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feat: add new samples to public projects
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fixes #1167
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@NRayya
NRayya committed Nov 1, 2024
1 parent 79bd14c commit 6b0d889
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Showing 7 changed files with 258 additions and 11 deletions.
22 changes: 17 additions & 5 deletions app/Http/Controllers/ProjectController.php
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Original file line number Diff line number Diff line change
Expand Up @@ -274,7 +274,7 @@ public function validation(Request $request, Project $project)
$validation = $project->validation;

if (! $validation) {
$validation = new Validation();
$validation = new Validation;
$validation->save();
$project->validation()->associate($validation);
$project->save();
Expand Down Expand Up @@ -302,7 +302,7 @@ public function validationReport(Request $request, Project $project)
$validation = $project->validation;

if (! $validation) {
$validation = new Validation();
$validation = new Validation;
$validation->save();
$project->validation()->associate($validation);
$project->save();
Expand All @@ -327,7 +327,13 @@ public function publish(Request $request, Project $project, PublishProject $publ
if ($project) {
$input = $request->all();
$release_date = $input['release_date'];
$enableProjectMode = $request->get('enableProjectMode');
$selected_project_id = $input['selected_project_id'];
$selected_project_license_id = $input['license_id'];
if ($selected_project_id) {
$enableProjectMode = false;
} else {
$enableProjectMode = $request->get('enableProjectMode');
}
if ($enableProjectMode) {
$validation = $project->validation;
$validation->process();
Expand Down Expand Up @@ -363,10 +369,15 @@ public function publish(Request $request, Project $project, PublishProject $publ
$validation = $validation->fresh();

foreach ($project->studies as $study) {
$study->license_id = $project->license_id;
if ($selected_project_id) {
$study->location = $selected_project_id;
$study->license_id = $selected_project_license_id;
} else {
$study->license_id = $project->license_id;
}
$study->save();
foreach ($study->datasets as $dataset) {
$dataset->license_id = $project->license_id;
$dataset->license_id = $study->license_id;
$dataset->save();
}
}
Expand All @@ -380,6 +391,7 @@ public function publish(Request $request, Project $project, PublishProject $publ
}
// add license check
if ($status) {

ProcessSubmission::dispatch($project);

return response()->json([
Expand Down
28 changes: 28 additions & 0 deletions app/Http/Controllers/UserController.php
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Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
<?php

namespace App\Http\Controllers;

use App\Models\Project;
use App\Models\User;

class UserController extends Controller
{
/**
* Retrieve the names of public projects owned by the user
*/
public function retrieveProjects(User $user)
{
return Project::where('owner_id', $user->id)
->where('is_public', true)
->get(['id', 'name', 'description', 'license_id'])
->map(function ($project) {
return [
'id' => $project->id,
'name' => $project->name,
'description' => $project->description,
'license_id' => $project->license_id,
];
})
->toArray();
}
}
29 changes: 25 additions & 4 deletions app/Jobs/ProcessSubmission.php
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ class ProcessSubmission implements ShouldBeUnique, ShouldQueue
public function __construct(Project $project)
{
$this->project = $project;

}

/**
Expand All @@ -45,7 +46,6 @@ public function __construct(Project $project)
public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishProject $projectPublisher, PublishStudy $studyPublisher)
{
$project = $this->project;

$project->status = 'processing';
$project->save();

Expand Down Expand Up @@ -117,16 +117,19 @@ public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishPr
$logs = 'Moving files in progress';

if ($project) {

$_studies = $project->studies;
if ($draft) {
$environment = env('APP_ENV', 'local');

foreach ($_studies as $study) {
// $study->users()->sync($project->user()->getDictionary());

$studyPath = preg_replace(
'~//+~',
'/',
$environment.'/samples/'.$study->uuid

);

$studyFSObjects = FileSystemObject::with('children')
Expand Down Expand Up @@ -154,11 +157,15 @@ public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishPr
}
$study->process_logs = $process_logs;
$study->draft_id = null;
$study->project_id = null;
if ($study->location) {
$study->project_id = $study->location;
} else {
$study->project_id = null;
}

foreach ($study->datasets as $dataset) {
$dataset->draft_id = null;
$dataset->project_id = null;
$dataset->project_id = $study->project_id;
$dataset->save();
}

Expand All @@ -167,7 +174,14 @@ public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishPr
}
}
$assigner->assign($_studies);

$release_date = Carbon::parse($project->release_date);
foreach ($_studies as $study) {
if ($study->location) {
$release_date = Carbon::now();
$study->release_date = $release_date;
}
}

if ($release_date->isPast()) {
foreach ($_studies as $study) {
Expand All @@ -176,7 +190,14 @@ public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishPr
}
$updater->update($_studies);
//Notification::send($this->prepareSendList($project), new StudyPublishNotification($_studies));
event(new StudyPublish($_studies, $this->prepareSendList($project)));

if ($study->location) {
$selected_project = Project::where([['id', $study->location]])->firstOrFail();
event(new StudyPublish($_studies, $this->prepareSendList($selected_project)));
$study->location = null;
} else {
event(new StudyPublish($_studies, $this->prepareSendList($project)));
}

$project->delete();
$draft->delete();
Expand Down
30 changes: 30 additions & 0 deletions resources/js/Pages/Publish.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,14 @@
@blur="updateDraft"
/>
</div>
<jet-button
v-if="publishForm.enableProjectMode"
class="bg-gray-500 -mt-10 hover:bg-gray-700 float-right"
@click="toggleManageProject"
>
{{ "+ Add to existing project" }}
</jet-button>

<div v-if="publishForm.enableProjectMode">
<div class="p-4 bg-gray-100 rounded-md">
<div id="project-name" class="mb-3">
Expand Down Expand Up @@ -677,6 +685,11 @@
ref="manageCitationElement"
:project="project"
/>
<manage-project
ref="manageProjectElement"
:project="project"
@selected_project="handleProjectSelected"
/>
</div>
</div>
</div>
Expand Down Expand Up @@ -790,6 +803,7 @@ import Validation from "@/Shared/Validation.vue";
import Datepicker from "@vuepic/vue-datepicker";
import "@vuepic/vue-datepicker/dist/main.css";
import ManageAuthor from "@/Shared/ManageAuthor.vue";
import ManageProject from "@/Shared/ManageProject.vue";
import ToolTip from "@/Shared/ToolTip.vue";
import ManageCitation from "@/Shared/ManageCitation.vue";
import Citation from "@/Shared/Citation.vue";
Expand Down Expand Up @@ -856,15 +870,19 @@ export default {
CitationCard,
JetConfirmationModal,
JetSuccessButton,
ManageProject,
},
props: ["user", "team", "project", "teamRole", "draft"],
setup() {
const manageAuthorElement = ref(null);
const manageCitationElement = ref(null);
const manageProjectElement = ref(null);
return {
manageAuthorElement,
manageCitationElement,
manageProjectElement,
};
},
Expand All @@ -886,6 +904,7 @@ export default {
terms: false,
enableProjectMode: false,
release_date: this.setReleaseDate(),
selected_project_id: null,
}),
licenses: null,
license: null,
Expand Down Expand Up @@ -1121,6 +1140,9 @@ export default {
toggleManageCitation() {
this.manageCitationElement.toggleDialog();
},
toggleManageProject() {
this.manageProjectElement.toggleDialog();
},
publish() {
this.showPublishConfirmationModal = false;
if (this.publishForm.conditions && this.publishForm.terms) {
Expand Down Expand Up @@ -1149,6 +1171,14 @@ export default {
return true;
}
},
handleProjectSelected(selected_project) {
this.publishForm.selected_project_id = selected_project.id;
this.publishForm.license_id = selected_project.license_id;
this.publishForm.conditions = true;
this.publishForm.terms = true;
this.publish();
},
// trackProject() {
// axios
// .get("/projects/status/" + this.project.id + "/queue")
Expand Down
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