Feature - stdout live reporting

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?: {

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 +8,13 @@
                 <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 ${action}`"
+                    @mousedown="mouseIsDown = true"
+                    @mousemove="mouseIsDown ? (mouseMoved = true) : (mouseMoved = false)"
+                    @mouseup="toggleExpanded()">
                     <FontAwesomeIcon :icon="iconClass" />
                 </b-col>
             </b-row>
@@ -40,6 +41,7 @@ export default {
             mouseIsDown: false,
             mouseMoved: false,
             expanded: false,
+            lastPos: 0,
         };
     },
     computed: {
@@ -53,6 +55,18 @@ export default {
             return this.expanded ? ["fas", "compress-alt"] : ["fas", "expand-alt"];
         },
     },
+    updated() {
+        try {
+            var codeDiv = this.$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 +86,8 @@ export default {
     padding: 0;
     margin: 0;
 }
+.code {
+    max-height: 50em;
+    overflow: auto;
+}
 </style>

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(() => {

client/src/components/JobInformation/JobInformation.vue

@@ -1,6 +1,13 @@
 <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 +48,8 @@
                     </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 +115,12 @@ 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 +139,15 @@ 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;
+            }
         },
     },
 };

client/src/components/providers/JobProvider.js

@@ -5,8 +5,10 @@ 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;

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 +73,10 @@
 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")
 
@@ -231,7 +236,9 @@ 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 +255,30 @@ 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 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
+            )
+            if stdout_length > 0 and stdout_position > -1:
+                try:
+                    stdout_path = Path(working_directory) / STDOUT_LOCATION
+                    stdout_file = open(stdout_path)
+                    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)
+                    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):

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()

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -178,15 +178,31 @@ 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
 
         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))
+        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(

lib/galaxy/webapps/galaxy/services/jobs.py

@@ -48,8 +48,14 @@ 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(