From 6b0d8891f1d368358b6bfc72fd98ced673265a11 Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Fri, 1 Nov 2024 21:44:58 +0100
Subject: [PATCH 1/2] feat: add new samples to public projects fixes #1167

---
 app/Http/Controllers/ProjectController.php |  22 ++-
 app/Http/Controllers/UserController.php    |  28 ++++
 app/Jobs/ProcessSubmission.php             |  29 +++-
 resources/js/Pages/Publish.vue             |  30 ++++
 resources/js/Shared/ManageProject.vue      | 154 +++++++++++++++++++++
 resources/js/Shared/SelectRich.vue         |   4 +-
 routes/web.php                             |   2 +
 7 files changed, 258 insertions(+), 11 deletions(-)
 create mode 100644 app/Http/Controllers/UserController.php
 create mode 100644 resources/js/Shared/ManageProject.vue

diff --git a/app/Http/Controllers/ProjectController.php b/app/Http/Controllers/ProjectController.php
index b8267610..090da985 100644
--- a/app/Http/Controllers/ProjectController.php
+++ b/app/Http/Controllers/ProjectController.php
@@ -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();
@@ -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();
@@ -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();
@@ -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();
                     }
                 }
@@ -380,6 +391,7 @@ public function publish(Request $request, Project $project, PublishProject $publ
                 }
                 // add license check
                 if ($status) {
+
                     ProcessSubmission::dispatch($project);
 
                     return response()->json([
diff --git a/app/Http/Controllers/UserController.php b/app/Http/Controllers/UserController.php
new file mode 100644
index 00000000..55d7107c
--- /dev/null
+++ b/app/Http/Controllers/UserController.php
@@ -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();
+    }
+}
diff --git a/app/Jobs/ProcessSubmission.php b/app/Jobs/ProcessSubmission.php
index b939d3b6..63c169a3 100644
--- a/app/Jobs/ProcessSubmission.php
+++ b/app/Jobs/ProcessSubmission.php
@@ -37,6 +37,7 @@ class ProcessSubmission implements ShouldBeUnique, ShouldQueue
     public function __construct(Project $project)
     {
         $this->project = $project;
+
     }
 
     /**
@@ -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();
 
@@ -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')
@@ -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();
                         }
 
@@ -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) {
@@ -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();
diff --git a/resources/js/Pages/Publish.vue b/resources/js/Pages/Publish.vue
index 01a091e0..df19c798 100644
--- a/resources/js/Pages/Publish.vue
+++ b/resources/js/Pages/Publish.vue
@@ -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">
@@ -677,6 +685,11 @@
                             ref="manageCitationElement"
                             :project="project"
                         />
+                        <manage-project
+                            ref="manageProjectElement"
+                            :project="project"
+                            @selected_project="handleProjectSelected"
+                        />
                     </div>
                 </div>
             </div>
@@ -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";
@@ -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,
         };
     },
 
@@ -886,6 +904,7 @@ export default {
                 terms: false,
                 enableProjectMode: false,
                 release_date: this.setReleaseDate(),
+                selected_project_id: null,
             }),
             licenses: null,
             license: null,
@@ -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) {
@@ -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")
diff --git a/resources/js/Shared/ManageProject.vue b/resources/js/Shared/ManageProject.vue
new file mode 100644
index 00000000..653a4ff8
--- /dev/null
+++ b/resources/js/Shared/ManageProject.vue
@@ -0,0 +1,154 @@
+<template>
+    <jet-dialog-modal
+        :show="showDialog"
+        :max-width="'6xl'"
+        @close="showDialog = false"
+    >
+        <template #title> Add Your Sample to a Published Project </template>
+        <template #content>
+            <div>
+                Find a project to publish your sample under. You can pick only a
+                project that has been published by you. <br />
+                The sample will get the same license as the chosen project and
+                will be made public shortly after publishing without embargo.
+                <br /><br />
+            </div>
+
+            <div v-if="projects && projects.length">
+                <select-rich
+                    v-model:selected="project_object"
+                    :items="projects"
+                    @update:selected="updateProjectName"
+                />
+            </div>
+            <div v-else>
+                <p>No projects available.</p>
+            </div>
+            <jet-secondary-button
+                class="float-left text-md font-bold text-white mt-8 mr-2 bg-green-600"
+                @click="showPublishConfirmationModal = true"
+            >
+                Publish now
+            </jet-secondary-button>
+            <jet-confirmation-modal
+                :show="showPublishConfirmationModal"
+                @close="showPublishConfirmationModal = false"
+            >
+                <template #title> Are you sure you want to publish? </template>
+                <template #content>
+                    Once the samples are published you will no longer be able to
+                    change their data or its location (the selected project).
+                </template>
+                <template #footer>
+                    <jet-secondary-button
+                        @click="showPublishConfirmationModal = false"
+                    >
+                        Cancel
+                    </jet-secondary-button>
+                    <jet-secondary-button
+                        class="ml-2 font-bold text-white bg-green-600"
+                        @click="save"
+                    >
+                        Publish now
+                    </jet-secondary-button>
+                </template>
+            </jet-confirmation-modal>
+        </template>
+        <template #footer>
+            <div class="flex">
+                <jet-secondary-button class="float-left" @click="onClose">
+                    Close
+                </jet-secondary-button>
+            </div>
+        </template>
+    </jet-dialog-modal>
+</template>
+
+<script>
+import JetDialogModal from "@/Jetstream/DialogModal.vue";
+import SelectRich from "@/Shared/SelectRich.vue";
+import axios from "axios";
+import JetSecondaryButton from "@/Jetstream/SecondaryButton.vue";
+import JetConfirmationModal from "@/Jetstream/ConfirmationModal.vue";
+
+export default {
+    components: {
+        JetDialogModal,
+        SelectRich,
+        JetSecondaryButton,
+        JetConfirmationModal,
+    },
+    props: {
+        project: Object,
+        study: Object,
+    },
+
+    data() {
+        return {
+            name: "",
+            showPublishConfirmationModal: false,
+            showDialog: false,
+            project_object: null,
+            project_id: null,
+            license_id: null,
+            projects: [],
+            studies: [],
+            user: null,
+        };
+    },
+
+    mounted() {
+        if (this.project) {
+            this.loadInitial();
+            this.user = this.project.owner_id;
+            this.loadProjects();
+        } else {
+            this.loadInitial();
+        }
+    },
+
+    methods: {
+        loadInitial() {
+            if (this.project_object) {
+                this.project_object = this.project_object;
+                this.project_id = this.project_object.id;
+                this.project_name = this.project_object.name;
+                this.license_id = this.project_object.license_id;
+            }
+        },
+        updateProjectName() {
+            this.project_id = this.project_object.id;
+            this.name = this.project_object.name;
+            this.license_id = this.project_object.license_id;
+        },
+        loadProjects() {
+            const url = route("user.publicProjects", { user: this.user });
+            axios
+                .get(url)
+                .then((res) => {
+                    this.projects = res.data;
+                })
+                .catch((error) => {
+                    console.error(
+                        "There was an error fetching the projects:",
+                        error
+                    );
+                });
+        },
+        toggleDialog() {
+            this.showDialog = !this.showDialog;
+        },
+        onClose() {
+            this.showDialog = false;
+        },
+
+        save() {
+            this.showPublishConfirmationModal = false;
+            if (this.project_id) {
+                this.$emit("selected_project", this.project_object);
+            }
+            this.onClose();
+        },
+    },
+};
+</script>
diff --git a/resources/js/Shared/SelectRich.vue b/resources/js/Shared/SelectRich.vue
index 891c9a95..de7dbeec 100644
--- a/resources/js/Shared/SelectRich.vue
+++ b/resources/js/Shared/SelectRich.vue
@@ -10,7 +10,7 @@
                 class="relative w-full bg-white border border-gray-300 rounded-md shadow-sm pl-3 pr-10 py-2 text-left cursor-default focus:outline-none focus:ring-1 focus:ring-teal-500 focus:border-teal-500 sm:text-sm"
             >
                 <span v-if="selected" class="block truncate">{{
-                    selected.title
+                    selected.title || selected.name
                 }}</span>
                 <span v-else class="block truncate">--Select--</span>
                 <span
@@ -51,7 +51,7 @@
                                     'block truncate',
                                 ]"
                             >
-                                <b>{{ item.title }}</b> <br />
+                                <b>{{ item.title || item.name }}</b> <br />
                                 <small
                                     v-if="item.description"
                                     v-html="item.description"
diff --git a/routes/web.php b/routes/web.php
index e7eefce7..31f2c56a 100644
--- a/routes/web.php
+++ b/routes/web.php
@@ -25,6 +25,7 @@
 use App\Http\Controllers\StudyMemberController;
 use App\Http\Controllers\TeamController;
 use App\Http\Controllers\UploadController;
+use App\Http\Controllers\UserController;
 use App\Models\Dataset;
 use App\Models\Molecule;
 use App\Models\Project;
@@ -395,3 +396,4 @@
 Route::get('services/oembed', [OEmbedController::class, 'spectra']);
 
 Route::get('embed/{id}', [OEmbedController::class, 'embed'])->name('embed');
+Route::get('{user}/public-projects', [UserController::class, 'retrieveProjects'])->name('user.publicProjects');

From 07b70ec72d52e4e4d6b027704fa6e40c36d95530 Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Sat, 2 Nov 2024 20:51:46 +0100
Subject: [PATCH 2/2] fix: update related identifiers of the published projects
 (datacite)

---
 app/Jobs/ProcessSubmission.php | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/Jobs/ProcessSubmission.php b/app/Jobs/ProcessSubmission.php
index 63c169a3..ee69149b 100644
--- a/app/Jobs/ProcessSubmission.php
+++ b/app/Jobs/ProcessSubmission.php
@@ -188,15 +188,16 @@ public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishPr
                         $studyPublisher->publish($study);
                     }
                 }
-                $updater->update($_studies);
                 //Notification::send($this->prepareSendList($project), new StudyPublishNotification($_studies));
 
                 if ($study->location) {
                     $selected_project = Project::where([['id', $study->location]])->firstOrFail();
+                    $updater->update($selected_project);
                     event(new StudyPublish($_studies, $this->prepareSendList($selected_project)));
                     $study->location = null;
                 } else {
                     event(new StudyPublish($_studies, $this->prepareSendList($project)));
+                    $updater->update($_studies);
                 }
 
                 $project->delete();