, then return stdout with status.
+        if job.state == job.states.RUNNING:
+            working_directory = trans.app.object_store.get_filename(
+                job, base_dir="job_work", dir_only=True, obj_dir=True
+            )
+            if stdout_length > 0 and stdout_position > -1:
+                try:
+                    stdout_path = Path(working_directory) / STDOUT_LOCATION
+                    stdout_file = open(stdout_path, "r")
+                    stdout_file.seek(stdout_position)
+                    job.job_stdout = stdout_file.read(stdout_length)
+                    job.tool_stdout = job.job_stdout
+                except Exception as e:
+                    log.error("Could not read STDOUT: %s", e)
+            if stderr_length > 0 and stderr_position > -1:
+                try:
+                    stderr_path = Path(working_directory) / STDERR_LOCATION
+                    stderr_file = open(stderr_path, "r")
+                    stderr_file.seek(stderr_position)
+                    job.job_stderr = stderr_file.read(stderr_length)
+                    job.tool_stderr = job.job_stderr
+                except Exception as e:
+                    log.error("Could not read STDERR: %s", e)
         return job
 
     def stop(self, job, message=None):
diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index ea52c5a59a49..2d6c56e30b30 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -104,7 +104,11 @@ def create(self, trans, job_id, payload, **kwargs):
         target_dir = os.path.dirname(path)
         util.safe_makedirs(target_dir)
         try:
-            shutil.move(input_file.name, path)
+            if os.path.exists(path):
+                with open(path, "ab") as destination:
+                    shutil.copyfileobj(open(input_file.name, "rb"), destination)
+            else:
+                shutil.move(input_file.name, path)
         finally:
             try:
                 input_file.close()
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 72a565b05ccd..441082287373 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -178,6 +178,10 @@ def show(
         id: DecodedDatabaseIdField,
         trans: ProvidesUserContext = DependsOnTrans,
         full: Optional[bool] = False,
+        stdout_position: Optional[int] = None,
+        stdout_length: Optional[int] = None,
+        stderr_position: Optional[int] = None,
+        stderr_length: Optional[int] = None,
     ) -> Dict[str, Any]:
         """
         Return dictionary containing description of job data
@@ -186,7 +190,15 @@ def show(
         - id: ID of job to return
         - full: Return extra information ?
         """
-        return self.service.show(trans, id, bool(full))
+        return self.service.show( 
+            trans,
+            id,
+            bool(full),
+            int(stdout_position) if stdout_position else 0,
+            int(stdout_length) if stdout_length else 0,
+            int(stderr_position) if stderr_position else 0,
+            int(stderr_length) if stderr_length else 0,
+        )
 
     @router.get("/api/jobs")
     def index(
diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
index 98ac5bbb8f9e..363f6c7291dc 100644
--- a/lib/galaxy/webapps/galaxy/services/jobs.py
+++ b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -48,8 +48,19 @@ def show(
         trans: ProvidesUserContext,
         id: DecodedDatabaseIdField,
         full: bool = False,
+        stdout_position: int = 0,
+        stdout_length: int = 0,
+        stderr_position: int = 0,
+        stderr_length: int = 0,
     ) -> Dict[str, Any]:
-        job = self.job_manager.get_accessible_job(trans, id)
+        job = self.job_manager.get_accessible_job(
+            trans, 
+            id, 
+            stdout_position, 
+            stdout_length, 
+            stderr_position, 
+            stderr_length
+        )
         return view_show_job(trans, job, bool(full))
 
     def index(

From 89cc78a682275952ae0d6515368222a1cc6a3869 Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 3 Nov 2023 11:20:31 -0400
Subject: [PATCH 02/24] Update api endpoint for jobs

---
 lib/galaxy/managers/jobs.py           | 2 +-
 lib/galaxy/webapps/galaxy/api/jobs.py | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 2f6225bd851d..cc329f3700b2 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -249,7 +249,7 @@ def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_l
                     raise ItemAccessibilityException("You are not allowed to rerun this job.")
         trans.sa_session.refresh(job)
 
-        # If stdout_length and stdout_position are legitimate values, then return stdout with status.
+        # If stdout and stderr parameters are legitimate values, then return with status.
         if job.state == job.states.RUNNING:
             working_directory = trans.app.object_store.get_filename(
                 job, base_dir="job_work", dir_only=True, obj_dir=True
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 441082287373..9254a412a7a3 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -16,7 +16,7 @@
     Optional,
     Union,
 )
-
+from pathlib import Path
 from fastapi import (
     Depends,
     Query,
@@ -189,6 +189,10 @@ def show(
         Parameters
         - id: ID of job to return
         - full: Return extra information ?
+        - stdout_position: The index of the character to begin reading stdout from
+        - stdout_length: How many characters of stdout to read
+        - stderr_position: The index of the character to begin reading stderr from
+        - stderr_length: How many characters of stderr to read
         """
         return self.service.show( 
             trans,

From 870917ba2da6adab21903b3facd16d7357625f6d Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 3 Nov 2023 13:48:07 -0400
Subject: [PATCH 03/24] Add missing variables and import

---
 lib/galaxy/managers/jobs.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index cc329f3700b2..060f3cc43377 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -5,6 +5,7 @@
     date,
     datetime,
 )
+from pathlib import Path
 
 from boltons.iterutils import remap
 from pydantic import (
@@ -72,6 +73,9 @@
 log = logging.getLogger(__name__)
 
 
+STDOUT_LOCATION = "outputs/tool_stdout"
+STDERR_LOCATION = "outputs/tool_stderr"
+
 class JobLock(BaseModel):
     active: bool = Field(title="Job lock status", description="If active, jobs will not dispatch")
 

From 6dfbc7a882818ae511bdc993f9a7d60af135484c Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 3 Nov 2023 13:48:55 -0400
Subject: [PATCH 04/24] Add capability for UI to load live job stdout and
 stderr

---
 .../src/components/JobInformation/CodeRow.vue | 31 ++++++++++++++-----
 .../JobInformation/JobInformation.vue         | 21 +++++++++++--
 .../src/components/providers/JobProvider.js   |  5 +--
 3 files changed, 45 insertions(+), 12 deletions(-)

diff --git a/client/src/components/JobInformation/CodeRow.vue b/client/src/components/JobInformation/CodeRow.vue
index e5b3e5d8ce82..4146958e9f3f 100644
--- a/client/src/components/JobInformation/CodeRow.vue
+++ b/client/src/components/JobInformation/CodeRow.vue
@@ -1,10 +1,5 @@
 <template>
-    <tr
-        v-b-tooltip.hover
-        :title="`click to ${action}`"
-        @mousedown="mouseIsDown = true"
-        @mousemove="mouseIsDown ? (mouseMoved = true) : (mouseMoved = false)"
-        @mouseup="toggleExpanded()">
+    <tr>
         <td>
             {{ codeLabel }}
         </td>
@@ -13,7 +8,12 @@
                 <b-col cols="11">
                     <pre :class="codeClass">{{ codeItem }}</pre>
                 </b-col>
-                <b-col class="nopadding pointer">
+                <b-col class="nopadding pointer"
+                    v-b-tooltip.hover
+                    :title="`click to ${action}`"
+                    @mousedown="mouseIsDown = true"
+                    @mousemove="mouseIsDown ? (mouseMoved = true) : (mouseMoved = false)"
+                    @mouseup="toggleExpanded()">
                     <FontAwesomeIcon :icon="iconClass" />
                 </b-col>
             </b-row>
@@ -40,6 +40,7 @@ export default {
             mouseIsDown: false,
             mouseMoved: false,
             expanded: false,
+            lastPos: 0,
         };
     },
     computed: {
@@ -53,6 +54,18 @@ export default {
             return this.expanded ? ["fas", "compress-alt"] : ["fas", "expand-alt"];
         },
     },
+    updated() {
+        try {
+            var codeDiv = this.$el.querySelector(".code");
+            if (codeDiv.scrollTop + codeDiv.offsetHeight >= this.lastPos - 5)  {
+                    // scroll is at the bottom
+                    codeDiv.scrollTop = codeDiv.scrollHeight;
+            }
+            this.lastPos = codeDiv.scrollHeight;
+        } catch(exception) {
+            console.debug("Code div is not present");
+        }
+    },
     methods: {
         toggleExpanded() {
             this.mouseIsDown = false;
@@ -72,4 +85,8 @@ export default {
     padding: 0;
     margin: 0;
 }
+.code {
+    max-height: 50em;
+    overflow: auto;
+}
 </style>
diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
index eef0dfc7195d..712fad35b5bc 100644
--- a/client/src/components/JobInformation/JobInformation.vue
+++ b/client/src/components/JobInformation/JobInformation.vue
@@ -1,6 +1,6 @@
 <template>
     <div>
-        <JobDetailsProvider auto-refresh :job-id="job_id" @update:result="updateJob" />
+        <JobDetailsProvider auto-refresh :job-id="job_id" :stdout_position=stdout_position :stdout_length=stdout_length :stderr_position=stderr_position :stderr_length=stderr_length @update:result="updateJob" />
         <h2 class="h-md">Job Information</h2>
         <table id="job-information" class="tabletip info_data_table">
             <tbody>
@@ -41,8 +41,8 @@
                     </td>
                 </tr>
                 <CodeRow v-if="job" id="command-line" :code-label="'Command Line'" :code-item="job.command_line" />
-                <CodeRow v-if="job" id="stdout" :code-label="'Tool Standard Output'" :code-item="job.tool_stdout" />
-                <CodeRow v-if="job" id="stderr" :code-label="'Tool Standard Error'" :code-item="job.tool_stderr" />
+                <CodeRow v-if="job" id="stdout" :code-label="'Tool Standard Output'" :code-item="stdout_text" />
+                <CodeRow v-if="job" id="stderr" :code-label="'Tool Standard Error'" :code-item="stderr_text" />
                 <CodeRow
                     v-if="job && job.traceback"
                     id="traceback"
@@ -108,6 +108,12 @@ export default {
     data() {
         return {
             job: null,
+            stdout_position: 0,
+            stdout_length: 50000,
+            stdout_text: "",
+            stderr_position: 0,
+            stderr_length: 50000,
+            stderr_text: "",
         };
     },
     computed: {
@@ -126,6 +132,15 @@ export default {
         },
         updateJob(job) {
             this.job = job;
+            // Keep stdout in memory and only fetch new text via JobProvider
+            if (job.tool_stdout != null) {
+                this.stdout_text += job.tool_stdout;
+                this.stdout_position += job.tool_stdout.length;
+            }
+            if (job.tool_stderr != null) {
+                this.stderr_text += job.tool_stderr;
+                this.stderr_position += job.tool_stderr.length;
+            }
         },
     },
 };
diff --git a/client/src/components/providers/JobProvider.js b/client/src/components/providers/JobProvider.js
index 09f3983c412e..a4eaa6aa0e13 100644
--- a/client/src/components/providers/JobProvider.js
+++ b/client/src/components/providers/JobProvider.js
@@ -5,8 +5,9 @@ import { rethrowSimple } from "utils/simple-error";
 
 import { cleanPaginationParameters, stateIsTerminal } from "./utils";
 
-async function jobDetails({ jobId }) {
-    const url = `${getAppRoot()}api/jobs/${jobId}?full=True`;
+async function jobDetails({ jobId, stdout_position = 0, stdout_length = 0, stderr_position = 0, stderr_length = 0 }) {
+    const url = `${getAppRoot()}api/jobs/${jobId}?full=True&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;

From de7cadf127e60c79f1a2f87867b0d02a2efb4ca0 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 08:21:52 -0500
Subject: [PATCH 05/24] Linting / format.

---
 client/src/components/JobInformation/CodeRow.vue      | 11 ++++++-----
 .../src/components/JobInformation/JobInformation.vue  |  9 ++++++++-
 client/src/components/providers/JobProvider.js        |  5 +++--
 lib/galaxy/managers/jobs.py                           |  9 ++++++---
 lib/galaxy/webapps/galaxy/api/jobs.py                 |  4 ++--
 lib/galaxy/webapps/galaxy/services/jobs.py            |  7 +------
 6 files changed, 26 insertions(+), 19 deletions(-)

diff --git a/client/src/components/JobInformation/CodeRow.vue b/client/src/components/JobInformation/CodeRow.vue
index 4146958e9f3f..8b69bfb37b80 100644
--- a/client/src/components/JobInformation/CodeRow.vue
+++ b/client/src/components/JobInformation/CodeRow.vue
@@ -8,8 +8,9 @@
                 <b-col cols="11">
                     <pre :class="codeClass">{{ codeItem }}</pre>
                 </b-col>
-                <b-col class="nopadding pointer"
+                <b-col
                     v-b-tooltip.hover
+                    class="nopadding pointer"
                     :title="`click to ${action}`"
                     @mousedown="mouseIsDown = true"
                     @mousemove="mouseIsDown ? (mouseMoved = true) : (mouseMoved = false)"
@@ -57,12 +58,12 @@ export default {
     updated() {
         try {
             var codeDiv = this.$el.querySelector(".code");
-            if (codeDiv.scrollTop + codeDiv.offsetHeight >= this.lastPos - 5)  {
-                    // scroll is at the bottom
-                    codeDiv.scrollTop = codeDiv.scrollHeight;
+            if (codeDiv.scrollTop + codeDiv.offsetHeight >= this.lastPos - 5) {
+                // scroll is at the bottom
+                codeDiv.scrollTop = codeDiv.scrollHeight;
             }
             this.lastPos = codeDiv.scrollHeight;
-        } catch(exception) {
+        } catch (exception) {
             console.debug("Code div is not present");
         }
     },
diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
index 712fad35b5bc..e3d3cbe6cb51 100644
--- a/client/src/components/JobInformation/JobInformation.vue
+++ b/client/src/components/JobInformation/JobInformation.vue
@@ -1,6 +1,13 @@
 <template>
     <div>
-        <JobDetailsProvider auto-refresh :job-id="job_id" :stdout_position=stdout_position :stdout_length=stdout_length :stderr_position=stderr_position :stderr_length=stderr_length @update:result="updateJob" />
+        <JobDetailsProvider
+            auto-refresh
+            :job-id="job_id"
+            :stdout_position="stdout_position"
+            :stdout_length="stdout_length"
+            :stderr_position="stderr_position"
+            :stderr_length="stderr_length"
+            @update:result="updateJob" />
         <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
index a4eaa6aa0e13..ef5f302e8080 100644
--- a/client/src/components/providers/JobProvider.js
+++ b/client/src/components/providers/JobProvider.js
@@ -6,8 +6,9 @@ import { rethrowSimple } from "utils/simple-error";
 import { cleanPaginationParameters, stateIsTerminal } from "./utils";
 
 async function jobDetails({ jobId, stdout_position = 0, stdout_length = 0, stderr_position = 0, stderr_length = 0 }) {
-    const url = `${getAppRoot()}api/jobs/${jobId}?full=True&stdout_position=${stdout_position}`+
-                `&stdout_length=${stdout_length}&stderr_position=${stderr_position}&stderr_length=${stderr_length}`;
+    const url =
+        `${getAppRoot()}api/jobs/${jobId}?full=True&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
index 060f3cc43377..b11c2f179802 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -76,6 +76,7 @@
 STDOUT_LOCATION = "outputs/tool_stdout"
 STDERR_LOCATION = "outputs/tool_stderr"
 
+
 class JobLock(BaseModel):
     active: bool = Field(title="Job lock status", description="If active, jobs will not dispatch")
 
@@ -235,7 +236,9 @@ def update_job_lock(self, job_lock: JobLock):
         )
         return self.job_lock()
 
-    def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0):
+    def get_accessible_job(
+        self, trans, decoded_job_id, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0
+    ):
         job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
         if job is None:
             raise ObjectNotFound()
@@ -261,7 +264,7 @@ def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_l
             if stdout_length > 0 and stdout_position > -1:
                 try:
                     stdout_path = Path(working_directory) / STDOUT_LOCATION
-                    stdout_file = open(stdout_path, "r")
+                    stdout_file = open(stdout_path)
                     stdout_file.seek(stdout_position)
                     job.job_stdout = stdout_file.read(stdout_length)
                     job.tool_stdout = job.job_stdout
@@ -270,7 +273,7 @@ def get_accessible_job(self, trans, decoded_job_id, stdout_position=-1, stdout_l
             if stderr_length > 0 and stderr_position > -1:
                 try:
                     stderr_path = Path(working_directory) / STDERR_LOCATION
-                    stderr_file = open(stderr_path, "r")
+                    stderr_file = open(stderr_path)
                     stderr_file.seek(stderr_position)
                     job.job_stderr = stderr_file.read(stderr_length)
                     job.tool_stderr = job.job_stderr
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 9254a412a7a3..26690562a885 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -16,7 +16,7 @@
     Optional,
     Union,
 )
-from pathlib import Path
+
 from fastapi import (
     Depends,
     Query,
@@ -194,7 +194,7 @@ def show(
         - stderr_position: The index of the character to begin reading stderr from
         - stderr_length: How many characters of stderr to read
         """
-        return self.service.show( 
+        return self.service.show(
             trans,
             id,
             bool(full),
diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
index 363f6c7291dc..7d2d87005fb2 100644
--- a/lib/galaxy/webapps/galaxy/services/jobs.py
+++ b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -54,12 +54,7 @@ def show(
         stderr_length: int = 0,
     ) -> Dict[str, Any]:
         job = self.job_manager.get_accessible_job(
-            trans, 
-            id, 
-            stdout_position, 
-            stdout_length, 
-            stderr_position, 
-            stderr_length
+            trans, id, stdout_position, stdout_length, stderr_position, stderr_length
         )
         return view_show_job(trans, job, bool(full))
 

From 31065a606b4dcd00934677f5747d5513e004e60e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 08:40:40 -0500
Subject: [PATCH 06/24] Fix jest test

---
 client/src/components/JobInformation/JobInformation.test.js | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/client/src/components/JobInformation/JobInformation.test.js b/client/src/components/JobInformation/JobInformation.test.js
index 0eab9f09f0e0..09f8a7bb57be 100644
--- a/client/src/components/JobInformation/JobInformation.test.js
+++ b/client/src/components/JobInformation/JobInformation.test.js
@@ -21,7 +21,11 @@ describe("JobInformation/JobInformation.vue", () => {
     beforeEach(() => {
         axiosMock = new MockAdapter(axios);
         axiosMock.onGet(new RegExp(`api/configuration/decode/*`)).reply(200, { decoded_id: 123 });
-        axiosMock.onGet("/api/jobs/test_id?full=True").reply(200, jobResponse);
+        axiosMock
+            .onGet(
+                "/api/jobs/test_id?full=True&stdout_position=0&stdout_length=50000&stderr_position=0&stderr_length=50000"
+            )
+            .reply(200, jobResponse);
     });
 
     afterEach(() => {

From 24e7d15b573a78461f7d7847bd3c7e389ee1a7da Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 08:53:40 -0500
Subject: [PATCH 07/24] Update API schema

---
 client/src/api/schema/schema.ts | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index 057ea7c8c031..031d322f40dc 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -901,6 +901,10 @@ export interface paths {
          * Parameters
          * - id: ID of job to return
          * - full: Return extra information ?
+         * - stdout_position: The index of the character to begin reading stdout from
+         * - stdout_length: How many characters of stdout to read
+         * - stderr_position: The index of the character to begin reading stderr from
+         * - stderr_length: How many characters of stderr to read
          */
         get: operations["show_api_jobs__id__get"];
     };
@@ -14596,10 +14600,18 @@ export interface operations {
          * Parameters
          * - id: ID of job to return
          * - full: Return extra information ?
+         * - stdout_position: The index of the character to begin reading stdout from
+         * - stdout_length: How many characters of stdout to read
+         * - stderr_position: The index of the character to begin reading stderr from
+         * - stderr_length: How many characters of stderr to read
          */
         parameters: {
             query?: {
                 full?: boolean;
+                stdout_position?: number;
+                stdout_length?: number;
+                stderr_position?: number;
+                stderr_length?: number;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {

From d336cadddba432e2e9427d4b772a946b30495750 Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 17 Nov 2023 13:41:59 -0500
Subject: [PATCH 08/24] Configure pulsar runner to read stdout from file if
 finish message stdout is none

---
 lib/galaxy/jobs/runners/pulsar.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 2bba3504024a..f3e4422c2b58 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -645,6 +645,18 @@ def finish_job(self, job_state: JobState):
             remote_metadata_directory = run_results.get("metadata_directory", None)
             tool_stdout = run_results.get("stdout", "")
             tool_stderr = run_results.get("stderr", "")
+            for file in ("tool_stdout", "tool_stderr"):
+                if tool_stdout and tool_stderr:
+                    pass
+                try:
+                    file_path = Path(job_wrapper.working_directory) / "outputs" / file
+                    file_content = open(file_path, "r")
+                    if tool_stdout is None and file == "tool_stdout":
+                        tool_stdout = file_content.read()
+                    elif tool_stderr is None and file == "tool_stderr":
+                        tool_stderr = file_content.read()
+                except Exception:
+                    pass
             job_stdout = run_results.get("job_stdout")
             job_stderr = run_results.get("job_stderr")
             exit_code = run_results.get("returncode")

From fd0237fdde1525d42dfe26c526322e37b13c091c Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 15 Dec 2023 13:52:31 -0500
Subject: [PATCH 09/24] Add new api endpoint to fetch job stdout and stderr

---
 lib/galaxy/managers/jobs.py                | 28 ++++++-----
 lib/galaxy/webapps/galaxy/api/jobs.py      | 56 +++++++++++++++++-----
 lib/galaxy/webapps/galaxy/buildapp.py      |  8 ++++
 lib/galaxy/webapps/galaxy/services/jobs.py |  8 +---
 4 files changed, 70 insertions(+), 30 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index b11c2f179802..2092cc66b033 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -236,9 +236,7 @@ def update_job_lock(self, job_lock: JobLock):
         )
         return self.job_lock()
 
-    def get_accessible_job(
-        self, trans, decoded_job_id, stdout_position=-1, stdout_length=0, stderr_position=-1, stderr_length=0
-    ):
+    def get_accessible_job(self, trans, decoded_job_id):
         job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
         if job is None:
             raise ObjectNotFound()
@@ -255,8 +253,15 @@ def get_accessible_job(
                 if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user):
                     raise ItemAccessibilityException("You are not allowed to rerun this job.")
         trans.sa_session.refresh(job)
+        return job
 
-        # If stdout and stderr parameters are legitimate values, then return with status.
+    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()
+
+        # If stdout_length and stdout_position are good values, then load standard out and add it to status
+        console_output = dict()
+        console_output["state"] = job.state
         if job.state == job.states.RUNNING:
             working_directory = trans.app.object_store.get_filename(
                 job, base_dir="job_work", dir_only=True, obj_dir=True
@@ -264,22 +269,23 @@ def get_accessible_job(
             if stdout_length > 0 and stdout_position > -1:
                 try:
                     stdout_path = Path(working_directory) / STDOUT_LOCATION
-                    stdout_file = open(stdout_path)
+                    stdout_file = open(stdout_path, "r")
                     stdout_file.seek(stdout_position)
-                    job.job_stdout = stdout_file.read(stdout_length)
-                    job.tool_stdout = job.job_stdout
+                    console_output["stdout"] = stdout_file.read(stdout_length)
                 except Exception as e:
                     log.error("Could not read STDOUT: %s", e)
             if stderr_length > 0 and stderr_position > -1:
                 try:
                     stderr_path = Path(working_directory) / STDERR_LOCATION
-                    stderr_file = open(stderr_path)
+                    stderr_file = open(stderr_path, "r")
                     stderr_file.seek(stderr_position)
-                    job.job_stderr = stderr_file.read(stderr_length)
-                    job.tool_stderr = job.job_stderr
+                    console_output["stderr"] = stderr_file.read(stderr_length)
                 except Exception as e:
                     log.error("Could not read STDERR: %s", e)
-        return job
+        else:
+            console_output["stdout"] = job.tool_stdout
+            console_output["stderr"] = job.tool_stderr
+        return console_output
 
     def stop(self, job, message=None):
         if not job.finished:
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 26690562a885..86c08dcfdfbd 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -178,10 +178,6 @@ def show(
         id: DecodedDatabaseIdField,
         trans: ProvidesUserContext = DependsOnTrans,
         full: Optional[bool] = False,
-        stdout_position: Optional[int] = None,
-        stdout_length: Optional[int] = None,
-        stderr_position: Optional[int] = None,
-        stderr_length: Optional[int] = None,
     ) -> Dict[str, Any]:
         """
         Return dictionary containing description of job data
@@ -189,19 +185,11 @@ def show(
         Parameters
         - id: ID of job to return
         - full: Return extra information ?
-        - stdout_position: The index of the character to begin reading stdout from
-        - stdout_length: How many characters of stdout to read
-        - stderr_position: The index of the character to begin reading stderr from
-        - stderr_length: How many characters of stderr to read
         """
         return self.service.show(
             trans,
             id,
             bool(full),
-            int(stdout_position) if stdout_position else 0,
-            int(stdout_length) if stdout_length else 0,
-            int(stderr_position) if stderr_position else 0,
-            int(stderr_length) if stderr_length else 0,
         )
 
     @router.get("/api/jobs")
@@ -345,6 +333,50 @@ def resume(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
             exceptions.RequestParameterInvalidException(f"Job with id '{job.tool_id}' is not paused")
         return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
 
+    @expose_api
+    def console_output(
+            self,
+            trans: ProvidesUserContext,
+            id,
+            stdout_position,
+            stdout_length,
+            stderr_position,
+            stderr_length,
+            **kwd
+    ):
+        """
+         * GET /api/jobs/{id}/console_output
+                Get the stdout and/or stderr of a job.
+
+        :type   id: string
+        :param  id: Encoded job id
+
+        :type   stdout_position: int
+        :param  stdout_position: The index of the character to begin reading stdout from
+
+        :type   stdout_length: int
+        :param  stdout_length: How many characters of stdout to read
+
+        :type   stderr_position: int
+        :param  stderr_position: The index of the character to begin reading stderr from
+
+        :type   stderr_length: int
+        :param  stderr_length: How many characters of stderr to read
+
+        :rtype:     dict
+        :returns:   dict containing stdout and stderr fields
+        """
+        job = self.__get_job(trans, id)
+        return self.job_manager.get_job_console_output(
+            trans,
+            job,
+            int(stdout_position),
+            int(stdout_length),
+            int(stderr_position),
+            int(stderr_length)
+        )
+
+
     @expose_api_anonymous
     def metrics(self, trans: ProvidesUserContext, **kwd):
         """
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 6dcd4c291613..bf0ab2243460 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -943,6 +943,14 @@ def connect_invocation_endpoint(endpoint_name, endpoint_suffix, action, conditio
     webapp.mapper.connect(
         "job_error", "/api/jobs/{id}/error", controller="jobs", action="error", conditions=dict(method=["POST"])
     )
+    webapp.mapper.connect(
+        "console_output",
+        "/api/jobs/{id}/console_output",
+        controller="jobs",
+        action="console_output",
+        conditions=dict(method=["GET"])
+    )
+
     webapp.mapper.connect(
         "common_problems",
         "/api/jobs/{id}/common_problems",
diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
index 7d2d87005fb2..750b7b0690c3 100644
--- a/lib/galaxy/webapps/galaxy/services/jobs.py
+++ b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -48,14 +48,8 @@ def show(
         trans: ProvidesUserContext,
         id: DecodedDatabaseIdField,
         full: bool = False,
-        stdout_position: int = 0,
-        stdout_length: int = 0,
-        stderr_position: int = 0,
-        stderr_length: int = 0,
     ) -> Dict[str, Any]:
-        job = self.job_manager.get_accessible_job(
-            trans, id, stdout_position, stdout_length, stderr_position, stderr_length
-        )
+        job = self.job_manager.get_accessible_job(trans, id,)
         return view_show_job(trans, job, bool(full))
 
     def index(

From 70bfcc4d310bff83a19aaf7fb1ac045aa6de56d0 Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 15 Dec 2023 14:57:12 -0500
Subject: [PATCH 10/24] Use stdout api endpoint in job info ui while job is
 running

---
 .../JobInformation/JobInformation.test.js     |  2 +-
 .../JobInformation/JobInformation.vue         | 37 ++++++++++++++-----
 .../src/components/providers/JobProvider.js   | 17 +++++++--
 3 files changed, 42 insertions(+), 14 deletions(-)

diff --git a/client/src/components/JobInformation/JobInformation.test.js b/client/src/components/JobInformation/JobInformation.test.js
index 09f8a7bb57be..4c0a5470f846 100644
--- a/client/src/components/JobInformation/JobInformation.test.js
+++ b/client/src/components/JobInformation/JobInformation.test.js
@@ -23,7 +23,7 @@ describe("JobInformation/JobInformation.vue", () => {
         axiosMock.onGet(new RegExp(`api/configuration/decode/*`)).reply(200, { decoded_id: 123 });
         axiosMock
             .onGet(
-                "/api/jobs/test_id?full=True&stdout_position=0&stdout_length=50000&stderr_position=0&stderr_length=50000"
+                "/api/jobs/test_id?full=True"
             )
             .reply(200, jobResponse);
     });
diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
index e3d3cbe6cb51..8848e31083c8 100644
--- a/client/src/components/JobInformation/JobInformation.vue
+++ b/client/src/components/JobInformation/JobInformation.vue
@@ -1,13 +1,14 @@
 <template>
     <div>
-        <JobDetailsProvider
+        <JobDetailsProvider auto-refresh :job-id="job_id" @update:result="updateJob"/>
+        <JobConsoleOutputProvider
             auto-refresh
             :job-id="job_id"
             :stdout_position="stdout_position"
             :stdout_length="stdout_length"
             :stderr_position="stderr_position"
             :stderr_length="stderr_length"
-            @update:result="updateJob" />
+            @update:result="updateConsoleOutputs"/>
         <h2 class="h-md">Job Information</h2>
         <table id="job-information" class="tabletip info_data_table">
             <tbody>
@@ -85,7 +86,7 @@
 
 <script>
 import CopyToClipboard from "components/CopyToClipboard";
-import { JobDetailsProvider } from "components/providers/JobProvider";
+import { JobDetailsProvider, JobConsoleOutputProvider } from "components/providers/JobProvider";
 import UtcDate from "components/UtcDate";
 import { formatDuration, intervalToDuration } from "date-fns";
 import { getAppRoot } from "onload/loadConfig";
@@ -99,6 +100,7 @@ export default {
         CodeRow,
         DecodedId,
         JobDetailsProvider,
+        JobConsoleOutputProvider,
         UtcDate,
         CopyToClipboard,
     },
@@ -139,14 +141,29 @@ export default {
         },
         updateJob(job) {
             this.job = job;
-            // Keep stdout in memory and only fetch new text via JobProvider
-            if (job.tool_stdout != null) {
-                this.stdout_text += job.tool_stdout;
-                this.stdout_position += job.tool_stdout.length;
+            // Load stored stdout and stderr
+            if (this.jobIsTerminal) {
+                if (job.tool_stdout) {
+                    this.stdout_text += job.tool_stdout;
+                    this.stdout_position += job.tool_stdout.length;
+                }
+                if (job.tool_stderr) {
+                    this.stderr_text += job.tool_stderr;
+                    this.stderr_position += job.tool_stderr.length;
+                }
             }
-            if (job.tool_stderr != null) {
-                this.stderr_text += job.tool_stderr;
-                this.stderr_position += job.tool_stderr.length;
+        },
+        updateConsoleOutputs(output) {
+            // Keep stdout in memory and only fetch new text via JobProvider
+            if (output && !this.jobIsTerminal) {
+                if (output.stdout != null) {
+                    this.stdout_text += output.stdout;
+                    this.stdout_position += output.stdout.length;
+                }
+                if (output.stderr != null) {
+                    this.stderr_text += output.stderr;
+                    this.stderr_position += output.stderr.length;
+                }
             }
         },
     },
diff --git a/client/src/components/providers/JobProvider.js b/client/src/components/providers/JobProvider.js
index ef5f302e8080..e736ebfc74bc 100644
--- a/client/src/components/providers/JobProvider.js
+++ b/client/src/components/providers/JobProvider.js
@@ -5,10 +5,20 @@ import { rethrowSimple } from "utils/simple-error";
 
 import { cleanPaginationParameters, stateIsTerminal } from "./utils";
 
-async function jobDetails({ jobId, stdout_position = 0, stdout_length = 0, stderr_position = 0, stderr_length = 0 }) {
+async function jobDetails({ jobId }) {
     const url =
-        `${getAppRoot()}api/jobs/${jobId}?full=True&stdout_position=${stdout_position}` +
-        `&stdout_length=${stdout_length}&stderr_position=${stderr_position}&stderr_length=${stderr_length}`;
+        `${getAppRoot()}api/jobs/${jobId}?full=True`;
+    try {
+        const { data } = await axios.get(url);
+        return data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
+
+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;
@@ -28,6 +38,7 @@ async function jobProblems({ jobId }) {
 }
 
 export const JobDetailsProvider = SingleQueryProvider(jobDetails, stateIsTerminal);
+export const JobConsoleOutputProvider = SingleQueryProvider(jobConsoleOutput, stateIsTerminal);
 export const JobProblemProvider = SingleQueryProvider(jobProblems, stateIsTerminal);
 
 export function jobsProvider(ctx, callback, extraParams = {}) {

From 791348a90500d80a26bc9473aba31332bd85ab5f Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Wed, 27 Mar 2024 11:44:54 -0400
Subject: [PATCH 11/24] Fix linting errors

---
 client/src/api/schema/schema.ts               | 66 ++++++++++++++++++-
 .../JobInformation/JobInformation.vue         |  6 +-
 lib/galaxy/jobs/runners/pulsar.py             |  4 +-
 lib/galaxy/managers/jobs.py                   |  6 +-
 lib/galaxy/schema/jobs.py                     |  2 +-
 5 files changed, 74 insertions(+), 10 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index c0d60b6b9a5d..6306fa45a3c0 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -1070,6 +1070,15 @@ export interface paths {
         /** Check inputs and job for common potential problems to aid in error reporting */
         get: operations["check_common_problems_api_jobs__job_id__common_problems_get"];
     };
+    "/api/jobs/{job_id}/console_output": {
+        /**
+         * Returns STDOUT and STDERR from job.
+         * @description Get the stdout and/or stderr of a job. The position parameters are the index
+         * of where to start reading stdout/stderr. The length parameterscontrol how much
+         * stdout/stderr is read.
+         */
+        get: operations["get_console_output_api_jobs__job_id__console_output_get"];
+    };
     "/api/jobs/{job_id}/destination_params": {
         /** Return destination parameters for specified job. */
         get: operations["destination_params_job_api_jobs__job_id__destination_params_get"];
@@ -8056,6 +8065,24 @@ export interface components {
              */
             update_time: string;
         };
+        /** JobConsoleOutput */
+        JobConsoleOutput: {
+            /**
+             * Job State
+             * @description The current job's state
+             */
+            state?: string;
+            /**
+             * STDERR
+             * @description Job STDERR text
+             */
+            stderr?: string | null;
+            /**
+             * STDOUT
+             * @description Job STDOUT text
+             */
+            stdout?: string | null;
+        };
         /** JobDestinationParams */
         JobDestinationParams: {
             /**
@@ -18832,6 +18859,43 @@ export interface operations {
             };
         };
     };
+    get_console_output_api_jobs__job_id__console_output_get: {
+        /**
+         * Returns STDOUT and STDERR from job.
+         * @description Get the stdout and/or stderr of a job. The position parameters are the index
+         * of where to start reading stdout/stderr. The length parameterscontrol how much
+         * stdout/stderr is read.
+         */
+        parameters: {
+            query: {
+                stdout_position: number;
+                stdout_length: number;
+                stderr_position: number;
+                stderr_length: number;
+            };
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string | null;
+            };
+            path: {
+                job_id: string;
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["JobConsoleOutput"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
     destination_params_job_api_jobs__job_id__destination_params_get: {
         /** Return destination parameters for specified job. */
         parameters: {
@@ -24301,4 +24365,4 @@ export interface operations {
             };
         };
     };
-}
\ No newline at end of file
+}
diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
index 6f733a19a3ff..f64917186b0f 100644
--- a/client/src/components/JobInformation/JobInformation.vue
+++ b/client/src/components/JobInformation/JobInformation.vue
@@ -35,10 +35,10 @@ const stdout_position = computed(() => stdout_text.value.length);
 const stderr_position = computed(() => stderr_text.value.length);
 
 const runTime = computed(() =>
-    formatDuration(intervalToDuration({ start: new Date(job.create_time), end: new Date(job.update_time) }))
+    formatDuration(intervalToDuration({ start: new Date(job.value.create_time), end: new Date(job.value.update_time) }))
 );
 
-const jobIsTerminal = computed(() => job.value && !NON_TERMINAL_STATES.includes(job.state));
+const jobIsTerminal = computed(() => job.value && !NON_TERMINAL_STATES.includes(job.value.state));
 
 const routeToInvocation = computed(() => `/workflows/invocations/${invocationId.value}`);
 
@@ -52,7 +52,7 @@ function updateJob(newJob) {
     if (newJob) {
         fetchInvocation(newJob.id);
     }
-    if (jobIsTerminal) {
+    if (jobIsTerminal.value) {
         if (newJob.tool_stdout) {
             stdout_text.value = newJob.tool_stdout;
         }
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 20ae553f71b4..8ed7b66ad8f9 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -650,8 +650,8 @@ def finish_job(self, job_state: JobState):
                 if tool_stdout and tool_stderr:
                     pass
                 try:
-                    file_path = Path(job_wrapper.working_directory) / "outputs" / file
-                    file_content = open(file_path, "r")
+                    file_path = os.path.join(job_wrapper.working_directory, "outputs", file)
+                    file_content = open(file_path)
                     if tool_stdout is None and file == "tool_stdout":
                         tool_stdout = file_content.read()
                     elif tool_stderr is None and file == "tool_stderr":
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 37ddfe8c4fb4..d5f71c850ac4 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -282,7 +282,7 @@ def get_job_console_output(self, trans, job, stdout_position=-1, stdout_length=0
             raise ObjectNotFound()
 
         # If stdout_length and stdout_position are good values, then load standard out and add it to status
-        console_output = dict()
+        console_output = {}
         console_output["state"] = job.state
         if job.state == job.states.RUNNING:
             working_directory = trans.app.object_store.get_filename(
@@ -291,7 +291,7 @@ def get_job_console_output(self, trans, job, stdout_position=-1, stdout_length=0
             if stdout_length > -1 and stdout_position > -1:
                 try:
                     stdout_path = Path(working_directory) / STDOUT_LOCATION
-                    stdout_file = open(stdout_path, "r")
+                    stdout_file = open(stdout_path)
                     stdout_file.seek(stdout_position)
                     console_output["stdout"] = stdout_file.read(stdout_length)
                 except Exception as e:
@@ -299,7 +299,7 @@ def get_job_console_output(self, trans, job, stdout_position=-1, stdout_length=0
             if stderr_length > -1 and stderr_position > -1:
                 try:
                     stderr_path = Path(working_directory) / STDERR_LOCATION
-                    stderr_file = open(stderr_path, "r")
+                    stderr_file = open(stderr_path)
                     stderr_file.seek(stderr_position)
                     console_output["stderr"] = stderr_file.read(stderr_length)
                 except Exception as e:
diff --git a/lib/galaxy/schema/jobs.py b/lib/galaxy/schema/jobs.py
index b48e92f51f90..52ba6a208d27 100644
--- a/lib/galaxy/schema/jobs.py
+++ b/lib/galaxy/schema/jobs.py
@@ -213,7 +213,7 @@ class JobOutput(Model):
 
 
 class JobConsoleOutput(Model):
-    state: str = Field(None, title="Job State", description="The current job's state")
+    state: Optional[JobState] = Field(None, title="Job State", description="The current job's state")
     stdout: Optional[str] = Field(None, title="STDOUT", description="Job STDOUT text")
     stderr: Optional[str] = Field(None, title="STDERR", description="Job STDERR text")
 

From 87f512637b0b2d2a0400e9059086ed408a9297a4 Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Wed, 27 Mar 2024 13:05:19 -0400
Subject: [PATCH 12/24] Fix more formatting and schema issues

---
 client/src/api/schema/schema.ts                  |  2 +-
 .../components/JobInformation/JobInformation.vue |  8 ++++----
 client/src/components/providers/JobProvider.js   | 16 +++++++++++-----
 lib/galaxy/managers/jobs.py                      |  4 +++-
 lib/galaxy/webapps/galaxy/api/jobs.py            | 14 +++++++-------
 lib/galaxy/webapps/galaxy/services/jobs.py       |  5 ++++-
 6 files changed, 30 insertions(+), 19 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index 6306fa45a3c0..9660be2fcda7 100644
--- 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
index f64917186b0f..0c68bc4d8190 100644
--- 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);
@@ -97,7 +97,7 @@ 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"
@@ -105,7 +105,7 @@ async function fetchInvocation(jobId) {
             :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
index e736ebfc74bc..b70cd152a004 100644
--- 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
index d5f71c850ac4..61d68d015f19 100644
--- 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
index c726becc42fa..de2dc7395c6a 100644
--- 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
index 76304a9742b2..cd12a8db599c 100644
--- 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(

From f1f8eec1965cb592c1cff133a805a158ad81ced8 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Fri, 3 May 2024 14:28:43 -0700
Subject: [PATCH 13/24] format imports

---
 lib/galaxy/managers/jobs.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index bf157d5e7c04..eec3a2c3b510 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -5,15 +5,12 @@
     date,
     datetime,
 )
-
 from pathlib import Path
-
 from typing import (
     cast,
     List,
 )
 
-
 import sqlalchemy
 from boltons.iterutils import remap
 from pydantic import (

From 6faf6839da5476922c3e79d2d9a5955b1f4dffee Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Thu, 9 May 2024 15:18:01 -0400
Subject: [PATCH 14/24] Fix issue where only one of stdout or stderr is present

---
 lib/galaxy/managers/jobs.py           | 2 ++
 lib/galaxy/webapps/galaxy/api/jobs.py | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 61d68d015f19..5476c68b39d5 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -298,6 +298,7 @@ def get_job_console_output(
                     console_output["stdout"] = stdout_file.read(stdout_length)
                 except Exception as e:
                     log.error("Could not read STDOUT: %s", e)
+                    console_output["stdout"] = ""
             if stderr_length > -1 and stderr_position > -1:
                 try:
                     stderr_path = Path(working_directory) / STDERR_LOCATION
@@ -306,6 +307,7 @@ def get_job_console_output(
                     console_output["stderr"] = stderr_file.read(stderr_length)
                 except Exception as e:
                     log.error("Could not read STDERR: %s", e)
+                    console_output["stderr"] = ""
         else:
             console_output["stdout"] = job.tool_stdout
             console_output["stderr"] = job.tool_stderr
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index de2dc7395c6a..7d3163de8092 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -385,7 +385,7 @@ def console_output(
     ) -> JobConsoleOutput:
         """
         Get the stdout and/or stderr of a job. The position parameters are the index
-        of where to start reading stdout/stderr. The length parameterscontrol how much
+        of where to start reading stdout/stderr. The length parameters control how much
         stdout/stderr is read.
         """
         job = self.service.get_job(trans, job_id)

From 63ede702ecf9f46016cd4f6037232b42309770fe Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Wed, 29 May 2024 15:04:49 -0400
Subject: [PATCH 15/24] Fix docstrings that refer to tool stdout as job stdout

---
 client/src/api/schema/schema.ts       | 14 +++++++-------
 lib/galaxy/schema/jobs.py             |  4 ++--
 lib/galaxy/webapps/galaxy/api/jobs.py |  4 ++--
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index a13a0673d97b..e5bb4b249806 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -1084,9 +1084,9 @@ export interface paths {
     };
     "/api/jobs/{job_id}/console_output": {
         /**
-         * Returns STDOUT and STDERR from job.
-         * @description Get the stdout and/or stderr of a job. The position parameters are the index
-         * of where to start reading stdout/stderr. The length parameterscontrol how much
+         * Returns STDOUT and STDERR from the tool running in a specific job.
+         * @description Get the stdout and/or stderr of a tool running in a specific job. The position parameters are the index
+         * of where to start reading stdout/stderr. The length parameters control how much
          * stdout/stderr is read.
          */
         get: operations["get_console_output_api_jobs__job_id__console_output_get"];
@@ -8478,12 +8478,12 @@ export interface components {
             state?: components["schemas"]["JobState"] | null;
             /**
              * STDERR
-             * @description Job STDERR text
+             * @description Tool STDERR text from the tool running in a specific job
              */
             stderr?: string | null;
             /**
              * STDOUT
-             * @description Job STDOUT text
+             * @description Tool STDOUT text from the tool running in a specific job
              */
             stdout?: string | null;
         };
@@ -19435,8 +19435,8 @@ export interface operations {
     };
     get_console_output_api_jobs__job_id__console_output_get: {
         /**
-         * Returns STDOUT and STDERR from job.
-         * @description Get the stdout and/or stderr of a job. The position parameters are the index
+         * Returns STDOUT and STDERR from the tool running in a specific job.
+         * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
          * of where to start reading stdout/stderr. The length parameterscontrol how much
          * stdout/stderr is read.
          */
diff --git a/lib/galaxy/schema/jobs.py b/lib/galaxy/schema/jobs.py
index 52ba6a208d27..b6d67b7d2a42 100644
--- a/lib/galaxy/schema/jobs.py
+++ b/lib/galaxy/schema/jobs.py
@@ -214,8 +214,8 @@ class JobOutput(Model):
 
 class JobConsoleOutput(Model):
     state: Optional[JobState] = Field(None, title="Job State", description="The current job's state")
-    stdout: Optional[str] = Field(None, title="STDOUT", description="Job STDOUT text")
-    stderr: Optional[str] = Field(None, title="STDERR", description="Job STDERR text")
+    stdout: Optional[str] = Field(None, title="STDOUT", description="Tool STDOUT from job.")
+    stderr: Optional[str] = Field(None, title="STDERR", description="Tool STDERR from job.")
 
 
 class JobParameter(Model):
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index b8ff2d8350a1..10242f38d75d 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -372,7 +372,7 @@ def outputs(
     @router.get(
         "/api/jobs/{job_id}/console_output",
         name="get_console_output",
-        summary="Returns STDOUT and STDERR from job.",
+        summary="Returns STDOUT and STDERR from the tool running in a specific job.",
     )
     def console_output(
         self,
@@ -384,7 +384,7 @@ def console_output(
         trans: ProvidesUserContext = DependsOnTrans,
     ) -> JobConsoleOutput:
         """
-        Get the stdout and/or stderr of a job. The position parameters are the index
+        Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
         of where to start reading stdout/stderr. The length parameters control how much
         stdout/stderr is read.
         """

From 735d5ef838016da1fcc72c7d2902ecfba14c1945 Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 14 Jun 2024 11:19:28 -0400
Subject: [PATCH 16/24] Restrict tool stdout updating to properly configured
 job destinations

---
 lib/galaxy/managers/jobs.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 4424b6efc4bd..2332533446af 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -30,6 +30,7 @@
 
 from galaxy import model
 from galaxy.exceptions import (
+    ConfigDoesNotAllowException,
     ItemAccessibilityException,
     ObjectNotFound,
     RequestParameterInvalidException,
@@ -69,6 +70,7 @@
     defaultdict,
     ExecutionTimer,
     listify,
+    string_as_bool_or_none,
 )
 from galaxy.util.search import (
     FilteredTerm,
@@ -284,6 +286,11 @@ def get_job_console_output(
         if job is None:
             raise ObjectNotFound()
 
+        # Check job destination params to see if stdout reporting is enabled
+        dest_params = job.destination_params
+        if not string_as_bool_or_none(dest_params.get("live_tool_output_reporting", False)):
+            raise ConfigDoesNotAllowException()
+
         # If stdout_length and stdout_position are good values, then load standard out and add it to status
         console_output = {}
         console_output["state"] = job.state

From deaba3918d01dd03e4682c10f02c050d93103e18 Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 14 Jun 2024 11:22:03 -0400
Subject: [PATCH 17/24] update client api schema

---
 client/src/api/schema/schema.ts | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index e5bb4b249806..baae4cbb3b01 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -1085,7 +1085,7 @@ export interface paths {
     "/api/jobs/{job_id}/console_output": {
         /**
          * Returns STDOUT and STDERR from the tool running in a specific job.
-         * @description Get the stdout and/or stderr of a tool running in a specific job. The position parameters are the index
+         * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
          * of where to start reading stdout/stderr. The length parameters control how much
          * stdout/stderr is read.
          */
@@ -8478,12 +8478,12 @@ export interface components {
             state?: components["schemas"]["JobState"] | null;
             /**
              * STDERR
-             * @description Tool STDERR text from the tool running in a specific job
+             * @description Tool STDERR from job.
              */
             stderr?: string | null;
             /**
              * STDOUT
-             * @description Tool STDOUT text from the tool running in a specific job
+             * @description Tool STDOUT from job.
              */
             stdout?: string | null;
         };
@@ -19437,7 +19437,7 @@ export interface operations {
         /**
          * Returns STDOUT and STDERR from the tool running in a specific job.
          * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
-         * of where to start reading stdout/stderr. The length parameterscontrol how much
+         * of where to start reading stdout/stderr. The length parameters control how much
          * stdout/stderr is read.
          */
         parameters: {

From 2e472a9c883094b9c91713bdcccf0b2ab06a66f4 Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Fri, 12 Jul 2024 14:41:57 -0400
Subject: [PATCH 18/24] Update client api schema

---
 client/src/api/schema/schema.ts | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index 16f3650da92b..cd21ff8bde9a 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -19802,13 +19802,13 @@ export interface operations {
             };
         };
     };
+    /**
+     * Returns STDOUT and STDERR from the tool running in a specific job.
+     * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
+     * of where to start reading stdout/stderr. The length parameters control how much
+     * stdout/stderr is read.
+     */
     get_console_output_api_jobs__job_id__console_output_get: {
-        /**
-         * Returns STDOUT and STDERR from the tool running in a specific job.
-         * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
-         * of where to start reading stdout/stderr. The length parameters control how much
-         * stdout/stderr is read.
-         */
         parameters: {
             query: {
                 stdout_position: number;
@@ -19816,8 +19816,8 @@ export interface operations {
                 stderr_position: number;
                 stderr_length: number;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {

From 53051e7868902acdc45088777c63d2c48f19390a Mon Sep 17 00:00:00 2001
From: Gregory Cage <cagege@ornl.gov>
Date: Mon, 23 Sep 2024 11:47:47 -0400
Subject: [PATCH 19/24] Update client api schema

---
 client/src/api/schema/schema.ts | 47 ++++++++++++++++++++++++---------
 1 file changed, 35 insertions(+), 12 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index 340356b740a4..35b2435ab92d 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -2770,13 +2770,26 @@ export interface paths {
         trace?: never;
     };
     "/api/jobs/{job_id}/console_output": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns STDOUT and STDERR from the tool running in a specific job.
          * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
-         * of where to start reading stdout/stderr. The length parameters control how much
-         * stdout/stderr is read.
+         *     of where to start reading stdout/stderr. The length parameters control how much
+         *     stdout/stderr is read.
          */
         get: operations["get_console_output_api_jobs__job_id__console_output_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/destination_params": {
         parameters: {
@@ -26632,12 +26645,6 @@ export interface operations {
             };
         };
     };
-    /**
-     * Returns STDOUT and STDERR from the tool running in a specific job.
-     * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
-     * of where to start reading stdout/stderr. The length parameters control how much
-     * stdout/stderr is read.
-     */
     get_console_output_api_jobs__job_id__console_output_get: {
         parameters: {
             query: {
@@ -26653,23 +26660,39 @@ export interface operations {
             path: {
                 job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["JobConsoleOutput"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    /** Return destination parameters for specified job. */
     destination_params_job_api_jobs__job_id__destination_params_get: {
         parameters: {
             query?: never;

From a2bffb849f02f498e12d40b9ae04bfdf456f1113 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2024 13:37:34 -0500
Subject: [PATCH 20/24] Update JobInformation.test.js for live console output.

---
 client/src/components/JobInformation/JobInformation.test.js | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/client/src/components/JobInformation/JobInformation.test.js b/client/src/components/JobInformation/JobInformation.test.js
index 0508a6485825..68602a1b6ffd 100644
--- a/client/src/components/JobInformation/JobInformation.test.js
+++ b/client/src/components/JobInformation/JobInformation.test.js
@@ -30,6 +30,12 @@ describe("JobInformation/JobInformation.vue", () => {
             }),
             http.get("/api/invocations", ({ response }) => {
                 return response(200).json([]);
+            }),
+            http.get("/api/jobs/{job_id}/console_output", ({ response }) => {
+                return response(200).json({
+                    stdout: "stdout",
+                    stderr: "stderr",
+                });
             })
         );
     });

From 8063632c30e4dcae43504ae21773e1da50f74ea8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 12 Nov 2024 14:02:21 -0500
Subject: [PATCH 21/24] Improved error handling for live console for tool
 execution.

---
 client/src/components/providers/JobProvider.js | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/client/src/components/providers/JobProvider.js b/client/src/components/providers/JobProvider.js
index 3be3df9e97e0..0cc077d83f10 100644
--- a/client/src/components/providers/JobProvider.js
+++ b/client/src/components/providers/JobProvider.js
@@ -26,7 +26,18 @@ async function jobConsoleOutput({
         `${getAppRoot()}api/jobs/${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);
+        const { status, data } = await axios.get(url, {
+            validateStatus: function (status) {
+                return status == 200 || status == 403;
+            },
+        });
+        if (status == 403) {
+            if (data.err_code == 403004) {
+                console.log("This job destination does not support console output");
+                return { state: "ok" };
+            }
+            throw Error("Problem fetching state");
+        }
         return data;
     } catch (e) {
         rethrowSimple(e);

From be1141206844bf0dea8914f296162821ad8d322a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 17 Nov 2024 20:50:56 -0500
Subject: [PATCH 22/24] xfail the test for the freeze.

Got permission from Marius in exchange for pledge to fix it before the release.
---
 test/integration/test_pulsar_embedded_mq.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/integration/test_pulsar_embedded_mq.py b/test/integration/test_pulsar_embedded_mq.py
index 19022a9b4b2f..b1f84a7ca407 100644
--- a/test/integration/test_pulsar_embedded_mq.py
+++ b/test/integration/test_pulsar_embedded_mq.py
@@ -78,6 +78,7 @@ def setUp(self) -> None:
     def handle_galaxy_config_kwds(cls, config):
         _handle_galaxy_config_kwds(cls, config)
 
+    @pytest.mark.xfail(reason="broken with https://github.com/galaxyproject/galaxy/pull/16975, @jmchilton must fix prior to full release 25.0")
     def test_purge_while_job_running(self):
         purge_while_job_running(self.dataset_populator)
 

From f0aa89a02846dc7f90f8f7a8717a66e5b9eadc3a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 17 Nov 2024 23:34:34 -0500
Subject: [PATCH 23/24] linting fix

---
 test/integration/test_pulsar_embedded_mq.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/test/integration/test_pulsar_embedded_mq.py b/test/integration/test_pulsar_embedded_mq.py
index b1f84a7ca407..f276f72062f1 100644
--- a/test/integration/test_pulsar_embedded_mq.py
+++ b/test/integration/test_pulsar_embedded_mq.py
@@ -78,7 +78,9 @@ def setUp(self) -> None:
     def handle_galaxy_config_kwds(cls, config):
         _handle_galaxy_config_kwds(cls, config)
 
-    @pytest.mark.xfail(reason="broken with https://github.com/galaxyproject/galaxy/pull/16975, @jmchilton must fix prior to full release 25.0")
+    @pytest.mark.xfail(
+        reason="broken with https://github.com/galaxyproject/galaxy/pull/16975, @jmchilton must fix prior to full release 25.0"
+    )
     def test_purge_while_job_running(self):
         purge_while_job_running(self.dataset_populator)
 

From 394fb16da329180d16bd0043e076dd6e6ca89bf3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 18 Nov 2024 00:08:00 -0500
Subject: [PATCH 24/24] Ahhh... the set metadata file is JSON and cannot be
 appended.

So lets restrict this new append in the job files behavior to just append for the tool_stdout and tool_stderr files.
---
 lib/galaxy/webapps/galaxy/api/job_files.py  | 2 +-
 test/integration/test_pulsar_embedded_mq.py | 3 ---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index f15bf4ec9faa..3d02ccfcf7be 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -133,7 +133,7 @@ def create(self, trans, job_id, payload, **kwargs):
         target_dir = os.path.dirname(path)
         util.safe_makedirs(target_dir)
         try:
-            if os.path.exists(path):
+            if os.path.exists(path) and (path.endswith("tool_stdout") or path.endswith("tool_stderr")):
                 with open(path, "ab") as destination:
                     shutil.copyfileobj(open(input_file.name, "rb"), destination)
             else:
diff --git a/test/integration/test_pulsar_embedded_mq.py b/test/integration/test_pulsar_embedded_mq.py
index f276f72062f1..19022a9b4b2f 100644
--- a/test/integration/test_pulsar_embedded_mq.py
+++ b/test/integration/test_pulsar_embedded_mq.py
@@ -78,9 +78,6 @@ def setUp(self) -> None:
     def handle_galaxy_config_kwds(cls, config):
         _handle_galaxy_config_kwds(cls, config)
 
-    @pytest.mark.xfail(
-        reason="broken with https://github.com/galaxyproject/galaxy/pull/16975, @jmchilton must fix prior to full release 25.0"
-    )
     def test_purge_while_job_running(self):
         purge_while_job_running(self.dataset_populator)