Some minor changes to the dataset show_params page #11244

simonbray · 2021-01-28T12:51:16Z

Implemented some of the suggestions in #11109

mvdbeek · 2021-01-28T14:04:01Z

client/src/components/DatasetInformation/DatasetInformation.vue

@@ -37,13 +37,25 @@
                    <tr v-if="dataset.id">
                        <td>History Content API ID</td>
                        <td>
-                            <div id="dataset-id">{{ dataset.id }} <decoded-id :id="dataset.id" /></div>
+                            <div id="dataset-id">
+                                {{ dataset.id }} <decoded-id :id="dataset.id" /> (<a


This should go into the JobInformation.vue file and it probably needs to use the job id?

mvdbeek · 2021-01-28T14:04:06Z

lib/galaxy/model/__init__.py

+        if self.workflow_invocation_step:
+            rval['created_by_workflow'] = True
+            rval['workflow_invocation_id'] = self.workflow_invocation_step.workflow_invocation.id
+            rval['workflow_id'] = self.workflow_invocation_step.workflow_invocation.workflow_id
+        else:
+            rval['created_by_workflow'] = False


This is really muddying the waters here, can you please remove this section?

While my initial reaction is that I don't like this, of course this would be useful, but this is a bit of a "details" view that we don't want to return whenever someone hits the job api endpoint.

I would suggest adding another view here and then serializing the workflow invocation step (rval['workflow_invocation_step'] = self.workflow_invocation_step.to_dict() if self.workflow_invocation_step else {}). You can to add the workflow_invocation_id in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/model/__init__.py#L5670-L5671.

The job component can then fetch the additional details from the vuex store if it is appropriate.

this is also hopefully been addressed

mvdbeek · 2021-01-28T14:51:15Z

client/src/components/DatasetInformation/DatasetInformation.vue

-                            <div id="history_id">{{ dataset.history_id }} <decoded-id :id="dataset.history_id" /></div>
+                            <div id="history_id">
+                                {{ dataset.history_id }} <decoded-id :id="dataset.history_id" /> (<a
+                                    :href="'/histories/view?id=' + dataset.history_id"


I think we want to get away from this direct navigation, but I'm not sure what the replacement is. @dannon is that how you would do this ? Might also be better to have a button for this ?

I guess, we kinda have to deal with it for now, not sure about global Vue router status

client/src/components/JobInformation/CodeRow.vue

client/src/components/JobInformation/JobInformation.vue

bgruening · 2021-02-25T11:26:39Z

We just discussed in a paper-cuts call the stderr/stdout display. I think it would be nice if we have a more scalable way to display files in this view. Not only stderr/stdout but also inputs and outputs.

From my bug-hunting perspective, when I try to answer user-report-mails I usually see the job-info page. And most of the time I need to see stderr and the input sites. It would be nice if we could open a modal (or the scratchbook?) to show those datasets. This would make the debugging way easier.

This should not go into this PR, but if you like the idea @mvdbeek Oleg could work on it he said.

mvdbeek · 2021-02-25T11:28:20Z

We just discussed in a paper-cuts call the stderr/stdout display. I think it would be nice if we have a more scalable way to display files in this view. Not only stderr/stdout but also inputs and outputs.

Can we discuss that in the next call ? I joined late ... have you seen how this looks like in 21.01 ?

This reverts commit 023dea1.

mvdbeek · 2021-04-08T13:52:06Z

client/src/components/DatasetInformation/DatasetInformation.vue

@@ -1,11 +1,11 @@
 <template>
    <DatasetProvider :id="hda_id" v-slot="{ item: dataset, loading }">
        <div v-if="!loading">
-            <h3>Dataset Information</h3>
+            <h3>Dataset Information (<a :href="'/datasets/edit?dataset_id=' + dataset.id" target="_top">edit</a>)</h3>


Can you add a edit button here ?

client/src/components/DatasetInformation/DatasetInformation.vue

mvdbeek · 2021-04-08T13:54:42Z

client/src/components/JobInformation/JobInformation.vue

@@ -6,7 +6,7 @@
                <tr v-if="job && job.tool_id">
                    <td>Galaxy Tool ID:</td>
                    <td id="galaxy-tool-id">
-                        {{ job.tool_id }}
+                        {{ job.tool_id }} (<a :href="'/root?tool_id=' + job.tool_id" target="_top">run</a>)


Can you add a button here as well ?

mvdbeek · 2021-04-08T13:55:32Z

client/src/components/JobInformation/JobInformation.vue

+                    <td>Workflow ID:</td>
+                    <td id="workflow-id">
+                        {{ job.workflow_invocation_step.id }} (<a
+                            :href="'/workflow/display_by_id?id=' + job.workflow_invocation_step.id"


This is probably the workflow id, not the Stored Workflow id. Are you sure this is correct ?

mvdbeek · 2021-04-08T14:00:18Z

client/src/store/jobStore.js

@@ -14,7 +14,7 @@ const getters = {

 const actions = {
    fetchJob: async ({ commit }, jobId) => {
-        const { data } = await axios.get(`${getAppRoot()}api/jobs/${jobId}?full=true`);
+        const { data } = await axios.get(`${getAppRoot()}api/jobs/${jobId}?full=true&view=workflow`);


This is going to fetch the expensive details for every job here. You need to make the view a variable.

mvdbeek · 2021-04-08T14:03:22Z

client/src/components/JobInformation/JobInformation.vue

@@ -47,7 +65,11 @@
                </tr>
                <tr v-if="job && job.id">
                    <td>Job API ID:</td>
-                    <td id="encoded-job-id">{{ job.id }} <decoded-id :id="job.id" /></td>
+                    <td id="encoded-job-id">
+                        {{ job.id }} <decoded-id :id="job.id" /> (<a :href="'/root?job_id=' + job.id" target="_top"


Can you make the rerun a button (like it is in the history panel)

lib/galaxy/model/__init__.py

mvdbeek · 2021-09-08T15:40:08Z

There's also a lot of different things in here, some more controversial than others. Could you break this up into one fix / improvement per PR ? That'll increase the chance to get things merged quickly

simonbray · 2021-09-08T15:49:52Z

Just checking I understand correctly: the controversial part is exposing the workflow and invocation ID in the jobs API?

mvdbeek · 2021-09-08T16:54:45Z

client/src/components/DatasetInformation/DatasetInformation.vue

+                </td>
+                <td>
+                    <b-button
+                        class="edit-button"


@simonbray there's more, this for instance probably doesn't make sense now that we display the dataset component in line, which already has the edit button

I removed the edit button as well as the job rerun button; both are already present in the newly embedded dataset / job components.

mvdbeek · 2021-09-08T16:55:42Z

client/src/components/JobInformation/JobInformation.vue

@@ -7,6 +7,9 @@
                    <td>Galaxy Tool ID:</td>
                    <td id="galaxy-tool-id">
                        {{ job.tool_id }}
+                        <a title="run" :href="`${getAppRoot()}root?tool_id=${job.tool_id}`" target="_top">
+                            <font-awesome-icon icon="play" />


This looks a bit odd without any spacing

mvdbeek · 2021-09-08T16:59:03Z

Just checking I understand correctly: the controversial part is exposing the workflow and invocation ID in the jobs API?

It's just generally a good strategy to create PRs that don't contain too many changes that don't depend on each other.

simonbray added 4 commits January 22, 2021 12:20

add links to dataset info page

3fd04aa

stop CodeRow recollapsing on click

023dea1

add workflow information to job API

fac42f5

add workflow information to show_params page

1f00680

github-actions bot added the area/UI-UX label Jan 28, 2021

github-actions bot added this to the 21.05 milestone Jan 28, 2021

simonbray added 2 commits January 28, 2021 14:21

fix testing and linting

d1c33c3

Merge remote-tracking branch 'upstream/dev' into show-params

7e4cd2d

simonbray force-pushed the show-params branch from 9b65361 to 7e4cd2d Compare January 28, 2021 13:23

mvdbeek reviewed Jan 28, 2021

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simonbray added 2 commits February 8, 2021 09:18

Merge remote-tracking branch 'upstream/dev' into show-params

71d1f62

some fixes

6d08759

simonbray added 2 commits February 25, 2021 12:34

add showWorkflowInfo param to JobInformation component

3b9c243

Revert "stop CodeRow recollapsing on click"

c248ffa

This reverts commit 023dea1.

simonbray force-pushed the show-params branch from 3d2a1fb to c248ffa Compare February 25, 2021 11:45

simonbray added 3 commits February 25, 2021 12:53

Merge remote-tracking branch 'upstream/dev' into show-params

718a692

js lint

3c5ae83

Merge remote-tracking branch 'upstream/dev' into show-params

ba31769

mvdbeek self-assigned this Apr 7, 2021

mvdbeek reviewed Apr 8, 2021

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simonbray mentioned this pull request Apr 26, 2021

Allow to filter /api/invocations by job_id #11882

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mvdbeek added the status/WIP label May 3, 2021

mvdbeek modified the milestones: 21.05, 21.09 May 3, 2021

OlegZharkov added 4 commits August 12, 2021 18:58

fix Created by workflow?

a77b3b2

change edit button

d016d43

fix root path

7cff66a

fix linting

33b6385

simonbray requested a review from mvdbeek August 19, 2021 12:52

mvdbeek removed this from the 21.09 milestone Sep 8, 2021

OlegZharkov modified the milestone: 21.09 Sep 8, 2021

dannon reviewed Sep 8, 2021

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Merge remote-tracking branch 'upstream/dev' into show-params

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simonbray force-pushed the show-params branch from a27a4e8 to 6daa29e Compare September 8, 2021 15:30

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simonbray added 4 commits September 9, 2021 10:58

update show_params buttons mouseover text

8d7196c

Merge remote-tracking branch 'upstream/dev' into show-params

3389afc

remove superfluous buttons

3417847

js lint

4a96b6d

simonbray force-pushed the show-params branch from 6a68789 to 4a96b6d Compare December 3, 2021 13:06

resolve conflict

bfadef7

mvdbeek marked this pull request as draft October 17, 2022 09:22

simonbray marked this pull request as ready for review December 22, 2022 11:41

github-actions bot added this to the 23.0 milestone Dec 22, 2022

simonbray marked this pull request as draft December 22, 2022 14:50

dannon modified the milestones: 23.0, 23.1 Jan 10, 2023

simonbray mentioned this pull request Feb 24, 2023

Provide way to get dataset collection id from the UI #15648

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Some minor changes to the dataset show_params page #11244

Some minor changes to the dataset show_params page #11244

simonbray commented Jan 28, 2021

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mvdbeek commented Sep 8, 2021

Some minor changes to the dataset show_params page #11244

Some minor changes to the dataset show_params page #11244

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