From bf7ae561400fcf36f757d84b031cf2b7ba520ff5 Mon Sep 17 00:00:00 2001
From: NishaSharma14 <sharmanis14@gmail.com>
Date: Wed, 24 Aug 2022 14:41:43 +0200
Subject: [PATCH 1/7] Citation WIP.

---
 .../Controllers/Admin/LicenseController.php   |   2 -
 app/Http/Controllers/CitationController.php   |   8 +
 app/Http/Controllers/StudyController.php      |   1 +
 app/Http/Resources/LicenseResource.php        |   1 +
 app/Models/Citation.php                       |  28 ++
 ...22_08_23_143935_create_citations_table.php |  36 ++
 ...4_111011_create_citation_project_table.php |  35 ++
 resources/js/Pages/Public/Project/Show.vue    |   6 +-
 resources/js/Shared/AddCitation.vue           | 425 ++++++++++++++++++
 9 files changed, 539 insertions(+), 3 deletions(-)
 create mode 100644 app/Http/Controllers/CitationController.php
 create mode 100644 app/Models/Citation.php
 create mode 100644 database/migrations/2022_08_23_143935_create_citations_table.php
 create mode 100644 database/migrations/2022_08_24_111011_create_citation_project_table.php
 create mode 100644 resources/js/Shared/AddCitation.vue

diff --git a/app/Http/Controllers/Admin/LicenseController.php b/app/Http/Controllers/Admin/LicenseController.php
index a7cb568c..938852b9 100644
--- a/app/Http/Controllers/Admin/LicenseController.php
+++ b/app/Http/Controllers/Admin/LicenseController.php
@@ -17,8 +17,6 @@ public function index(Request $request)
         $licenses = Cache::rememberForever('licenses', function () {
             return License::select('id', 'title', 'description')->get();
         });
-
-        // $licenses = License::select('id','title')->get();
         return $licenses;
     }
 
diff --git a/app/Http/Controllers/CitationController.php b/app/Http/Controllers/CitationController.php
new file mode 100644
index 00000000..ca7f338e
--- /dev/null
+++ b/app/Http/Controllers/CitationController.php
@@ -0,0 +1,8 @@
+<?php
+
+namespace App\Http\Controllers;
+
+class CitationController extends Controller
+{
+    //
+}
diff --git a/app/Http/Controllers/StudyController.php b/app/Http/Controllers/StudyController.php
index 3cf72979..b3e4ec96 100644
--- a/app/Http/Controllers/StudyController.php
+++ b/app/Http/Controllers/StudyController.php
@@ -140,6 +140,7 @@ public function moleculeDetach(Request $request, Study $study, Molecule $molecul
             $sample = $study->sample;
             $sample->molecules()->detach([$molecule->id]);
             $sample = $sample->fresh();
+
             return $sample->molecules;
         }
     }
diff --git a/app/Http/Resources/LicenseResource.php b/app/Http/Resources/LicenseResource.php
index f2075ac4..b000ed97 100644
--- a/app/Http/Resources/LicenseResource.php
+++ b/app/Http/Resources/LicenseResource.php
@@ -22,6 +22,7 @@ public function toArray($request)
             'html_url' => $this->html_url,
             'permissions' => $this->permissions,
             'description' => $this->description,
+            'body' => $this->body,
         ];
     }
 }
diff --git a/app/Models/Citation.php b/app/Models/Citation.php
new file mode 100644
index 00000000..5ebadd23
--- /dev/null
+++ b/app/Models/Citation.php
@@ -0,0 +1,28 @@
+<?php
+
+namespace App\Models;
+
+use Illuminate\Database\Eloquent\Factories\HasFactory;
+use Illuminate\Database\Eloquent\Model;
+
+class Citation extends Model
+{
+    use HasFactory;
+
+    protected $fillable = [
+        'doi',
+        'title',
+        'abstract',
+        'citation_text',
+    ];
+
+    /**
+     * Projects that belongs to citations.
+     *
+     * @return \Illuminate\Database\Eloquent\Relations\belongsToMany
+     */
+    public function projects()
+    {
+        return $this->belongsToMany(Project::class);
+    }
+}
diff --git a/database/migrations/2022_08_23_143935_create_citations_table.php b/database/migrations/2022_08_23_143935_create_citations_table.php
new file mode 100644
index 00000000..080db538
--- /dev/null
+++ b/database/migrations/2022_08_23_143935_create_citations_table.php
@@ -0,0 +1,36 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+return new class extends Migration
+{
+    /**
+     * Run the migrations.
+     *
+     * @return void
+     */
+    public function up()
+    {
+        Schema::create('citations', function (Blueprint $table) {
+            $table->id();
+            $table->string('doi');
+            $table->string('title');
+            $table->longText('authors');
+            $table->longText('abstract');
+            $table->longText('citation_text');
+            $table->timestamps();
+        });
+    }
+
+    /**
+     * Reverse the migrations.
+     *
+     * @return void
+     */
+    public function down()
+    {
+        Schema::dropIfExists('citations');
+    }
+};
diff --git a/database/migrations/2022_08_24_111011_create_citation_project_table.php b/database/migrations/2022_08_24_111011_create_citation_project_table.php
new file mode 100644
index 00000000..d8e86ddc
--- /dev/null
+++ b/database/migrations/2022_08_24_111011_create_citation_project_table.php
@@ -0,0 +1,35 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+return new class extends Migration
+{
+    /**
+     * Run the migrations.
+     *
+     * @return void
+     */
+    public function up()
+    {
+        Schema::create('citation_project', function (Blueprint $table) {
+            $table->id();
+            $table->foreignId('project_id');
+            $table->foreignId('citation_id');
+            $table->string('user')->nullable();
+            $table->timestamps();
+            $table->unique(['project_id', 'citation_id']);
+        });
+    }
+
+    /**
+     * Reverse the migrations.
+     *
+     * @return void
+     */
+    public function down()
+    {
+        Schema::dropIfExists('citation_project');
+    }
+};
diff --git a/resources/js/Pages/Public/Project/Show.vue b/resources/js/Pages/Public/Project/Show.vue
index bd7c9fb2..11172464 100644
--- a/resources/js/Pages/Public/Project/Show.vue
+++ b/resources/js/Pages/Public/Project/Show.vue
@@ -66,7 +66,11 @@
                                                 user.last_name
                                             }}
                                         </p>
-                                        <p class="text-sm text-gray-500 truncate">@ {{ user.username }}</p>
+                                        <p
+                                            class="text-sm text-gray-500 truncate"
+                                        >
+                                            @ {{ user.username }}
+                                        </p>
                                     </a>
                                 </div>
                             </div>
diff --git a/resources/js/Shared/AddCitation.vue b/resources/js/Shared/AddCitation.vue
new file mode 100644
index 00000000..4f09ef93
--- /dev/null
+++ b/resources/js/Shared/AddCitation.vue
@@ -0,0 +1,425 @@
+<template>
+    <jet-dialog-modal
+        :show="addCitationDialog"
+        :max-width="'6xl'"
+        @close="addCitationDialog = false"
+    >
+        <template #title> New Citation </template>
+        <template #content>
+            <div
+                class="relative grid grid-cols-1 gap-x-16 max-w-7xl mx-auto lg:grid-cols-2 divide-x"
+            >
+                <div
+                    class="pb-36 px-4 sm:px-6 lg:pb-16 lg:px-0 lg:row-start-1 lg:col-start-1"
+                >
+                    <!-- Import Section-->
+                    <div>
+                        <p class="text-sm leading-6 font-bold text-gray-900">
+                            Import From
+                        </p>
+                        <div
+                            class="mt-1 grid grid-cols-1 gap-y-6 gap-x-4 sm:grid-cols-2"
+                        >
+                            <div class="sm:col-span-2">
+                                <label
+                                    for="name"
+                                    class="block text-sm font-medium text-gray-700"
+                                >
+                                    DOI
+                                </label>
+                                <div class="mt-1 flex rounded-md shadow-sm">
+                                    <input
+                                        id="name"
+                                        v-model="importCitationForm.doi"
+                                        type="text"
+                                        name="name"
+                                        autocomplete="off"
+                                        class="flex-1 focus:ring-teal-500 focus:border-teal-500 block w-full min-w-0 rounded sm:text-sm border-gray-300"
+                                    />
+                                </div>
+                                <jet-input-error
+                                    :message="importCitationForm.errors.doi"
+                                    class="mt-2"
+                                />
+                            </div>
+                        </div>
+                        <div class="sm:col-span-2 mt-4">
+                            <jet-secondary-button @click="importAuthors">
+                                Import
+                            </jet-secondary-button>
+                        </div>
+                        <div
+                            v-if="loading && importCitationForm.doi"
+                            class="sm:col-span-9 mt-4 align-centre"
+                        >
+                            <loading-button :loading="loading" />
+                        </div>
+                        <div
+                            v-if="authorsListDOI.length > 0 && !loading"
+                            class="sm:col-span-9 mt-4"
+                        >
+                            <author-checkbox
+                                v-model:checked="doiSelectedAuthorList"
+                                :items="authorsListDOI"
+                            />
+                        </div>
+                        <div
+                            v-if="authorsListDOI.length > 0"
+                            class="sm:col-span-6 pt-3"
+                        >
+                            <jet-secondary-button
+                                class="float-right text-md font-bold text-teal-900"
+                                @click="addAuthor('DOI')"
+                            >
+                                Add
+                            </jet-secondary-button>
+                        </div>
+                    </div>
+                </div>
+                <div
+                    class="pb-36 px-4 sm:px-6 lg:pb-16 lg:px-0 lg:row-start-1 lg:col-start-2"
+                >
+                    <div class="p-2">
+                        <!--Add Manual Section-->
+                        <p class="text-sm leading-6 font-bold text-gray-900">
+                            Add Manually
+                        </p>
+                        <div
+                            class="mt-1 grid grid-cols-1 gap-y-6 gap-x-4 sm:grid-cols-2"
+                        >
+                            <div class="sm:col-span-2">
+                                <label
+                                    for="title"
+                                    class="block text-sm font-medium text-gray-700"
+                                >
+                                    Title
+                                </label>
+                                <div class="mt-1">
+                                    <input
+                                        id="title"
+                                        v-model="manualAddCitationForm.title"
+                                        type="text"
+                                        name="title"
+                                        autocomplete="title"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
+                                    />
+                                </div>
+                            </div>
+                            <div class="sm:col-span-2">
+                                <label
+                                    for="family-name"
+                                    class="block text-sm font-medium text-gray-700 after:content-['*'] after:ml-0.5 after:text-red-500"
+                                >
+                                    Family Name
+                                </label>
+                                <div class="mt-1">
+                                    <input
+                                        id="family-name"
+                                        v-model="
+                                            manualAddCitationForm.family_name
+                                        "
+                                        type="text"
+                                        name="family-name"
+                                        autocomplete="family-name"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
+                                    />
+                                </div>
+                                <jet-input-error
+                                    :message="
+                                        manualAddCitationForm.errors.family_name
+                                    "
+                                    class="mt-2"
+                                />
+                            </div>
+
+                            <div class="sm:col-span-2">
+                                <label
+                                    for="given-name"
+                                    class="block text-sm font-medium text-gray-700 after:content-['*'] after:ml-0.5 after:text-red-500"
+                                >
+                                    Given Name
+                                </label>
+                                <div class="mt-1">
+                                    <input
+                                        id="given-name"
+                                        v-model="
+                                            manualAddCitationForm.given_name
+                                        "
+                                        type="text"
+                                        name="given-name"
+                                        autocomplete="given-name"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
+                                    />
+                                </div>
+                                <jet-input-error
+                                    :message="
+                                        manualAddCitationForm.errors.given_name
+                                    "
+                                    class="mt-2"
+                                />
+                            </div>
+                            <div class="sm:col-span-3">
+                                <label
+                                    for="email"
+                                    class="block text-sm font-medium text-gray-700"
+                                >
+                                    Email address
+                                </label>
+                                <div class="mt-1">
+                                    <input
+                                        id="email"
+                                        v-model="manualAddCitationForm.email_id"
+                                        name="email"
+                                        type="email"
+                                        autocomplete="email"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
+                                        @blur="validateEmail"
+                                    />
+                                    <jet-input-error
+                                        :message="
+                                            manualAddCitationForm.errors
+                                                .email_id
+                                        "
+                                        class="mt-2"
+                                    />
+                                </div>
+                            </div>
+                            <div class="sm:col-span-3">
+                                <label
+                                    for="orcid"
+                                    class="block text-sm font-medium text-gray-700"
+                                >
+                                    ORCID ID
+                                </label>
+                                <div class="mt-1">
+                                    <input
+                                        id="orcid"
+                                        v-model="manualAddCitationForm.orcid_id"
+                                        name="orcid"
+                                        autocomplete="orcid"
+                                        type="text"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
+                                    />
+                                </div>
+                            </div>
+                            <div class="sm:col-span-6">
+                                <label
+                                    for="about"
+                                    class="block text-sm font-medium text-gray-700 after:content-['*'] after:ml-0.5 after:text-red-500"
+                                >
+                                    Affiliation
+                                </label>
+                                <div class="mt-1">
+                                    <textarea
+                                        id="affiliation"
+                                        v-model="
+                                            manualAddCitationForm.affiliation
+                                        "
+                                        name="affiliation"
+                                        rows="3"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border border-gray-300 rounded-md"
+                                        placeholder="Name and address of affiliated University and Department. e.g. Institut für Anorganische und Analytische Chemie,Friedrich-Schiller-Universität,Schloßgasse 10, 07743 Jena"
+                                    />
+                                </div>
+                                <jet-input-error
+                                    :message="
+                                        manualAddCitationForm.errors.affiliation
+                                    "
+                                    class="mt-2"
+                                />
+                            </div>
+                            <div class="sm:col-span-6 float-left">
+                                <jet-secondary-button
+                                    class="float-right text-md font-bold text-teal-900"
+                                    @click="addAuthor('Manual')"
+                                >
+                                    Add
+                                </jet-secondary-button>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+            <!-- Added Author Summary -->
+            <div v-if="selectedAuthorsList.length > 0">
+                <div class="ml-2 mt-2 overflow-y-scroll h-64">
+                    <table
+                        class="divide-y divide-gray-200 w-full table-fixed overflow-y-scroll"
+                    >
+                        <thead class="bg-gray-50 sticky top-0">
+                            <tr>
+                                <th
+                                    colspan="3"
+                                    scope="col"
+                                    class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider"
+                                >
+                                    Author
+                                </th>
+                                <th
+                                    scope="col"
+                                    class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider"
+                                >
+                                    Actions
+                                </th>
+                            </tr>
+                        </thead>
+                        <tbody class="bg-white divide-y divide-gray-200">
+                            <tr
+                                v-for="author in selectedAuthorsList"
+                                :key="author.id"
+                            >
+                                <td colspan="3" class="py-4">
+                                    <div class="ml-4">
+                                        <h3
+                                            class="text-sm leading-6 font-medium text-gray-900"
+                                        >
+                                            {{ author.title }}
+                                            {{ author.given_name }}
+                                            {{ author.family_name }}
+                                        </h3>
+                                        <p
+                                            class="mt-1 text-xs font-small text-blue-gray-900 break-words"
+                                        >
+                                            {{ author.affiliation }}
+                                        </p>
+                                        <div
+                                            v-if="author.orcid_id"
+                                            class="text-xs leading-6 font-medium text-gray-900"
+                                        >
+                                            <p>
+                                                Orcid Id -
+                                                <a
+                                                    :href="author.orcid_id"
+                                                    class="text-teal-900"
+                                                    >{{ author.orcid_id }}</a
+                                                >
+                                            </p>
+                                        </div>
+                                        <div
+                                            v-if="author.email_id"
+                                            class="text-xs leading-6 font-medium text-gray-900"
+                                        >
+                                            <p>
+                                                Email Id - {{ author.email_id }}
+                                            </p>
+                                        </div>
+                                    </div>
+                                </td>
+                                <td
+                                    class="px-6 py-4 text-sm leading-5 text-gray-500 whitespace-no-wrap border-gray-200"
+                                >
+                                    <button
+                                        type="button"
+                                        class="inline-flex items-center p-1 border border-transparent"
+                                        @click="editAuthor(author)"
+                                    >
+                                        <PencilIcon
+                                            class="w-5 h-5 mr-1 text-gray-600"
+                                        />
+                                    </button>
+                                    <button
+                                        type="button"
+                                        class="inline-flex items-center p-1 border border-transparent"
+                                        @click="
+                                            confirmAuthorDeletion(author.id)
+                                        "
+                                    >
+                                        <TrashIcon
+                                            class="w-5 h-5 mr-1 text-gray-600"
+                                        />
+                                    </button>
+                                </td>
+                            </tr>
+                        </tbody>
+                    </table>
+                </div>
+            </div>
+            <jet-dialog-modal
+                :show="confirmingAuthorDeletion"
+                @close="closeModal"
+            >
+                <template #title> Delete Author </template>
+
+                <template #content>
+                    Are you sure you want to delete this author?
+                    <div class="mt-4"></div>
+                </template>
+
+                <template #footer>
+                    <jet-secondary-button @click="closeModal">
+                        Cancel
+                    </jet-secondary-button>
+
+                    <jet-danger-button
+                        class="ml-2"
+                        :class="{ 'opacity-25': form.processing }"
+                        :disabled="form.processing"
+                        @click="deleteAuthor(authorId)"
+                    >
+                        Delete Author
+                    </jet-danger-button>
+                </template>
+            </jet-dialog-modal>
+        </template>
+
+        <template #footer>
+            <jet-secondary-button class="float-left" @click="onClose">
+                Close
+            </jet-secondary-button>
+
+            <jet-button class="ml-2" @click="updateCitation"> Save </jet-button>
+        </template>
+    </jet-dialog-modal>
+</template>
+
+<script>
+import JetDialogModal from "@/Jetstream/DialogModal.vue";
+import JetSecondaryButton from "@/Jetstream/SecondaryButton.vue";
+import JetButton from "@/Jetstream/Button.vue";
+import AuthorCheckbox from "@/Shared/AuthorCheckbox.vue";
+import { TrashIcon, PencilIcon } from "@heroicons/vue/solid";
+import JetInputError from "@/Jetstream/InputError.vue";
+import LoadingButton from "@/Shared/LoadingButton.vue";
+import JetDangerButton from "@/Jetstream/DangerButton.vue";
+export default {
+    components: {
+        JetDialogModal,
+        JetSecondaryButton,
+        JetDangerButton,
+        JetButton,
+        AuthorCheckbox,
+        PencilIcon,
+        TrashIcon,
+        JetInputError,
+        LoadingButton,
+    },
+
+    props: ["project"],
+
+    data() {
+        return {
+            importCitationForm: this.$inertia.form({
+                doi: "",
+                errors: {},
+            }),
+            manualAddCitationForm: this.$inertia.form({
+                _method: "POST",
+                errors: {},
+            }),
+        };
+    },
+    mounted() {
+        const initialise = () => {
+            this.addCitationDialog = true;
+        };
+        this.emitter.all.set("openAddCitationDialog", [initialise]);
+    },
+    methods: {
+        updateCitation() {},
+        onClose() {
+            this.addCitationDialog = false;
+            //this.resetData();
+        },
+    },
+};
+</script>

From 7acdea2b4c32b52a5283f051ea671b7c32ab933e Mon Sep 17 00:00:00 2001
From: NishaSharma14 <sharmanis14@gmail.com>
Date: Wed, 24 Aug 2022 15:04:36 +0200
Subject: [PATCH 2/7] Merge conflict

---
 database/seeders/DatabaseSeeder.php           |  6 ++---
 database/seeders/LicenseSeeder.php            | 25 +++++++++++--------
 resources/js/Pages/Public/Project/License.vue |  2 +-
 3 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/database/seeders/DatabaseSeeder.php b/database/seeders/DatabaseSeeder.php
index ba56fc49..d3757cea 100644
--- a/database/seeders/DatabaseSeeder.php
+++ b/database/seeders/DatabaseSeeder.php
@@ -13,9 +13,9 @@ class DatabaseSeeder extends Seeder
      */
     public function run()
     {
-        $this->call(RolesAndPermissionsSeeder::class);
-        $this->call(UsersSeeder::class);
-        $this->call(AnnouncementSeeder::class);
+        // $this->call(RolesAndPermissionsSeeder::class);
+        // $this->call(UsersSeeder::class);
+        // $this->call(AnnouncementSeeder::class);
         $this->call(LicenseSeeder::class);
     }
 }
diff --git a/database/seeders/LicenseSeeder.php b/database/seeders/LicenseSeeder.php
index 05c7b4c2..e3e97941 100644
--- a/database/seeders/LicenseSeeder.php
+++ b/database/seeders/LicenseSeeder.php
@@ -270,16 +270,19 @@ public function run()
             ],
 
         ];
-        foreach ($licenses as $license) {
-            $license = License::create([
-                'title' => $license['title'],
-                'slug' => $license['slug'],
-                'spdx_id' => $license['spdx_id'],
-                'url' => $license['url'],
-                'description' => $license['description'],
-                'body' => $license['body'],
-                'category' => $license['category'],
-            ]);
+        License::truncate();
+        if($licenses){
+            foreach ($licenses as $license) {
+                $license = License::create([
+                    'title' => $license['title'],
+                    'slug' => $license['slug'],
+                    'spdx_id' => $license['spdx_id'],
+                    'url' => $license['url'],
+                    'description' => $license['description'],
+                    'body' => $license['body'],
+                    'category' => $license['category'],
+                ]);
+            }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/resources/js/Pages/Public/Project/License.vue b/resources/js/Pages/Public/Project/License.vue
index 64a3f4fa..86c466f7 100644
--- a/resources/js/Pages/Public/Project/License.vue
+++ b/resources/js/Pages/Public/Project/License.vue
@@ -41,4 +41,4 @@ export default {
     mounted() {},
     methods: {},
 };
-</script>
+</script>
\ No newline at end of file

From c43b9a002293a714d89696ac0be56321e798bf03 Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Thu, 25 Aug 2022 15:58:51 +0200
Subject: [PATCH 3/7] Route the project, Study, Dataset schemas Define project
 as bioschema study Implement the project schema

---
 .../API/Bioschema/ProjectController.php       |  72 +++++
 app/Models/Bioschema/Project.php              | 274 ++++++++++++++++++
 routes/api.php                                |   3 +
 3 files changed, 349 insertions(+)
 create mode 100644 app/Http/Controllers/API/Bioschema/ProjectController.php
 create mode 100644 app/Models/Bioschema/Project.php

diff --git a/app/Http/Controllers/API/Bioschema/ProjectController.php b/app/Http/Controllers/API/Bioschema/ProjectController.php
new file mode 100644
index 00000000..c064778d
--- /dev/null
+++ b/app/Http/Controllers/API/Bioschema/ProjectController.php
@@ -0,0 +1,72 @@
+<?php
+
+namespace App\Http\Controllers\API\Bioschema;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Http\Request;
+use Spatie\SchemaOrg\Schema;
+use App\Models\Project;
+use App\Models\Study;
+
+use App\Models\User;
+use App\Models\Author;
+
+
+
+class ProjectController extends Controller
+{
+    public function schema(Request $request, $username, $projectName, $studyName = null, $datasetName = null)
+    {
+        $user = User::where('username', $username)->firstOrFail();
+        if($user){
+            $project = Project::where([['slug', $projectName], ['owner_id', $user->id]])->firstOrFail();
+            
+        }
+
+        if($project){
+            $creativeWork = Schema::creativeWork();
+            $creativeWork['@id'] = 'https://bioschemas.org/profiles/Study/0.2-DRAFT';
+            $confromsTo = [];
+            $confromsTo['http://purl.org/dc/terms/conformsTo'] = $creativeWork;
+
+            $projectSchema = Schema::Project(); 
+            $projectSchema['@id']= $project->uuid;
+            $projectSchema['dct:conformsTo'] = $confromsTo;
+            $authors = [];
+            foreach ($project->authors as &$author) {
+                $authorSchema = Schema::Person(); 
+                $authorSchema-> givenName($author->given_name);
+                $authorSchema->familyName($author->family_name);
+                $authorSchema->identifier($author->orcid_id);
+                $authorSchema-> email($author->email_id);
+                $authorSchema-> affiliation($author->affiliation);
+                array_push($authors, $authorSchema);
+            }
+            $projectSchema['author']  = $authors;
+            $projectSchema->datePublished($project->release_date);
+            $projectSchema->description($project->description);
+            $projectSchema->name($project->name);
+            $projectSchema->dateCreated($project->created_at);
+            $tags = [];
+            foreach ($project->tags as &$tag) {
+                $tag = $tag->name; 
+                array_push($tags, $tag);
+            }
+            $projectSchema->keywords($tags);
+            $projectSchema->url($project->url);
+            
+            if($studyName && !$datasetName){
+                $study = Study::where([['slug', $studyName], ['owner_id', $user->id], ['project_id', $project->id]])->firstOrFail();
+                // send study back with project info added to it\
+                return [];
+            }else if($studyName && $datasetName){
+                $dataset = Dataset::where([['slug', $datasetName], ['owner_id', $user->id], ['project_id', $project->id], ['study_id', $study->id]])->firstOrFail();
+                // send dataset with project and study details
+                return [];
+            }else{
+                // add studies and associated datasets
+                return $projectSchema;
+            }
+        }
+    }
+}
diff --git a/app/Models/Bioschema/Project.php b/app/Models/Bioschema/Project.php
new file mode 100644
index 00000000..30936678
--- /dev/null
+++ b/app/Models/Bioschema/Project.php
@@ -0,0 +1,274 @@
+<?php
+
+namespace Spatie\SchemaOrg;
+
+use \Spatie\SchemaOrg\Contracts\DatasetContract;
+use \Spatie\SchemaOrg\Contracts\CreativeWorkContract;
+use \Spatie\SchemaOrg\Contracts\ThingContract;
+
+/**
+ * A body of structured information describing some topic(s) of interest.
+ *
+ * @see https://bioschemas.org/profiles/Study/0.2-DRAFT
+ * @link http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources
+ *
+ */
+class Project extends BaseType implements CreativeWorkContract, ThingContract
+{
+    /**
+     * The author of this content or rating. Please note that author is special
+     * in that HTML 5 provides a special mechanism for indicating authorship via
+     * the rel tag. That is equivalent to this and may be used interchangeably.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\OrganizationContract|\Spatie\SchemaOrg\Contracts\OrganizationContract[]|\Spatie\SchemaOrg\Contracts\PersonContract|\Spatie\SchemaOrg\Contracts\PersonContract[] $author
+     *
+     * @return static
+     *
+     * @see https://schema.org/author
+     */
+    public function author($author)
+    {
+        return $this->setProperty('author', $author);
+    }
+
+    /**
+     * Date of first broadcast/publication.
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $datePublished
+     *
+     * @return static
+     *
+     * @see https://schema.org/datePublished
+     */
+    public function datePublished($datePublished)
+    {
+        return $this->setProperty('datePublished', $datePublished);
+    }
+
+    /**
+     * A description of the item.
+     *
+     * @param string|string[] $description
+     *
+     * @return static
+     *
+     * @see https://schema.org/description
+     */
+    public function description($description)
+    {
+        return $this->setProperty('description', $description);
+    }
+
+    /**
+     * The identifier property represents any kind of identifier for any kind of
+     * [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides
+     * dedicated properties for representing many of these, either as textual
+     * strings or as URL (URI) links. See [background
+     * notes](/docs/datamodel.html#identifierBg) for more details.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $identifier
+     *
+     * @return static
+     *
+     * @see https://schema.org/identifier
+     */
+    public function identifier($identifier)
+    {
+        return $this->setProperty('identifier', $identifier);
+    }
+
+    /**
+     * The name of the item.
+     *
+     * @param string|string[] $name
+     *
+     * @return static
+     *
+     * @see https://schema.org/name
+     */
+    public function name($name)
+    {
+        return $this->setProperty('name', $name);
+    }
+
+    /**
+     * Define the domain of the study. For example, the domain could be astrophysics,
+     * functional genomics or earth science. Those domains can also have an ontology
+     * reference.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyDomain
+     *
+     * @return static
+     *
+     */
+    public function studyDomain($studyDomain)
+    {
+        return $this->setProperty('studyDomain', $studyDomain);
+    }
+
+    /**
+     * A subject of the study, i.e. one of the medical conditions, therapies, devices,
+     * drugs, etc. investigated by the study.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\BioChemEntityContract|\Spatie\SchemaOrg\Contracts\MedicalEntityContract[] $studySubject
+
+     * @return static
+     *
+     */
+    public function studySubject($studySubject)
+    {
+        return $this->setProperty('studySubject', $studySubject);
+    }
+
+    /**
+     * The subject matter of the content.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\ThingContract|\Spatie\SchemaOrg\Contracts\ThingContract[] $about
+     *
+     * @return static
+     *
+     * @see https://schema.org/about
+     * @link https://github.com/schemaorg/schemaorg/issues/1670
+     */
+    public function about($about)
+    {
+        return $this->setProperty('about', $about);
+    }
+
+    /**
+     * A property-value pair representing an additional characteristics of the 
+     * entitity, e.g. a product feature or another characteristic for which there 
+     * is no matching property in schema.org. Note: Publishers should be aware that 
+     * applications designed to use specific schema.org properties (e.g. http://schema.org/width, 
+     * http://schema.org/color, http://schema.org/gtin13, …) will typically expect 
+     * such data to be provided using those properties, rather than using the generic 
+     * property/value mechanism.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[] $additionalProperty
+     *
+     * @return static
+     *
+     * @see https://schema.org/additionalProperty
+     */
+    public function additionalProperty($additionalProperty)
+    {
+        return $this->setProperty('additionalProperty', $additionalProperty);
+    }
+
+    /**
+     * A citation or reference to another creative work, such as another
+     * publication, web page, scholarly article, etc.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\CreativeWorkContract|\Spatie\SchemaOrg\Contracts\CreativeWorkContract[]|string|string[] $citation
+     *
+     * @return static
+     *
+     * @see https://schema.org/citation
+     */
+    public function citation($citation)
+    {
+        return $this->setProperty('citation', $citation);
+    }
+
+    /**
+     * The creator/author of this CreativeWork. This is the same as the Author
+     * property for CreativeWork.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\OrganizationContract|\Spatie\SchemaOrg\Contracts\OrganizationContract[]|\Spatie\SchemaOrg\Contracts\PersonContract|\Spatie\SchemaOrg\Contracts\PersonContract[] $creator
+     *
+     * @return static
+     *
+     * @see https://schema.org/creator
+     */
+    public function creator($creator)
+    {
+        return $this->setProperty('creator', $creator);
+    }
+
+    /**
+     * The date on which the CreativeWork was created or the item was added to a
+     * DataFeed.
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $dateCreated
+     *
+     * @return static
+     *
+     * @see https://schema.org/dateCreated
+     */
+    public function dateCreated($dateCreated)
+    {
+        return $this->setProperty('dateCreated', $dateCreated);
+    }
+
+    /**
+     * The end date and time of the item (in ISO 8601 date format).
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $endDate
+     *
+     * @return static
+     *
+     * @see https://schema.org/endDate
+     */
+    public function endDate($endDate)
+    {
+        return $this->setProperty('endDate', $endDate);
+    }
+
+    /**
+     * The start date and time of the item (in ISO 8601 date format).
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $startDate
+     *
+     * @return static
+     *
+     * @see https://schema.org/startDate
+     */
+    public function startDate($startDate)
+    {
+        return $this->setProperty('startDate', $startDate);
+    }
+
+    /**
+     * Keywords or tags used to describe some item. Multiple textual entries in
+     * a keywords list are typically delimited by commas, or by repeating the
+     * property.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\DefinedTermContract|\Spatie\SchemaOrg\Contracts\DefinedTermContract[]|string|string[] $keywords
+     *
+     * @return static
+     *
+     * @see https://schema.org/keywords
+     */
+    public function keywords($keywords)
+    {
+        return $this->setProperty('keywords', $keywords);
+    }
+
+    /**
+     * TA process performed as part of an experiment or wider study, i.e. intentionally
+     * designed. These processes can have ontology URL attached to.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyProcess
+     *
+     * @return static
+     *
+     */
+    public function studyProcess($studyProcess)
+    {
+        return $this->setProperty('studyProcess', $studyProcess);
+    }
+
+    /**
+     * URL of the item.
+     *
+     * @param string|string[] $url
+     *
+     * @return static
+     *
+     * @see https://schema.org/url
+     */
+    public function url($url)
+    {
+        return $this->setProperty('url', $url);
+    }
+}
diff --git a/routes/api.php b/routes/api.php
index 3a12594f..0f4440fb 100644
--- a/routes/api.php
+++ b/routes/api.php
@@ -4,6 +4,8 @@
 use App\Http\Controllers\API\Auth\RegisterController;
 use App\Http\Controllers\API\Auth\UserController;
 use App\Http\Controllers\API\Bioschema\DataCatalogController;
+use App\Http\Controllers\API\Bioschema\DatasetController;
+use App\Http\Controllers\API\Bioschema\ProjectController as ProjectSchemaController;
 use App\Http\Controllers\API\FileSystemController;
 use App\Http\Controllers\API\ProjectController;
 use Illuminate\Support\Facades\Route;
@@ -36,6 +38,7 @@
     Route::prefix('schemas')->group(function () {
         Route::prefix('bioschema')->group(function () {
             Route::get('/', [DataCatalogController::class, 'schema']);
+            Route::get('/{username}/{project}/{study?}/{dataset?}', [ProjectSchemaController::class, 'schema']);
         });
     });
 });

From 7dc60cf082544de3ed31a863045f31aa28960bc5 Mon Sep 17 00:00:00 2001
From: NishaSharma14 <sharmanis14@gmail.com>
Date: Thu, 25 Aug 2022 16:03:00 +0200
Subject: [PATCH 4/7] Associate Citation to Project.

---
 app/Actions/Project/UpdateProject.php         |   7 +
 app/Http/Controllers/CitationController.php   |  30 +-
 app/Http/Controllers/ProjectController.php    |   6 +-
 app/Http/Middleware/HandleInertiaRequests.php |   1 +
 app/Http/Resources/CitationResource.php       |  25 +
 app/Http/Resources/ProjectResource.php        |  12 +-
 app/Models/Citation.php                       |   1 +
 app/Models/Project.php                        |   4 +
 ...22_08_23_143935_create_citations_table.php |   2 +-
 database/seeders/DatabaseSeeder.php           |   6 +-
 resources/js/Pages/Project/Show.vue           |  82 +++
 resources/js/Pages/Public/Project/Show.vue    |  57 ++
 resources/js/Shared/AddCitation.vue           | 502 +++++++++++++-----
 resources/js/Shared/AuthorCheckbox.vue        |   2 +-
 routes/web.php                                |   5 +
 15 files changed, 600 insertions(+), 142 deletions(-)
 create mode 100644 app/Http/Resources/CitationResource.php

diff --git a/app/Actions/Project/UpdateProject.php b/app/Actions/Project/UpdateProject.php
index 4d36685c..ec48aad8 100644
--- a/app/Actions/Project/UpdateProject.php
+++ b/app/Actions/Project/UpdateProject.php
@@ -116,4 +116,11 @@ public function updateAuthors(Project $project, $authors)
             $authors
         );
     }
+
+    public function updateCitation(Project $project, $citations, $user)
+    {
+        $project->citations()->syncWithPivotValues(
+            $citations,['user' => $user->id]
+        );
+    }
 }
diff --git a/app/Http/Controllers/CitationController.php b/app/Http/Controllers/CitationController.php
index ca7f338e..853ade8b 100644
--- a/app/Http/Controllers/CitationController.php
+++ b/app/Http/Controllers/CitationController.php
@@ -2,7 +2,35 @@
 
 namespace App\Http\Controllers;
 
+
+use App\Actions\Project\UpdateProject;
+use App\Models\Citation;
+use App\Models\Project;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\DB;
+
 class CitationController extends Controller
 {
-    //
+    public function updateCitation(Request $request, UpdateProject $updater, Project $project)
+    {
+        $input = $request->citationList;
+        $user = $request->user();
+        //dd($request->citationList);
+        //DB transaction
+        $citations = [];
+
+        foreach ($input as $item) {
+            $citation = Citation::create([
+                'doi' => array_key_exists('doi', $item) ? $item['doi'] : null,
+                'title' => array_key_exists('title', $item) ? $item['title'] : null,
+                'authors' => array_key_exists('authors', $item) ? $item['authors'] : null,
+                'abstract' => array_key_exists('abstract', $item) ? $item['abstract'] : null,
+                'citation_text' => array_key_exists('citation_text', $item) ? $item['citation_text'] : null,
+                ]);
+            array_push($citations, $citation->id);
+        }
+        $updater->updateCitation($project, $citations, $user);
+
+        return $request->wantsJson() ? new JsonResponse('', 200) : back()->with('success', 'Citation updated successfully');
+    }
 }
diff --git a/app/Http/Controllers/ProjectController.php b/app/Http/Controllers/ProjectController.php
index c4867806..ffa314d6 100644
--- a/app/Http/Controllers/ProjectController.php
+++ b/app/Http/Controllers/ProjectController.php
@@ -40,7 +40,7 @@ public function publicProjectView(Request $request, $owner, $slug)
 
         if ($tab == 'info') {
             return Inertia::render('Public/Project/Show', [
-                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors']),
+                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors', 'citations']),
                 'tab' => $tab,
             ]);
         } elseif ($tab == 'studies') {
@@ -69,7 +69,7 @@ public function publicProjectView(Request $request, $owner, $slug)
             ]);
         } else {
             return Inertia::render('Public/Project/Show', [
-                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors']),
+                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors', 'citations']),
                 'tab' => 'info',
             ]);
         }
@@ -110,7 +110,7 @@ public function show(Request $request, Project $project, GetLicense $getLicense)
         }
 
         return Inertia::render('Project/Show', [
-            'project' => $project->load('projectInvitations', 'tags', 'authors'),
+            'project' => $project->load('projectInvitations', 'tags', 'authors', 'citations'),
             'team' => $team ? $team->load(['users', 'owner']) : null,
             'members' => $project->allUsers(),
             'availableRoles' => array_values(Jetstream::$roles),
diff --git a/app/Http/Middleware/HandleInertiaRequests.php b/app/Http/Middleware/HandleInertiaRequests.php
index 3c6a5f60..d602e2a8 100644
--- a/app/Http/Middleware/HandleInertiaRequests.php
+++ b/app/Http/Middleware/HandleInertiaRequests.php
@@ -70,6 +70,7 @@ public function share(Request $request)
             'MEILISEARCH_PUBLICKEY' => (env('MEILISEARCH_PUBLICKEY')),
             'SCOUT_PREFIX' => (env('SCOUT_PREFIX')),
             'getDetailsbyDOIApi' => (env('GET_DETAILS_BY_DOI_API')),
+            'getCitationbyDOIApi' => (env('GET_CITATION_BY_DOI_API')),
         ]);
     }
 }
diff --git a/app/Http/Resources/CitationResource.php b/app/Http/Resources/CitationResource.php
new file mode 100644
index 00000000..77403fd1
--- /dev/null
+++ b/app/Http/Resources/CitationResource.php
@@ -0,0 +1,25 @@
+<?php
+
+namespace App\Http\Resources;
+
+use Illuminate\Http\Resources\Json\JsonResource;
+
+class CitationResource extends JsonResource
+{
+    /**
+     * Transform the resource into an array.
+     *
+     * @param  \Illuminate\Http\Request  $request
+     * @return array|\Illuminate\Contracts\Support\Arrayable|\JsonSerializable
+     */
+    public function toArray($request)
+    {
+        return [
+            'doi' => $this->doi,
+            'title' => $this->title,
+            'authors' => $this->authors,
+            'abstract' => $this->abstract,
+            'citation_text' => $this->citation_text,
+        ];
+    }
+}
diff --git a/app/Http/Resources/ProjectResource.php b/app/Http/Resources/ProjectResource.php
index bdca17ae..39200cf4 100644
--- a/app/Http/Resources/ProjectResource.php
+++ b/app/Http/Resources/ProjectResource.php
@@ -9,7 +9,7 @@ class ProjectResource extends JsonResource
 {
     private bool $lite = true;
 
-    private array $properties = ['users', 'studies', 'files', 'authors'];
+    private array $properties = ['users', 'studies', 'files', 'authors', 'citations'];
 
     public function lite(bool $lite, array $properties): self
     {
@@ -94,6 +94,16 @@ function () {
                             ];
                         }
                     ),
+                    $this->mergeWhen(
+                        in_array('citations', $this->properties),
+                        function () {
+                            return [
+                                'citations' => CitationResource::collection(
+                                    $this->citations
+                                ),
+                            ];
+                        }
+                    ),
                 ];
             }),
         ];
diff --git a/app/Models/Citation.php b/app/Models/Citation.php
index 5ebadd23..b621026b 100644
--- a/app/Models/Citation.php
+++ b/app/Models/Citation.php
@@ -12,6 +12,7 @@ class Citation extends Model
     protected $fillable = [
         'doi',
         'title',
+        'authors',
         'abstract',
         'citation_text',
     ];
diff --git a/app/Models/Project.php b/app/Models/Project.php
index 4b203302..368a4717 100644
--- a/app/Models/Project.php
+++ b/app/Models/Project.php
@@ -270,4 +270,8 @@ public function scopeFilter($query, array $filters)
             }
         });
     }
+    public function citations()
+    {
+        return $this->belongsToMany(Citation::class);
+    }
 }
diff --git a/database/migrations/2022_08_23_143935_create_citations_table.php b/database/migrations/2022_08_23_143935_create_citations_table.php
index 080db538..2ed5a1a3 100644
--- a/database/migrations/2022_08_23_143935_create_citations_table.php
+++ b/database/migrations/2022_08_23_143935_create_citations_table.php
@@ -15,7 +15,7 @@ public function up()
     {
         Schema::create('citations', function (Blueprint $table) {
             $table->id();
-            $table->string('doi');
+            $table->string('doi')->nullable();
             $table->string('title');
             $table->longText('authors');
             $table->longText('abstract');
diff --git a/database/seeders/DatabaseSeeder.php b/database/seeders/DatabaseSeeder.php
index d3757cea..ba56fc49 100644
--- a/database/seeders/DatabaseSeeder.php
+++ b/database/seeders/DatabaseSeeder.php
@@ -13,9 +13,9 @@ class DatabaseSeeder extends Seeder
      */
     public function run()
     {
-        // $this->call(RolesAndPermissionsSeeder::class);
-        // $this->call(UsersSeeder::class);
-        // $this->call(AnnouncementSeeder::class);
+        $this->call(RolesAndPermissionsSeeder::class);
+        $this->call(UsersSeeder::class);
+        $this->call(AnnouncementSeeder::class);
         $this->call(LicenseSeeder::class);
     }
 }
diff --git a/resources/js/Pages/Project/Show.vue b/resources/js/Pages/Project/Show.vue
index c5365e83..4a5a002a 100644
--- a/resources/js/Pages/Project/Show.vue
+++ b/resources/js/Pages/Project/Show.vue
@@ -140,6 +140,10 @@
                                     ref="addAuthorElement"
                                     :project="project"
                                 />
+                                <add-citation
+                                    ref="addCitationElement"
+                                    :project="project"
+                                />
                                 <span
                                     class="capitalize inline-flex pr-4 ml-7 inline-flex items-center px-2.5 py-0.5 rounded-full text-xs font-medium bg-gray-100 text-gray-800"
                                 >
@@ -377,6 +381,76 @@
                         </dd>
                     </div>
                 </div>
+                <!-- Citation -->
+                <div class="mb-8">
+                    <div class="relative">
+                        <div
+                            class="absolute inset-0 flex items-center"
+                            aria-hidden="true"
+                        >
+                            <div class="w-full border-t border-gray-300"></div>
+                        </div>
+                        <div class="relative flex items-center justify-between">
+                            <span
+                                class="px-3 -ml-4 rounded text-sm bg-gray-100 font-medium text-gray-500"
+                            >
+                                Citation
+                            </span>
+                            <button
+                                v-if="canUpdateProject"
+                                type="button"
+                                class="inline-flex items-center shadow-sm px-4 py-1.5 border border-gray-300 text-sm leading-5 font-medium rounded-full text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-teal-500"
+                                @click="toggleAddCitation"
+                            >
+                                <PencilIcon
+                                    class="w-4 h-4 mr-1 text-gray-600"
+                                />
+                                <span>Edit</span>
+                            </button>
+                        </div>
+                    </div>
+                    <dd class="mt-2 text-md text-gray-900 space-y-5">
+                        <div class="mt-1 grid grid-cols-1 gap-4 sm:grid-cols-2">
+                            <div
+                                v-for="citation in project.citations"
+                                :key="citation.id"
+                                class="relative rounded-lg border border-gray-300 bg-white px-6 py-5 shadow-sm flex items-center space-x-3 hover:border-gray-400 focus-within:ring-2 focus-within:ring-offset-2 focus-within:ring-pink-500"
+                            >
+                                <div class="flex-1 min-w-0">
+                                    <a class="focus:outline-none">
+                                        <span
+                                            class="absolute inset-0"
+                                            aria-hidden="true"
+                                        ></span>
+                                        <p
+                                            class="text-sm font-medium text-gray-900"
+                                        >
+                                            {{ citation.title }}
+                                        </p>
+                                        <p class="text-sm text-teal-500">
+                                            {{ citation.authors }}
+                                        </p>
+                                        <p class="text-sm text-gray-500">
+                                            {{ citation.citation_text }}
+                                        </p>
+                                        <p
+                                            v-if="citation.doi"
+                                            class="text-sm font-bold text-gray-500"
+                                        >
+                                            DOI - {{ citation.doi }}
+                                        </p>
+                                        <p
+                                            class="text-sm text-gray-500 truncate ..."
+                                        >
+                                            {{ citation.abstract }} ...
+                                        </p>
+                                    </a>
+                                </div>
+                            </div>
+                        </div>
+                    </dd>
+                </div>
+
                 <!-- Author -->
                 <div class="mb-8">
                     <div class="relative">
@@ -472,6 +546,7 @@ import { ref } from "vue";
 import { StarIcon, PencilIcon } from "@heroicons/vue/solid";
 import AddAuthor from "@/Shared/AddAuthor.vue";
 import ToolTip from "@/Shared/ToolTip.vue";
+import AddCitation from "@/Shared/AddCitation.vue";
 
 export default {
     components: {
@@ -484,6 +559,7 @@ export default {
         AccessDialogue,
         AddAuthor,
         ToolTip,
+        AddCitation,
     },
     props: [
         "project",
@@ -497,9 +573,11 @@ export default {
     setup() {
         const projectDetailsElement = ref(null);
         const addAuthorElement = ref(null);
+        const addCitationElement = ref(null);
         return {
             projectDetailsElement,
             addAuthorElement,
+            addCitationElement,
         };
     },
     mounted() {},
@@ -534,6 +612,10 @@ export default {
         toggleAddAuthor() {
             this.addAuthorElement.toggleAddAuthorDialog();
         },
+        toggleAddCitation() {
+            this.addCitationElement.toggleAddCitationDialog();
+            //this.emitter.emit("openAddCitationDialog", {});
+        },
     },
 };
 </script>
diff --git a/resources/js/Pages/Public/Project/Show.vue b/resources/js/Pages/Public/Project/Show.vue
index 11172464..c06e4497 100644
--- a/resources/js/Pages/Public/Project/Show.vue
+++ b/resources/js/Pages/Public/Project/Show.vue
@@ -76,6 +76,63 @@
                             </div>
                         </div>
                     </div>
+                    <div
+                        v-if="
+                            project.data.citations &&
+                            project.data.citations.length > 0
+                        "
+                        class="pt-8 gap-y-6 sm:grid-cols-6 sm:gap-x-6"
+                    >
+                        <div class="sm:col-span-6">
+                            <h2
+                                class="text-xl font-extrabold mb-3 text-blue-gray-900"
+                            >
+                                Citation(s)
+                            </h2>
+                            <!-- <p class="mt-1 text-sm text-blue-gray-500">
+                      This information will be displayed publicly so be careful what you
+                      share.
+                    </p> -->
+                        </div>
+                        <div class="mt-1 grid grid-cols-1 gap-4 sm:grid-cols-2">
+                            <div
+                                v-for="citation in project.data.citations"
+                                :key="citation.id"
+                                class="relative rounded-lg border border-gray-300 bg-white px-6 py-5 shadow-sm flex items-center space-x-3 hover:border-gray-400 focus-within:ring-2 focus-within:ring-offset-2 focus-within:ring-pink-500"
+                            >
+                                <div class="flex-1 min-w-0">
+                                    <a class="focus:outline-none">
+                                        <span
+                                            class="absolute inset-0"
+                                            aria-hidden="true"
+                                        ></span>
+                                        <p
+                                            class="text-sm font-medium text-gray-900"
+                                        >
+                                            {{ citation.title }}
+                                        </p>
+                                        <p class="text-sm text-teal-500">
+                                            {{ citation.authors }}
+                                        </p>
+                                        <p class="text-sm text-gray-500">
+                                            {{ citation.citation_text }}
+                                        </p>
+                                        <p
+                                            v-if="citation.doi"
+                                            class="text-sm font-bold text-gray-500"
+                                        >
+                                            DOI - {{ citation.doi }}
+                                        </p>
+                                        <p
+                                            class="text-sm text-gray-500 truncate ..."
+                                        >
+                                            {{ citation.abstract }} ...
+                                        </p>
+                                    </a>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
                     <div
                         v-if="
                             project.data.authors &&
diff --git a/resources/js/Shared/AddCitation.vue b/resources/js/Shared/AddCitation.vue
index 4f09ef93..96782953 100644
--- a/resources/js/Shared/AddCitation.vue
+++ b/resources/js/Shared/AddCitation.vue
@@ -4,10 +4,10 @@
         :max-width="'6xl'"
         @close="addCitationDialog = false"
     >
-        <template #title> New Citation </template>
+        <template #title> Update Citation </template>
         <template #content>
             <div
-                class="relative grid grid-cols-1 gap-x-16 max-w-7xl mx-auto lg:grid-cols-2 divide-x"
+                class="relative grid grid-cols-1 gap-x-5 max-w-7xl mx-auto lg:grid-cols-2 divide-x"
             >
                 <div
                     class="pb-36 px-4 sm:px-6 lg:pb-16 lg:px-0 lg:row-start-1 lg:col-start-1"
@@ -18,7 +18,7 @@
                             Import From
                         </p>
                         <div
-                            class="mt-1 grid grid-cols-1 gap-y-6 gap-x-4 sm:grid-cols-2"
+                            class="mt-3 grid grid-cols-1 gap-y-6 gap-x-4 sm:grid-cols-2"
                         >
                             <div class="sm:col-span-2">
                                 <label
@@ -44,7 +44,7 @@
                             </div>
                         </div>
                         <div class="sm:col-span-2 mt-4">
-                            <jet-secondary-button @click="importAuthors">
+                            <jet-secondary-button @click="importCitation">
                                 Import
                             </jet-secondary-button>
                         </div>
@@ -54,22 +54,74 @@
                         >
                             <loading-button :loading="loading" />
                         </div>
+                        <!-- List Imported Citation -->
                         <div
-                            v-if="authorsListDOI.length > 0 && !loading"
-                            class="sm:col-span-9 mt-4"
-                        >
-                            <author-checkbox
-                                v-model:checked="doiSelectedAuthorList"
-                                :items="authorsListDOI"
-                            />
-                        </div>
-                        <div
-                            v-if="authorsListDOI.length > 0"
-                            class="sm:col-span-6 pt-3"
+                            v-if="this.formattedCitationRes != null && !loading"
+                            class="mt-4"
                         >
+                            <fieldset
+                                class="border rounded border-gray-200 overflow-auto"
+                            >
+                                <legend class="sr-only">Notifications</legend>
+                                <div
+                                    style="height: 40vh"
+                                    class="divide-y divide-gray-200"
+                                >
+                                    <div class="relative flex items-start p-4">
+                                        <div class="min-w-0 flex-1 text-sm">
+                                            <label
+                                                for="citation"
+                                                class="font-medium text-gray-700"
+                                            >
+                                                {{ formattedCitationRes.title }}
+                                            </label>
+                                            <p
+                                                id="citation-authors"
+                                                class="text-teal-500"
+                                            >
+                                                {{
+                                                    formattedCitationRes.authors
+                                                }}
+                                            </p>
+                                            <p
+                                                id="citation-text"
+                                                class="text-gray-500"
+                                            >
+                                                {{
+                                                    formattedCitationRes.citation_text
+                                                }}
+                                            </p>
+                                            <p
+                                                id="citation-doi"
+                                                class="text-gray-500 font-bold"
+                                            >
+                                                DOI -
+                                                {{ formattedCitationRes.doi }}
+                                            </p>
+                                            <p
+                                                v-if="
+                                                    formattedCitationRes.abstract
+                                                "
+                                                id="citation-doi"
+                                                class="font-bold text-gray-500 mt-2"
+                                            >
+                                                Abstract
+                                            </p>
+                                            <p
+                                                id="citation-abstract"
+                                                class="text-xs text-gray-500"
+                                            >
+                                                {{
+                                                    formattedCitationRes.abstract
+                                                }}
+                                            </p>
+                                        </div>
+                                    </div>
+                                </div>
+                            </fieldset>
                             <jet-secondary-button
-                                class="float-right text-md font-bold text-teal-900"
-                                @click="addAuthor('DOI')"
+                                class="float-right text-md font-bold text-teal-900 mt-4"
+                                @click="addCitationTemp('DOI')"
                             >
                                 Add
                             </jet-secondary-button>
@@ -87,143 +139,121 @@
                         <div
                             class="mt-1 grid grid-cols-1 gap-y-6 gap-x-4 sm:grid-cols-2"
                         >
-                            <div class="sm:col-span-2">
+                            <div class="sm:col-span-1">
                                 <label
-                                    for="title"
+                                    for="doi"
                                     class="block text-sm font-medium text-gray-700"
                                 >
-                                    Title
+                                    DOI
                                 </label>
                                 <div class="mt-1">
                                     <input
-                                        id="title"
-                                        v-model="manualAddCitationForm.title"
+                                        id="doi"
+                                        v-model="manualAddCitationForm.doi"
                                         type="text"
-                                        name="title"
-                                        autocomplete="title"
+                                        name="doi"
+                                        autocomplete="doi"
                                         class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
                                     />
                                 </div>
                             </div>
-                            <div class="sm:col-span-2">
+                            <div class="sm:col-span-4">
                                 <label
-                                    for="family-name"
+                                    for="title"
                                     class="block text-sm font-medium text-gray-700 after:content-['*'] after:ml-0.5 after:text-red-500"
                                 >
-                                    Family Name
+                                    Title
                                 </label>
                                 <div class="mt-1">
                                     <input
-                                        id="family-name"
-                                        v-model="
-                                            manualAddCitationForm.family_name
-                                        "
+                                        id="title"
+                                        v-model="manualAddCitationForm.title"
                                         type="text"
-                                        name="family-name"
-                                        autocomplete="family-name"
+                                        name="title"
+                                        autocomplete="title"
                                         class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
                                     />
                                 </div>
                                 <jet-input-error
                                     :message="
-                                        manualAddCitationForm.errors.family_name
+                                        manualAddCitationForm.errors.title
                                     "
                                     class="mt-2"
                                 />
                             </div>
-
-                            <div class="sm:col-span-2">
+                            <div class="sm:col-span-6">
                                 <label
-                                    for="given-name"
+                                    for="authors"
                                     class="block text-sm font-medium text-gray-700 after:content-['*'] after:ml-0.5 after:text-red-500"
                                 >
-                                    Given Name
+                                    Authors
                                 </label>
                                 <div class="mt-1">
-                                    <input
-                                        id="given-name"
-                                        v-model="
-                                            manualAddCitationForm.given_name
-                                        "
-                                        type="text"
-                                        name="given-name"
-                                        autocomplete="given-name"
-                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
+                                    <textarea
+                                        id="authors"
+                                        v-model="manualAddCitationForm.authors"
+                                        name="authors"
+                                        rows="3"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border border-gray-300 rounded-md"
+                                        placeholder=""
                                     />
                                 </div>
                                 <jet-input-error
                                     :message="
-                                        manualAddCitationForm.errors.given_name
+                                        manualAddCitationForm.errors.authors
                                     "
                                     class="mt-2"
                                 />
                             </div>
-                            <div class="sm:col-span-3">
-                                <label
-                                    for="email"
-                                    class="block text-sm font-medium text-gray-700"
-                                >
-                                    Email address
-                                </label>
-                                <div class="mt-1">
-                                    <input
-                                        id="email"
-                                        v-model="manualAddCitationForm.email_id"
-                                        name="email"
-                                        type="email"
-                                        autocomplete="email"
-                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
-                                        @blur="validateEmail"
-                                    />
-                                    <jet-input-error
-                                        :message="
-                                            manualAddCitationForm.errors
-                                                .email_id
-                                        "
-                                        class="mt-2"
-                                    />
-                                </div>
-                            </div>
-                            <div class="sm:col-span-3">
+
+                            <div class="sm:col-span-6">
                                 <label
-                                    for="orcid"
-                                    class="block text-sm font-medium text-gray-700"
+                                    for="abstract"
+                                    class="block text-sm font-medium text-gray-700 after:content-['*'] after:ml-0.5 after:text-red-500"
                                 >
-                                    ORCID ID
+                                    Abstract
                                 </label>
                                 <div class="mt-1">
-                                    <input
-                                        id="orcid"
-                                        v-model="manualAddCitationForm.orcid_id"
-                                        name="orcid"
-                                        autocomplete="orcid"
-                                        type="text"
-                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border-gray-300 rounded-md"
+                                    <textarea
+                                        id="abstract"
+                                        v-model="manualAddCitationForm.abstract"
+                                        name="abstract"
+                                        rows="3"
+                                        class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border border-gray-300 rounded-md"
+                                        placeholder=""
                                     />
                                 </div>
+                                <jet-input-error
+                                    :message="
+                                        manualAddCitationForm.errors.abstract
+                                    "
+                                    class="mt-2"
+                                />
                             </div>
+
                             <div class="sm:col-span-6">
                                 <label
-                                    for="about"
+                                    for="citation-text"
                                     class="block text-sm font-medium text-gray-700 after:content-['*'] after:ml-0.5 after:text-red-500"
                                 >
-                                    Affiliation
+                                    Citation Text
                                 </label>
                                 <div class="mt-1">
                                     <textarea
-                                        id="affiliation"
+                                        id="citation-text"
                                         v-model="
-                                            manualAddCitationForm.affiliation
+                                            manualAddCitationForm.citation_text
                                         "
-                                        name="affiliation"
+                                        name="citation-text"
                                         rows="3"
                                         class="shadow-sm focus:ring-teal-500 focus:border-teal-500 block w-full sm:text-sm border border-gray-300 rounded-md"
-                                        placeholder="Name and address of affiliated University and Department. e.g. Institut für Anorganische und Analytische Chemie,Friedrich-Schiller-Universität,Schloßgasse 10, 07743 Jena"
+                                        placeholder=""
                                     />
                                 </div>
                                 <jet-input-error
                                     :message="
-                                        manualAddCitationForm.errors.affiliation
+                                        manualAddCitationForm.errors
+                                            .citation_text
                                     "
                                     class="mt-2"
                                 />
@@ -231,7 +261,7 @@
                             <div class="sm:col-span-6 float-left">
                                 <jet-secondary-button
                                     class="float-right text-md font-bold text-teal-900"
-                                    @click="addAuthor('Manual')"
+                                    @click="addCitationTemp('Manual')"
                                 >
                                     Add
                                 </jet-secondary-button>
@@ -240,8 +270,8 @@
                     </div>
                 </div>
             </div>
-            <!-- Added Author Summary -->
-            <div v-if="selectedAuthorsList.length > 0">
+            <!-- Added Citation Summary -->
+            <div v-if="selectedCitationList.length > 0">
                 <div class="ml-2 mt-2 overflow-y-scroll h-64">
                     <table
                         class="divide-y divide-gray-200 w-full table-fixed overflow-y-scroll"
@@ -253,7 +283,7 @@
                                     scope="col"
                                     class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider"
                                 >
-                                    Author
+                                    Citation
                                 </th>
                                 <th
                                     scope="col"
@@ -265,63 +295,57 @@
                         </thead>
                         <tbody class="bg-white divide-y divide-gray-200">
                             <tr
-                                v-for="author in selectedAuthorsList"
-                                :key="author.id"
+                                v-for="citation in selectedCitationList"
+                                :key="citation.id"
                             >
                                 <td colspan="3" class="py-4">
                                     <div class="ml-4">
                                         <h3
                                             class="text-sm leading-6 font-medium text-gray-900"
                                         >
-                                            {{ author.title }}
-                                            {{ author.given_name }}
-                                            {{ author.family_name }}
+                                            {{ citation.title }}
                                         </h3>
+                                        <p
+                                            class="mt-1 text-xs font-small text-teal-900 break-words"
+                                        >
+                                            {{ citation.authors }}
+                                        </p>
                                         <p
                                             class="mt-1 text-xs font-small text-blue-gray-900 break-words"
                                         >
-                                            {{ author.affiliation }}
+                                            {{ citation.citation_text }}
                                         </p>
                                         <div
-                                            v-if="author.orcid_id"
-                                            class="text-xs leading-6 font-medium text-gray-900"
+                                            v-if="citation.doi"
+                                            class="text-xs font-bold leading-6 font-medium text-gray-900"
                                         >
-                                            <p>
-                                                Orcid Id -
-                                                <a
-                                                    :href="author.orcid_id"
-                                                    class="text-teal-900"
-                                                    >{{ author.orcid_id }}</a
-                                                >
-                                            </p>
+                                            <p>DOI - {{ citation.doi }}</p>
                                         </div>
                                         <div
-                                            v-if="author.email_id"
-                                            class="text-xs leading-6 font-medium text-gray-900"
+                                            v-if="citation.abstract"
+                                            class="text-xs text-gray-500 truncate ..."
                                         >
-                                            <p>
-                                                Email Id - {{ author.email_id }}
-                                            </p>
+                                            <p>{{ citation.abstract }} ...</p>
                                         </div>
                                     </div>
                                 </td>
                                 <td
                                     class="px-6 py-4 text-sm leading-5 text-gray-500 whitespace-no-wrap border-gray-200"
                                 >
-                                    <button
+                                    <!-- <button
                                         type="button"
                                         class="inline-flex items-center p-1 border border-transparent"
-                                        @click="editAuthor(author)"
+                                        @click="editCitation(citation)"
                                     >
                                         <PencilIcon
                                             class="w-5 h-5 mr-1 text-gray-600"
                                         />
-                                    </button>
+                                    </button> -->
                                     <button
                                         type="button"
                                         class="inline-flex items-center p-1 border border-transparent"
                                         @click="
-                                            confirmAuthorDeletion(author.id)
+                                            confirmCitationDeletion(citation)
                                         "
                                     >
                                         <TrashIcon
@@ -335,13 +359,13 @@
                 </div>
             </div>
             <jet-dialog-modal
-                :show="confirmingAuthorDeletion"
+                :show="confirmingCitationDeletion"
                 @close="closeModal"
             >
-                <template #title> Delete Author </template>
+                <template #title> Delete Citation </template>
 
                 <template #content>
-                    Are you sure you want to delete this author?
+                    Are you sure you want to delete this citation?
                     <div class="mt-4"></div>
                 </template>
 
@@ -354,14 +378,13 @@
                         class="ml-2"
                         :class="{ 'opacity-25': form.processing }"
                         :disabled="form.processing"
-                        @click="deleteAuthor(authorId)"
+                        @click="deleteCitation()"
                     >
-                        Delete Author
+                        Delete Citation
                     </jet-danger-button>
                 </template>
             </jet-dialog-modal>
         </template>
-
         <template #footer>
             <jet-secondary-button class="float-left" @click="onClose">
                 Close
@@ -398,27 +421,242 @@ export default {
 
     data() {
         return {
+            form: this.$inertia.form({}),
             importCitationForm: this.$inertia.form({
-                doi: "",
+                doi: "10.1021/acs.jmedchem.5b01009",
+                _method: "POST",
                 errors: {},
             }),
+            updateCitationForm: this.$inertia.form({
+                _method: "POST",
+                citationList: [],
+            }),
             manualAddCitationForm: this.$inertia.form({
                 _method: "POST",
+                doi: "",
+                title: "",
+                authors: "",
+                abstract: "",
+                citation_text: "",
                 errors: {},
             }),
+            formattedCitationRes: null,
+            importedCitationByDOI: [],
+            addCitationDialog: false,
+            selectedCitationList: [],
+            confirmingCitationDeletion: false,
+            selectedCitationforDelete: {},
+            loading: false,
         };
     },
-    mounted() {
+    /* mounted() {
+        console.log('citation called..')
         const initialise = () => {
             this.addCitationDialog = true;
         };
         this.emitter.all.set("openAddCitationDialog", [initialise]);
-    },
+    },*/
     methods: {
-        updateCitation() {},
+        toggleAddCitationDialog() {
+            this.selectedCitationList = [];
+            this.addCitationDialog = !this.addCitationDialog;
+            if (this.project.citations) {
+                for (var i = 0; i < this.project.citations.length; i++) {
+                    this.selectedCitationList.push(this.project.citations[i]);
+                }
+            }
+        },
+        /*Add citations to temp list either added Manually or imported from DOI.*/
+        addCitationTemp(source) {
+            if (source == "Manual") {
+                this.validateForm();
+                if (!this.manualAddCitationForm.hasErrors) {
+                    this.selectedCitationList.push(this.manualAddCitationForm);
+                    this.manualAddCitationForm = this.$inertia.form({});
+                }
+            } else if (source == "DOI") {
+                //Adding citation to tmp list imported from DOI.
+                this.selectedCitationList.push(this.formattedCitationRes);
+            }
+
+            //filtering duplicate values from the temp list.
+            if (this.selectedCitationList.length > 0) {
+                const keys = ["doi"];
+                this.selectedCitationList = this.selectedCitationList.filter(
+                    (value, index, self) =>
+                        self.findIndex((v) =>
+                            keys.every((k) => v[k] === value[k])
+                        ) === index
+                );
+            }
+        },
+        /*Import Citation from DOI*/
+        importCitation() {
+            this.loading = true;
+            this.importedCitationByDOI = [];
+            this.importCitationForm.errors = {};
+            this.formattedCitationRes = null;
+            if (!this.importCitationForm.doi) {
+                this.importCitationForm.errors.doi =
+                    "The DOI field is required.";
+            } else {
+                axios
+                    .get(this.$page.props.getCitationbyDOIApi, {
+                        params: {
+                            query: this.importCitationForm.doi,
+                            format: "json",
+                            pageSize: "1",
+                            resulttype: "core",
+                            synonym: "true",
+                        },
+                    })
+                    .then((res) => {
+                        this.formattedCitationRes = this.formatCitationResponse(
+                            res.data.resultList.result[0]
+                        );
+                    })
+                    .catch((error) => {
+                        this.importCitationForm.errors.doi =
+                            "Something went wrong. Please check the DOI and try again.";
+                    })
+                    .finally(() => {
+                        if (this.formattedCitationRes == null) {
+                            this.importCitationForm.errors.doi =
+                                "Something went wrong. Please check the DOI and try again.";
+                        }
+                        this.loading = false;
+                    });
+            }
+        },
+        formatCitationResponse(obj) {
+            var journalTitle = "";
+            var yearofPublication = "";
+            var volume = "";
+            var issue = "";
+            var pageInfo = "";
+            if (obj) {
+                this.formattedCitationRes = {};
+                if (obj.journalInfo) {
+                    journalTitle = obj.journalInfo.journal.title
+                        ? obj.journalInfo.journal.title
+                        : "";
+                    yearofPublication = obj.journalInfo.yearOfPublication
+                        ? obj.journalInfo.yearOfPublication
+                        : "";
+                    volume = obj.journalInfo.volume
+                        ? obj.journalInfo.volume
+                        : "";
+                    issue = obj.journalInfo.issue ? obj.journalInfo.issue : "";
+                }
+                pageInfo = obj.pageInfo ? obj.pageInfo : "";
+                this.formattedCitationRes.title = obj.title ? obj.title : "";
+                this.formattedCitationRes.authors = obj.authorString
+                    ? obj.authorString
+                    : "";
+                this.formattedCitationRes.citation_text =
+                    journalTitle +
+                    " " +
+                    yearofPublication +
+                    " " +
+                    volume +
+                    " ( " +
+                    issue +
+                    " ) " +
+                    pageInfo;
+                this.formattedCitationRes.doi = obj.doi ? obj.doi : "";
+                this.formattedCitationRes.abstract = obj.abstractText
+                    ? obj.abstractText
+                    : "";
+            }
+            return this.formattedCitationRes;
+        },
+        /*Update the Citation table and relationship*/
+        updateCitation() {
+            this.updateCitationForm.reset();
+            for (var i = 0; i < this.selectedCitationList.length; i++) {
+                this.updateCitationForm.citationList.push(
+                    this.selectedCitationList[i]
+                );
+            }
+            this.updateCitationForm.post(
+                route("update-citation", this.project.id),
+                {
+                    preserveScroll: true,
+                    onSuccess: () => {
+                        this.addCitationDialog = false;
+                        this.resetData();
+                    },
+                    onError: (err) => console.error(err),
+                }
+            );
+        },
+        /*Validation form*/
+        validateForm() {
+            this.manualAddCitationForm.errors = {};
+            this.manualAddCitationForm.hasErrors = false;
+            var hasErrors = false;
+            if (!this.manualAddCitationForm.title) {
+                this.manualAddCitationForm.errors.title =
+                    "The title field is required.";
+                hasErrors = true;
+            }
+            if (!this.manualAddCitationForm.authors) {
+                this.manualAddCitationForm.errors.authors =
+                    "The authors field is required.";
+                hasErrors = true;
+            }
+            if (!this.manualAddCitationForm.abstract) {
+                this.manualAddCitationForm.errors.abstract =
+                    "The abstract field is required.";
+                hasErrors = true;
+            }
+            if (!this.manualAddCitationForm.citation_text) {
+                this.manualAddCitationForm.errors.citation_text =
+                    "The citation text field is required.";
+                hasErrors = true;
+            }
+            if (hasErrors) {
+                this.manualAddCitationForm.hasErrors = true;
+            }
+        },
+        editCitation() {
+            //
+        },
+        /*Confirming before deletion*/
+        confirmCitationDeletion(citation) {
+            this.selectedCitationforDelete = citation;
+            this.confirmingCitationDeletion = true;
+        },
+        /*Delete citation from the temp list*/
+        deleteCitation(citation) {
+            var index = this.selectedCitationforDelete
+                ? this.selectedCitationList.indexOf(
+                      this.selectedCitationforDelete
+                  )
+                : null;
+            if (index > -1) {
+                this.selectedCitationList.splice(index, 1);
+            }
+            this.closeModal();
+        },
+        closeModal() {
+            this.confirmingCitationDeletion = false;
+        },
+        /*Resetting local variables and forms*/
+        resetData() {
+            this.importCitationForm = this.$inertia.form({});
+            this.manualAddCitationForm = this.$inertia.form({});
+            this.formattedCitationRes = null;
+            this.importedCitationByDOI = [];
+            this.addCitationDialog = false;
+            this.selectedCitationList = [];
+            this.confirmingCitationDeletion = false;
+            this.selectedCitationforDelete = {};
+            this.loading = false;
+        },
         onClose() {
             this.addCitationDialog = false;
-            //this.resetData();
+            this.resetData();
         },
     },
 };
diff --git a/resources/js/Shared/AuthorCheckbox.vue b/resources/js/Shared/AuthorCheckbox.vue
index 3f942305..52c54329 100644
--- a/resources/js/Shared/AuthorCheckbox.vue
+++ b/resources/js/Shared/AuthorCheckbox.vue
@@ -1,5 +1,5 @@
 <template>
-    <fieldset class="border border-gray-200 overflow-auto">
+    <fieldset class="border rounded border-gray-200 overflow-auto">
         <legend class="sr-only">Notifications</legend>
         <div style="height: 40vh" class="divide-y divide-gray-200">
             <div
diff --git a/routes/web.php b/routes/web.php
index 1d844307..ee8d1782 100644
--- a/routes/web.php
+++ b/routes/web.php
@@ -6,6 +6,7 @@
 use App\Http\Controllers\Admin\UsersController;
 use App\Http\Controllers\Auth\SocialController;
 use App\Http\Controllers\AuthorController;
+use App\Http\Controllers\CitationController;
 use App\Http\Controllers\DashboardController;
 use App\Http\Controllers\DatasetController;
 use App\Http\Controllers\DownloadController;
@@ -82,6 +83,10 @@
     // Authors
     Route::post('authors/{project}', [AuthorController::class, 'updateAuthor'])
                 ->name('update-author');
+    
+    //Citation
+    Route::post('citation/{project}', [CitationController::class, 'updateCitation'])
+    ->name('update-citation');
 
     Route::post('/onboarding/{status}', [DashboardController::class, 'onboardingStatus'])
             ->name('onboarding.complete');

From 955f536cf6222be44e6d9412a0b80f471f1eedb5 Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Thu, 25 Aug 2022 17:38:01 +0200
Subject: [PATCH 5/7] Add study class Add study schema

---
 ...tController.php => BiochemaController.php} |  42 ++-
 app/Models/Bioschema/BioSchema.php            |  17 ++
 app/Models/Bioschema/Project.php              |   2 +-
 app/Models/Bioschema/Study.php                | 275 ++++++++++++++++++
 routes/api.php                                |   5 +-
 5 files changed, 331 insertions(+), 10 deletions(-)
 rename app/Http/Controllers/API/Bioschema/{ProjectController.php => BiochemaController.php} (63%)
 create mode 100644 app/Models/Bioschema/BioSchema.php
 create mode 100644 app/Models/Bioschema/Study.php

diff --git a/app/Http/Controllers/API/Bioschema/ProjectController.php b/app/Http/Controllers/API/Bioschema/BiochemaController.php
similarity index 63%
rename from app/Http/Controllers/API/Bioschema/ProjectController.php
rename to app/Http/Controllers/API/Bioschema/BiochemaController.php
index c064778d..10fbc3f2 100644
--- a/app/Http/Controllers/API/Bioschema/ProjectController.php
+++ b/app/Http/Controllers/API/Bioschema/BiochemaController.php
@@ -5,22 +5,22 @@
 use App\Http\Controllers\Controller;
 use Illuminate\Http\Request;
 use Spatie\SchemaOrg\Schema;
+use App\Models\Bioschema\BioSchema;
 use App\Models\Project;
 use App\Models\Study;
-
+use App\Models\Bioschema\Study as StudySchema;
 use App\Models\User;
 use App\Models\Author;
 
 
 
-class ProjectController extends Controller
+class BiochemaController extends Controller
 {
     public function schema(Request $request, $username, $projectName, $studyName = null, $datasetName = null)
     {
         $user = User::where('username', $username)->firstOrFail();
         if($user){
-            $project = Project::where([['slug', $projectName], ['owner_id', $user->id]])->firstOrFail();
-            
+            $project = Project::where([['slug', $projectName], ['owner_id', $user->id]])->firstOrFail();  
         }
 
         if($project){
@@ -53,18 +53,48 @@ public function schema(Request $request, $username, $projectName, $studyName = n
                 array_push($tags, $tag);
             }
             $projectSchema->keywords($tags);
-            $projectSchema->url($project->url);
+            $projectSchema->url($project->public_url);
             
+
+
             if($studyName && !$datasetName){
                 $study = Study::where([['slug', $studyName], ['owner_id', $user->id], ['project_id', $project->id]])->firstOrFail();
                 // send study back with project info added to it\
-                return [];
+                if($study){
+                    $studySchema = BioSchema::Study(); 
+                    $studySchema['@id']= $study->uuid;
+                    $studySchema['dct:conformsTo'] = $confromsTo;
+                    $studySchema->description($study->description);
+                    $studySchema->name($study->name);
+                    $tags = [];
+                    foreach ($study->tags as &$tag) {
+                        $tag = $tag->name; 
+                        array_push($tags, $tag);
+                    }
+                    $studySchema->keywords($tags);
+                    $studySchema->url($study->public_url);
+
+                    $projectSchema->relatedStudy($studySchema);
+
+                    return $projectSchema;
+                }
+                
             }else if($studyName && $datasetName){
                 $dataset = Dataset::where([['slug', $datasetName], ['owner_id', $user->id], ['project_id', $project->id], ['study_id', $study->id]])->firstOrFail();
                 // send dataset with project and study details
                 return [];
             }else{
                 // add studies and associated datasets
+                $studies = [];
+                foreach ($project->studies as &$study) {
+                    $studySchema = BioSchema::Study(); 
+                    $studySchema['@id']= $study->uuid;
+                    $studySchema['dct:conformsTo'] = $confromsTo;
+                    $studySchema->name($study->name);
+                    $studySchema->url($study->public_url);
+                    array_push($studies, $studySchema);   
+                }
+                $projectSchema->relatedStudy($studies);
                 return $projectSchema;
             }
         }
diff --git a/app/Models/Bioschema/BioSchema.php b/app/Models/Bioschema/BioSchema.php
new file mode 100644
index 00000000..3cc96f16
--- /dev/null
+++ b/app/Models/Bioschema/BioSchema.php
@@ -0,0 +1,17 @@
+<?php
+
+namespace App\Models\Bioschema;
+
+use App\Models\Bioschema\Study;
+use \Spatie\SchemaOrg\Schema;
+
+/**
+ * Factory class for all Schema.org types.
+ */
+class BioSchema extends Schema
+{
+    public static function study(): Study
+    {
+        return new Study();
+    }
+}
\ No newline at end of file
diff --git a/app/Models/Bioschema/Project.php b/app/Models/Bioschema/Project.php
index 30936678..cc33a374 100644
--- a/app/Models/Bioschema/Project.php
+++ b/app/Models/Bioschema/Project.php
@@ -1,6 +1,6 @@
 <?php
 
-namespace Spatie\SchemaOrg;
+namespace App\Models\Bioschema;
 
 use \Spatie\SchemaOrg\Contracts\DatasetContract;
 use \Spatie\SchemaOrg\Contracts\CreativeWorkContract;
diff --git a/app/Models/Bioschema/Study.php b/app/Models/Bioschema/Study.php
new file mode 100644
index 00000000..9587268f
--- /dev/null
+++ b/app/Models/Bioschema/Study.php
@@ -0,0 +1,275 @@
+<?php
+
+namespace App\Models\Bioschema;
+
+use \Spatie\SchemaOrg\Contracts\DatasetContract;
+use \Spatie\SchemaOrg\Contracts\CreativeWorkContract;
+use \Spatie\SchemaOrg\Contracts\ThingContract;
+use \Spatie\SchemaOrg\BaseType;
+
+/**
+ * A body of structured information describing some topic(s) of interest.
+ *
+ * @see https://bioschemas.org/profiles/Study/0.2-DRAFT
+ * @link http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources
+ *
+ */
+class Study extends BaseType
+{
+    /**
+     * The author of this content or rating. Please note that author is special
+     * in that HTML 5 provides a special mechanism for indicating authorship via
+     * the rel tag. That is equivalent to this and may be used interchangeably.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\OrganizationContract|\Spatie\SchemaOrg\Contracts\OrganizationContract[]|\Spatie\SchemaOrg\Contracts\PersonContract|\Spatie\SchemaOrg\Contracts\PersonContract[] $author
+     *
+     * @return static
+     *
+     * @see https://schema.org/author
+     */
+    public function author($author)
+    {
+        return $this->setProperty('author', $author);
+    }
+
+    /**
+     * Date of first broadcast/publication.
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $datePublished
+     *
+     * @return static
+     *
+     * @see https://schema.org/datePublished
+     */
+    public function datePublished($datePublished)
+    {
+        return $this->setProperty('datePublished', $datePublished);
+    }
+
+    /**
+     * A description of the item.
+     *
+     * @param string|string[] $description
+     *
+     * @return static
+     *
+     * @see https://schema.org/description
+     */
+    public function description($description)
+    {
+        return $this->setProperty('description', $description);
+    }
+
+    /**
+     * The identifier property represents any kind of identifier for any kind of
+     * [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides
+     * dedicated properties for representing many of these, either as textual
+     * strings or as URL (URI) links. See [background
+     * notes](/docs/datamodel.html#identifierBg) for more details.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $identifier
+     *
+     * @return static
+     *
+     * @see https://schema.org/identifier
+     */
+    public function identifier($identifier)
+    {
+        return $this->setProperty('identifier', $identifier);
+    }
+
+    /**
+     * The name of the item.
+     *
+     * @param string|string[] $name
+     *
+     * @return static
+     *
+     * @see https://schema.org/name
+     */
+    public function name($name)
+    {
+        return $this->setProperty('name', $name);
+    }
+
+    /**
+     * Define the domain of the study. For example, the domain could be astrophysics,
+     * functional genomics or earth science. Those domains can also have an ontology
+     * reference.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyDomain
+     *
+     * @return static
+     *
+     */
+    public function studyDomain($studyDomain)
+    {
+        return $this->setProperty('studyDomain', $studyDomain);
+    }
+
+    /**
+     * A subject of the study, i.e. one of the medical conditions, therapies, devices,
+     * drugs, etc. investigated by the study.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\BioChemEntityContract|\Spatie\SchemaOrg\Contracts\MedicalEntityContract[] $studySubject
+
+     * @return static
+     *
+     */
+    public function studySubject($studySubject)
+    {
+        return $this->setProperty('studySubject', $studySubject);
+    }
+
+    /**
+     * The subject matter of the content.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\ThingContract|\Spatie\SchemaOrg\Contracts\ThingContract[] $about
+     *
+     * @return static
+     *
+     * @see https://schema.org/about
+     * @link https://github.com/schemaorg/schemaorg/issues/1670
+     */
+    public function about($about)
+    {
+        return $this->setProperty('about', $about);
+    }
+
+    /**
+     * A property-value pair representing an additional characteristics of the 
+     * entitity, e.g. a product feature or another characteristic for which there 
+     * is no matching property in schema.org. Note: Publishers should be aware that 
+     * applications designed to use specific schema.org properties (e.g. http://schema.org/width, 
+     * http://schema.org/color, http://schema.org/gtin13, …) will typically expect 
+     * such data to be provided using those properties, rather than using the generic 
+     * property/value mechanism.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[] $additionalProperty
+     *
+     * @return static
+     *
+     * @see https://schema.org/additionalProperty
+     */
+    public function additionalProperty($additionalProperty)
+    {
+        return $this->setProperty('additionalProperty', $additionalProperty);
+    }
+
+    /**
+     * A citation or reference to another creative work, such as another
+     * publication, web page, scholarly article, etc.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\CreativeWorkContract|\Spatie\SchemaOrg\Contracts\CreativeWorkContract[]|string|string[] $citation
+     *
+     * @return static
+     *
+     * @see https://schema.org/citation
+     */
+    public function citation($citation)
+    {
+        return $this->setProperty('citation', $citation);
+    }
+
+    /**
+     * The creator/author of this CreativeWork. This is the same as the Author
+     * property for CreativeWork.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\OrganizationContract|\Spatie\SchemaOrg\Contracts\OrganizationContract[]|\Spatie\SchemaOrg\Contracts\PersonContract|\Spatie\SchemaOrg\Contracts\PersonContract[] $creator
+     *
+     * @return static
+     *
+     * @see https://schema.org/creator
+     */
+    public function creator($creator)
+    {
+        return $this->setProperty('creator', $creator);
+    }
+
+    /**
+     * The date on which the CreativeWork was created or the item was added to a
+     * DataFeed.
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $dateCreated
+     *
+     * @return static
+     *
+     * @see https://schema.org/dateCreated
+     */
+    public function dateCreated($dateCreated)
+    {
+        return $this->setProperty('dateCreated', $dateCreated);
+    }
+
+    /**
+     * The end date and time of the item (in ISO 8601 date format).
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $endDate
+     *
+     * @return static
+     *
+     * @see https://schema.org/endDate
+     */
+    public function endDate($endDate)
+    {
+        return $this->setProperty('endDate', $endDate);
+    }
+
+    /**
+     * The start date and time of the item (in ISO 8601 date format).
+     *
+     * @param \DateTimeInterface|\DateTimeInterface[] $startDate
+     *
+     * @return static
+     *
+     * @see https://schema.org/startDate
+     */
+    public function startDate($startDate)
+    {
+        return $this->setProperty('startDate', $startDate);
+    }
+
+    /**
+     * Keywords or tags used to describe some item. Multiple textual entries in
+     * a keywords list are typically delimited by commas, or by repeating the
+     * property.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\DefinedTermContract|\Spatie\SchemaOrg\Contracts\DefinedTermContract[]|string|string[] $keywords
+     *
+     * @return static
+     *
+     * @see https://schema.org/keywords
+     */
+    public function keywords($keywords)
+    {
+        return $this->setProperty('keywords', $keywords);
+    }
+
+    /**
+     * TA process performed as part of an experiment or wider study, i.e. intentionally
+     * designed. These processes can have ontology URL attached to.
+     *
+     * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyProcess
+     *
+     * @return static
+     *
+     */
+    public function studyProcess($studyProcess)
+    {
+        return $this->setProperty('studyProcess', $studyProcess);
+    }
+
+    /**
+     * URL of the item.
+     *
+     * @param string|string[] $url
+     *
+     * @return static
+     *
+     * @see https://schema.org/url
+     */
+    public function url($url)
+    {
+        return $this->setProperty('url', $url);
+    }
+}
diff --git a/routes/api.php b/routes/api.php
index 0f4440fb..e0f19634 100644
--- a/routes/api.php
+++ b/routes/api.php
@@ -4,8 +4,7 @@
 use App\Http\Controllers\API\Auth\RegisterController;
 use App\Http\Controllers\API\Auth\UserController;
 use App\Http\Controllers\API\Bioschema\DataCatalogController;
-use App\Http\Controllers\API\Bioschema\DatasetController;
-use App\Http\Controllers\API\Bioschema\ProjectController as ProjectSchemaController;
+use App\Http\Controllers\API\Bioschema\BiochemaController;
 use App\Http\Controllers\API\FileSystemController;
 use App\Http\Controllers\API\ProjectController;
 use Illuminate\Support\Facades\Route;
@@ -38,7 +37,7 @@
     Route::prefix('schemas')->group(function () {
         Route::prefix('bioschema')->group(function () {
             Route::get('/', [DataCatalogController::class, 'schema']);
-            Route::get('/{username}/{project}/{study?}/{dataset?}', [ProjectSchemaController::class, 'schema']);
+            Route::get('/{username}/{project}/{study?}/{dataset?}', [BiochemaController::class, 'schema']);
         });
     });
 });

From 094736d81e9c197ac193d2671c23410f1224f5bc Mon Sep 17 00:00:00 2001
From: NRayya <82588017+NRayya@users.noreply.github.com>
Date: Thu, 25 Aug 2022 21:15:34 +0200
Subject: [PATCH 6/7] Add dataset schema Modify project schema Modify study
 schema

---
 .../API/Bioschema/BiochemaController.php      | 86 +++++++++++++------
 1 file changed, 60 insertions(+), 26 deletions(-)

diff --git a/app/Http/Controllers/API/Bioschema/BiochemaController.php b/app/Http/Controllers/API/Bioschema/BiochemaController.php
index 10fbc3f2..eae43926 100644
--- a/app/Http/Controllers/API/Bioschema/BiochemaController.php
+++ b/app/Http/Controllers/API/Bioschema/BiochemaController.php
@@ -8,6 +8,7 @@
 use App\Models\Bioschema\BioSchema;
 use App\Models\Project;
 use App\Models\Study;
+use App\Models\Dataset;
 use App\Models\Bioschema\Study as StudySchema;
 use App\Models\User;
 use App\Models\Author;
@@ -22,12 +23,12 @@ public function schema(Request $request, $username, $projectName, $studyName = n
         if($user){
             $project = Project::where([['slug', $projectName], ['owner_id', $user->id]])->firstOrFail();  
         }
-
         if($project){
             $creativeWork = Schema::creativeWork();
             $creativeWork['@id'] = 'https://bioschemas.org/profiles/Study/0.2-DRAFT';
             $confromsTo = [];
             $confromsTo['http://purl.org/dc/terms/conformsTo'] = $creativeWork;
+            
 
             $projectSchema = Schema::Project(); 
             $projectSchema['@id']= $project->uuid;
@@ -54,18 +55,35 @@ public function schema(Request $request, $username, $projectName, $studyName = n
             }
             $projectSchema->keywords($tags);
             $projectSchema->url($project->public_url);
+            $projectSchema->license($project->license->url);
             
-
-
-            if($studyName && !$datasetName){
-                $study = Study::where([['slug', $studyName], ['owner_id', $user->id], ['project_id', $project->id]])->firstOrFail();
+            $studies = [];
+            foreach ($project->studies as &$study) {
+                $studySchema = BioSchema::Study(); 
+                $studySchema->name($study->name);
+                $studySchema->url($study->public_url);
+                
+                $datasets = [];
+                foreach ($study->datasets as &$dataset) {
+                    $datasetSchema = Schema::Dataset(); 
+                    $datasetSchema->name($dataset->name);
+                    $datasetSchema->url($dataset->public_url);
+                    array_push($datasets, $datasetSchema);
+                }
+                $studySchema->hasPart($datasets);
+                array_push($studies, $studySchema);   
+            }
+            $projectSchema->hasPart($studies);
+            
+            if($studyName){
                 // send study back with project info added to it\
+                $study = Study::where([['slug', $studyName], ['owner_id', $user->id], ['project_id', $project->id]])->firstOrFail();
                 if($study){
                     $studySchema = BioSchema::Study(); 
                     $studySchema['@id']= $study->uuid;
                     $studySchema['dct:conformsTo'] = $confromsTo;
-                    $studySchema->description($study->description);
                     $studySchema->name($study->name);
+                    $studySchema->description($study->description);
                     $tags = [];
                     foreach ($study->tags as &$tag) {
                         $tag = $tag->name; 
@@ -73,30 +91,46 @@ public function schema(Request $request, $username, $projectName, $studyName = n
                     }
                     $studySchema->keywords($tags);
                     $studySchema->url($study->public_url);
-
+                    $studySchema->license($study->license->url);
+                    $datasets = [];
+                    foreach ($study->datasets as &$dataset) {
+                        $datasetSchema = Schema::Dataset(); 
+                        $datasetSchema->name($dataset->name);
+                        $datasetSchema->url($dataset->public_url);
+                        array_push($datasets, $datasetSchema);
+                    }
+                    $studySchema->hasPart($datasets);
                     $projectSchema->relatedStudy($studySchema);
+                    
+                    
+                    if($datasetName){
+                        $dataset = Dataset::where([['slug', $datasetName], ['owner_id', $user->id], ['project_id', $project->id], ['study_id', $study->id]])->firstOrFail();
+                        // send dataset with project and study details
+                        if($dataset){
+                            $dataCatalog = Schema::dataCatalog();
+                            $dataCatalog->name(env('APP_NAME'));
+                            $dataCatalog->url('https://nmrxiv.org');
 
-                    return $projectSchema;
-                }
-                
-            }else if($studyName && $datasetName){
-                $dataset = Dataset::where([['slug', $datasetName], ['owner_id', $user->id], ['project_id', $project->id], ['study_id', $study->id]])->firstOrFail();
-                // send dataset with project and study details
-                return [];
-            }else{
-                // add studies and associated datasets
-                $studies = [];
-                foreach ($project->studies as &$study) {
-                    $studySchema = BioSchema::Study(); 
-                    $studySchema['@id']= $study->uuid;
-                    $studySchema['dct:conformsTo'] = $confromsTo;
-                    $studySchema->name($study->name);
-                    $studySchema->url($study->public_url);
-                    array_push($studies, $studySchema);   
+                            $creativeWorkDataset = Schema::creativeWork();
+                            $creativeWorkDataset['@id'] = 'https://bioschemas.org/profiles/Dataset/1.0-RELEASE';
+                            $DatasetconfromsTo = [];
+                            $DatasetconfromsTo['http://purl.org/dc/terms/conformsTo'] = $creativeWorkDataset;
+                            $datasetSchema = Schema::Dataset(); 
+                            $datasetSchema['@id']= $dataset->uuid;
+                            $datasetSchema['dct:conformsTo'] = $DatasetconfromsTo;
+                            $datasetSchema->description($dataset->description);
+                            $datasetSchema->name($dataset->name);
+                            $datasetSchema->url($dataset->public_url);
+                            $datasetSchema->license($study->license->url);
+                            $datasetSchema->includedInDataCatalog($dataCatalog);
+                            $datasetSchema->measurementTechnique("https://terminology.nfdi4chem.de/ts/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000591");
+                            $datasetSchema->isPartOf([$projectSchema]);
+                            return $datasetSchema;
+                        }
+                    }
                 }
-                $projectSchema->relatedStudy($studies);
-                return $projectSchema;
             }
+            return $projectSchema;
         }
     }
 }

From a270c810c7f1c93fb3c8dedfdccbd57b104b4ccb Mon Sep 17 00:00:00 2001
From: Venkata Chandra Sekhar Nainala <mailcs76@gmail.com>
Date: Fri, 26 Aug 2022 12:01:58 +0200
Subject: [PATCH 7/7] Added tour steps for the dataset upload - Initial version

---
 resources/js/App/Tour.vue                     | 139 ++++++++++++++-
 resources/js/Layouts/AppLayout.vue            |  12 +-
 resources/js/Pages/Dashboard.vue              |   8 +-
 resources/js/Shared/Submission.vue            | 164 ++++++++++++++----
 .../components/support-bubble.blade.php       |   2 +-
 5 files changed, 287 insertions(+), 38 deletions(-)

diff --git a/resources/js/App/Tour.vue b/resources/js/App/Tour.vue
index 66df87d5..3e7419ab 100644
--- a/resources/js/App/Tour.vue
+++ b/resources/js/App/Tour.vue
@@ -15,8 +15,145 @@ export default {
                     header: {
                         title: "Get Started",
                     },
-                    content: `Click to create project, <br/> study or dataset!`,
+                    content: `Click to start uploading <br/> your datasets to nmrXiv. <br/> <small>Check out our guides  <br/>to prepare datasets <br/>for uploading <a class="text-green-400 hover:text-decoration-line" href="https://docs.nmrxiv.org">here</a>.</small>`,
                 },
+                {
+                    target: "#v-step-1",
+                    header: {
+                        title: "Your space: Dashboard",
+                    },
+                    content: `You can find all your work<br/> organised under this section.<br/> <small>All your active projects <br/>and quicklinks are accessible <br/> from your dashboard. <br/>Please remember you will have <br/>dedicated dashboards for you <br/>and your teams.</small>`,
+                },
+                {
+                    target: "#v-step-2",
+                    header: {
+                        title: "Your space: Shared with me",
+                    },
+                    content: `Projects and studies shared<br/> with you can be accessed from here.`,
+                },
+                {
+                    target: "#v-step-3",
+                    header: {
+                        title: "Your space: Recent",
+                    },
+                    content: `Quick access to recently<br/> edited projects and studies.`,
+                },
+                {
+                    target: "#v-step-4",
+                    header: {
+                        title: "Your space: Starred",
+                    },
+                    content: `Projects, studies that you starred<br/> can be accessed quickly from this view.`,
+                },
+                {
+                    target: "#v-step-5",
+                    header: {
+                        title: "Your space: Trash",
+                    },
+                    content: `Projects, studies deleted will<br/> be available here for you to restore if need.`,
+                },
+                {
+                    target: "#v-step-6",
+                    header: {
+                        title: "Guides on Submission",
+                    },
+                    content: `Check out our submission guides any time for more information. Here is a quick link for you right from your dashboard.`,
+                },
+                {
+                    target: "#v-step-7",
+                    header: {
+                        title: "API",
+                    },
+                    content: `Developing a tool? want to access data or submit programmatically? Check out our API`,
+                },
+                {
+                    target: "#v-step-8",
+                    header: {
+                        title: "Spectra Challenges",
+                    },
+                    content: `Are you proficient in structure ellucidation? Stay tuned for new challenges.`,
+                },
+                {
+                    target: "#v-step-9",
+                    header: {
+                        title: "Need help! Email us",
+                    },
+                    content: `You can write to us via email for any further queries. We are happy to help!`,
+                },
+                {
+                    target: "#v-step-10",
+                    header: {
+                        title: "Help! Chat window",
+                    },
+                    content: `Reach out to us with any questions, suggestions or bugs. We will get back to you as soon as we can`,
+                },
+                {
+                    target: "#v-step-11",
+                    header: {
+                        title: "Documentation site",
+                    },
+                    content: `Check out our documentation site for our installation & submission guies, design principles and architectural overview.`,
+                },
+                {
+                    target: "#v-step-12",
+                    header: {
+                        title: "Tour",
+                    },
+                    content: `You can always comeback and start this tour using this tour button`,
+                },
+                {
+                    target: "#v-step-13",
+                    header: {
+                        title: "Account management",
+                    },
+                    content: `You can manage your teams, profile and other settings from the drop down here.`,
+                },
+                {
+                    target: "#v-step-0",
+                    header: {
+                        title: "Let's upload a demo dataset",
+                    },
+                    content: `Click here to start uploading`,
+                    before: type => new Promise((resolve, reject) => {
+                        this.emitter.emit("openDatasetCreateDialog", {});
+                        resolve("upload dialog open");
+                    })
+                },
+                {
+                    target: "#v-step-14",
+                    header: {
+                        title: "Files upload",
+                    },
+                    content: `Lets provide some basic details about your submission and then upload files`,
+                },
+                {
+                    target: "#v-step-15",
+                    header: {
+                        title: "Name",
+                    },
+                    content: `Project name`,
+                },
+                {
+                    target: "#v-step-16",
+                    header: {
+                        title: "Description",
+                    },
+                    content: `Project Description`,
+                },
+                {
+                    target: "#v-step-17",
+                    header: {
+                        title: "Keywords",
+                    },
+                    content: `Project keywords`,
+                },
+                {
+                    target: "#v-step-18",
+                    header: {
+                        title: "Spectra files",
+                    },
+                    content: `Lets start uploading your spectra data. Here is an example dataset. Download and then drag and drop the files here. Once uploaded press next.`,
+                }
             ],
         };
     },
diff --git a/resources/js/Layouts/AppLayout.vue b/resources/js/Layouts/AppLayout.vue
index 2fd5d935..7e937998 100644
--- a/resources/js/Layouts/AppLayout.vue
+++ b/resources/js/Layouts/AppLayout.vue
@@ -181,6 +181,7 @@
                             </div>
                             <Link
                                 :href="item.href"
+                                :id="item.id"
                                 :class="[
                                     $page.url === item.href
                                         ? ' border-r-4 bg-gray-200 border-r-black'
@@ -199,6 +200,7 @@
                             <Link
                                 v-for="child in item.children"
                                 :key="child.name"
+                                :id="child.id"
                                 :href="child.href"
                                 :class="[
                                     $page.url === child.href
@@ -271,7 +273,7 @@
                     <flash-messages />
                     <div class="ml-4 flex items-center md:ml-6">
                         <div>
-                            <a href="https://docs.nmrxiv.org" target="_blank"
+                            <a id="v-step-11" href="https://docs.nmrxiv.org" target="_blank"
                                 ><svg
                                     xmlns="http://www.w3.org/2000/svg"
                                     viewBox="0 0 24 24"
@@ -291,7 +293,7 @@
                             v-if="$page.props.user.first_name != null"
                             class="ml-5"
                         >
-                            <a
+                            <a id="v-step-12"
                                 class="cursor-pointer text-gray-600"
                                 target="_blank"
                                 @click="startTour"
@@ -314,6 +316,7 @@
                             class="ml-3 relative"
                         >
                             <div
+                                id="v-step-13"
                                 v-if="
                                     $page.props.user.current_team &&
                                     $page.props.user.current_team.personal_team
@@ -713,6 +716,7 @@ const navigation = [
         name: "Dashboard",
         href: "/dashboard",
         prefix: "Your Space",
+        id: "v-step-1",
         icon: HomeIcon,
         bg: "bg-gray-50",
         children: [
@@ -720,6 +724,7 @@ const navigation = [
                 auth: true,
                 name: "Shared with me",
                 href: "/dashboard/shared-with-me",
+                id: "v-step-2",
                 icon: UsersIcon,
                 bg: "bg-white",
             },
@@ -727,6 +732,7 @@ const navigation = [
                 auth: false,
                 name: "Recent",
                 href: "/dashboard/recent",
+                id: "v-step-3",
                 icon: ClockIcon,
                 bg: "bg-white",
             },
@@ -734,6 +740,7 @@ const navigation = [
                 auth: false,
                 name: "Starred",
                 href: "/dashboard/starred",
+                id: "v-step-4",
                 icon: StarIcon,
                 bg: "bg-white",
             },
@@ -741,6 +748,7 @@ const navigation = [
                 auth: false,
                 name: "Trash",
                 href: "/dashboard/trashed",
+                id: "v-step-5",
                 icon: TrashIcon,
                 bg: "bg-white",
             },
diff --git a/resources/js/Pages/Dashboard.vue b/resources/js/Pages/Dashboard.vue
index 60e68f9d..ce1211d9 100644
--- a/resources/js/Pages/Dashboard.vue
+++ b/resources/js/Pages/Dashboard.vue
@@ -82,7 +82,7 @@
                 role="list"
                 class="mt-6 border-b border-gray-200 divide-y divide-gray-200"
             >
-                <li>
+                <li id="v-step-6">
                     <div class="relative group py-4 flex items-start space-x-3">
                         <div class="flex-shrink-0">
                             <span
@@ -143,7 +143,7 @@
                     </div>
                 </li>
 
-                <li>
+                <li id="v-step-7">
                     <div class="relative group py-4 flex items-start space-x-3">
                         <div class="flex-shrink-0">
                             <span
@@ -205,7 +205,7 @@
                     </div>
                 </li>
 
-                <li>
+                <li id="v-step-8">
                     <div class="relative group py-4 flex items-start space-x-3">
                         <div class="flex-shrink-0">
                             <span
@@ -264,7 +264,7 @@
                     </div>
                 </li>
             </ul>
-            <div class="mt-6 flex">
+            <div class="mt-6 flex" id="v-step-9">
                 <a
                     href="mailto:info@nmrxiv.org"
                     class="text-sm font-medium text-indigo-600 hover:text-indigo-500"
diff --git a/resources/js/Shared/Submission.vue b/resources/js/Shared/Submission.vue
index ec59f185..1d1fe5a9 100644
--- a/resources/js/Shared/Submission.vue
+++ b/resources/js/Shared/Submission.vue
@@ -9,7 +9,7 @@
                 v-if="!loading && currentDraft"
                 class="lg:border-b lg:border-gray-200 pb-3 pr-5 -mx-6"
             >
-                <div class="flex items-left justify-start pl-5 float-left">
+                <div id="v-step-14" class="flex items-left justify-start pl-5 float-left">
                     <b>{{
                         steps.find((step) => step.status === "current").name
                     }}</b>
@@ -175,7 +175,7 @@
                             id="submission-dropzone"
                         >
                             <div v-if="currentDraft">
-                                <div class="mb-3">
+                                <div id="v-step-15" class="mb-3">
                                     <label
                                         for="project-name"
                                         class="block text-sm font-medium text-gray-700"
@@ -195,7 +195,7 @@
                                         class="mt-2"
                                     />
                                 </div>
-                                <div class="mb-3">
+                                <div id="v-step-16" class="mb-3">
                                     <label
                                         for="description"
                                         class="block text-sm font-medium text-gray-700"
@@ -223,7 +223,7 @@
                                         class="mt-2"
                                     />
                                 </div>
-                                <div class="mb-3">
+                                <div id="v-step-17" class="mb-3">
                                     <label
                                         for="description"
                                         class="block text-sm font-medium text-gray-700"
@@ -254,7 +254,7 @@
                                             >Draft ID:
                                             {{ currentDraft.key }}</small
                                         >
-                                        <div>
+                                        <div id="v-step-18">
                                             <file-system-browser
                                                 ref="fsbRef"
                                                 :readonly="false"
@@ -278,10 +278,14 @@
                                         class="hidden flex-shrink-0 w-64 bg-white border-r border-blue-gray-200 md:flex md:flex-col"
                                     >
                                         <div
-                                            @click="autoImport()"
-                                            class="border-gray-200 px-4 py-3 border-b border-gray-200 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider flex-shrink-0 border-b border-blue-gray-200 flex items-center"
+                                            class="border-gray-200 px-4 py-3 border-b border-gray-200 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider flex-shrink-0 border-b border-blue-gray-200"
                                         >
                                             STUDY ({{ studies.length }})
+
+                                            <span class="float-right" @click="toggleAutoImport()">
+                                                <PlayIcon v-if="!$page.props.autoimport" class="w-5 h-5"></PlayIcon>
+                                                <PauseIcon v-else class="w-5 h-5"></PauseIcon>
+                                            </span>
                                         </div>
                                         <div
                                             style="
@@ -463,6 +467,10 @@
                                                                     >
                                                                         Study
                                                                         Name
+
+                                                                        <span class="float-right border rounded-full px-2 py-1 mb-2" @click="autoGenerateDescription()">
+                                                                            Auto generate
+                                                                        </span>
                                                                     </label>
                                                                     <div
                                                                         class="mt-1"
@@ -1206,22 +1214,15 @@
                                                                                             "
                                                                                             class="relative"
                                                                                         >
-                                                                                            <img
-                                                                                                class="h-10 w-10 rounded-full bg-gray-400 flex items-center justify-center ring-8 ring-white"
-                                                                                                :src="
-                                                                                                    'https://ui-avatars.com/api/?name=' +
-                                                                                                    (
-                                                                                                        '0' +
-                                                                                                        molecule
-                                                                                                            .pivot
-                                                                                                            .percentage_composition
-                                                                                                    ).slice(
-                                                                                                        -2
-                                                                                                    ) +
-                                                                                                    '%2BUser&color=7F9CF5&background=EBF4FF'
-                                                                                                "
-                                                                                                alt=""
-                                                                                            />
+                                                                                            <div
+                                                                            class="rounded-full border p-2 z-10 bg-gray-100 text-sm"
+                                                                        >
+                                                                            {{
+                                                                                molecule
+                                                                                    .pivot
+                                                                                    .percentage_composition
+                                                                            }}%
+                                                                        </div>
                                                                                             <!-- <span
                                                 class="absolute -bottom-0.5 -right-1 bg-white rounded-tl px-0.5 py-px"
                                               >
@@ -1274,12 +1275,31 @@
                                                                                                         "
                                                                                                     ></span>
                                                                                                 </div>
+                                                                                                <button
+                                                                            class="inline-flex items-center px-2.5 py-1.5 border border-gray-300 shadow-sm text-xs font-medium rounded text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-indigo-500"
+                                                                            @click="
+                                                                                deleteMolecule(
+                                                                                    molecule
+                                                                                )
+                                                                            "
+                                                                        >
+                                                                            <TrashIcon
+                                                                                class="w-4 h-4 inline mr-1"
+                                                                            ></TrashIcon
+                                                                            >Delete
+                                                                        </button>
                                                                                             </div>
                                                                                         </div>
                                                                                     </div>
                                                                                 </div>
                                                                             </li>
                                                                         </ul>
+                                                                        <div
+                                                        class="rounded-full border p-2 z-10 bg-gray-100 text-sm mt-14 text-center"
+                                                    >
+                                                        Sample chemical
+                                                        composition
+                                                    </div>
                                                                     </div>
                                                                     <div v-else>
                                                                         <div
@@ -1353,6 +1373,16 @@
                                                                                 "
                                                                             />
                                                                         </div>
+                                                                        <button
+                                                                            v-if="
+                                                                                smiles &&
+                                                                                smiles != ''
+                                                                            "
+                                                                            class="inline-flex items-center px-2.5 py-1.5 border border-gray-300 shadow-sm text-xs font-medium rounded text-gray-700 bg-white hover:bg-gray-50 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-indigo-500 mt-2"
+                                                                            @click="loadSmiles"
+                                                                        >
+                                                                            Load Structure
+                                                                        </button>
                                                                     </div>
                                                                     <div
                                                                         class="relative"
@@ -1419,7 +1449,7 @@
                                                                             saveMolecule
                                                                         "
                                                                     >
-                                                                        SAVE
+                                                                        ADD
                                                                     </button>
                                                                 </div>
                                                             </div>
@@ -2314,8 +2344,12 @@ import {
     ClipboardCopyIcon,
     QuestionMarkCircleIcon,
     ExclamationIcon,
+    TrashIcon,
+    PlayIcon,
+    PauseIcon
 } from "@heroicons/vue/solid";
 import { Link } from "@inertiajs/inertia-vue3";
+import { isString } from '@vueuse/core';
 
 export default {
     components: {
@@ -2333,6 +2367,9 @@ export default {
         ClipboardCopyIcon,
         QuestionMarkCircleIcon,
         ExclamationIcon,
+        TrashIcon,
+        PlayIcon,
+        PauseIcon
     },
     props: [],
     data() {
@@ -2357,6 +2394,7 @@ export default {
             steps: [
                 {
                     id: "01",
+                    step: "v-step-14",
                     name: "Files Upload",
                     description: "Vitae sed mi luctus laoreet.",
                     href: "#",
@@ -2526,6 +2564,55 @@ export default {
     },
     unmounted() {},
     methods: {
+        autoGenerateDescription(){
+            let desc = "This dataset contains NMR spectra obtained for the sample -" + this.selectedStudy.name + "</br>"
+            let sampleNames = []
+            let sampleTags = []
+            this.selectedStudy.datasets.forEach(ds => {
+                let nmriuminfo = JSON.parse(ds.nmrium_info)
+                if(nmriuminfo){
+                    let spectra = nmriuminfo.spectra
+                    spectra.forEach(sp => {
+                        desc = desc + "Experiment: " + sp.info.experiment + "</br>"
+                        desc = desc + "Nucleus: " +sp.info.nucleus + "</br>"
+                        desc = desc + "Type: " +sp.info.type + "</br>"
+                        desc = desc + "Temperature: " +sp.info.temperature + "</br>"
+                        desc = desc + "Solvent: " +sp.info.solvent + "</br>"
+                        desc = desc + "Origin Frequency: " +sp.info.originFrequency + "</br>"
+                        desc = desc + "Probe Name: " +sp.info.probeName + "</br>"
+                        sampleTags.push(this.isString(sp.info.nucleus) ? sp.info.nucleus : sp.info.nucleus.join(" - "))
+                        if(sp.info.sampleName){
+                            sampleNames.push(sp.info.sampleName)
+                        }
+                        desc = desc + "Sample Name: " +sp.info.sampleName + "</br>"
+                    })
+                    desc = desc + "</br></br>"
+                }
+                
+            })
+            this.studyForm.description = desc
+            if(sampleNames.length > 0){
+                sampleNames = [...new Set(sampleNames)];
+                let sampleName = sampleNames.join(", ")
+                console.log(sampleName)
+                if(sampleName!= ''){
+                    this.studyForm.name = sampleNames.join(", ")
+                }
+            }
+            if(sampleTags.length > 0){
+                sampleTags = [...new Set(sampleTags)];
+                this.studyForm.name = sampleNames.join(", ")
+                let tags = []
+                sampleTags.forEach((t) => {
+                    tags.push({
+                        text: t,
+                    });
+                });
+                this.studyForm.tags = tags;
+            }
+
+        },  
+
         loadMol(molFile) {
             let svgString = null;
             let mol = OCL.Molecule.fromMolfile(molFile);
@@ -2549,6 +2636,22 @@ export default {
             return info;
         },
 
+        deleteMolecule(mol) {
+            axios
+                .delete(
+                    "/dashboard/studies/" +
+                        this.selectedStudy.id +
+                        "/molecule/" +
+                        mol.id
+                )
+                .then((res) => {
+                    this.selectedStudy.sample.molecules = res.data;
+                    this.smiles = "";
+                    this.percentage = 0;
+                    this.editor.setSmiles("");
+                });
+        },
+
         updateProject() {
             this.updateProjectForm.clearErrors();
             this.loadingStep = true;
@@ -2911,14 +3014,14 @@ export default {
                                             key +
                                             "</b>: " +
                                             this.draftForm.errors[key] +
-                                            "<br/>";
+                                            "</br>";
                                     } else {
                                         this.errorMessage +=
                                             "<b class='capitalize'>" +
                                             key +
                                             "</b>: " +
                                             this.draftForm.errors[key] +
-                                            "<br/>";
+                                            "</br>";
                                     }
                                 }
                             );
@@ -3119,10 +3222,11 @@ export default {
             }
         },
 
-        autoImport() {
-            this.$page.props.autoimport = true;
-            console.log("autoimporting");
-            this.selectStudy(this.studies[0], 0);
+        toggleAutoImport() {
+            this.$page.props.autoimport = !this.$page.props.autoimport;
+            if(this.$page.props.autoimport){
+                this.selectStudy(this.studies[0], 0);
+            }
         },
 
         fetchDrafts() {
diff --git a/resources/views/vendor/support-bubble/components/support-bubble.blade.php b/resources/views/vendor/support-bubble/components/support-bubble.blade.php
index c07b11ef..b065dcb0 100644
--- a/resources/views/vendor/support-bubble/components/support-bubble.blade.php
+++ b/resources/views/vendor/support-bubble/components/support-bubble.blade.php
@@ -9,7 +9,7 @@
         </div>
     </div>
 
-    <div class="spatie-support-bubble__button | pointer-events-auto">
+    <div id="v-step-10" class="spatie-support-bubble__button | pointer-events-auto">
         @include('support-bubble::includes.bubble')
     </div>
 </div>