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Merge pull request #576 from NFDI4Chem/development
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@NishaSharma14
NishaSharma14 authored Nov 8, 2022
2 parents a8c3656 + 7203837 commit 49bfa47
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Showing 14 changed files with 1,425 additions and 1,078 deletions.
15 changes: 15 additions & 0 deletions app/Http/Controllers/DashboardController.php
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Expand Up @@ -113,4 +113,19 @@ public function onboardingStatus(Request $request, $status)
}
}
}

/**
* Update the database to skip displaying primer
*
* @return void
*/
public function skipPrimer(Request $request)
{
$user = $request->user();

if ($user) {
$user->primed = true;
$user->save();
}
}
}
4 changes: 2 additions & 2 deletions app/Http/Resources/DatasetResource.php
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Expand Up @@ -35,11 +35,11 @@ public function toArray($request)
'identifier' => $this->identifier,
'doi' => $this->doi,
'project' => [
'name' => $this->project ? $this->project->slug : '',
'name' => $this->project ? $this->project->name : '',
'public_url' => $this->project ? $this->project->public_url : null,
],
'study' => [
'name' => $this->study ? $this->study->slug : '',
'name' => $this->study ? $this->study->name : '',
'public_url' => $this->study ? $this->study->public_url : null,
],
'owner' => new UserResource($this->owner),
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2 changes: 1 addition & 1 deletion app/Models/Validation.php
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Expand Up @@ -179,7 +179,7 @@ public function process()
];

$values = [
'files' => $dataset->fsObject->instrument_type,
'files' => $dataset->fsObject ? $dataset->fsObject->instrument_type : null,
'nmrium_info' => $dataset->has_nmrium ? $dataset->has_nmrium : null,
'assay' => $dataset->assay,
'assignments' => $dataset->has_nmrium ? $dataset->has_nmrium : null,
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32 changes: 32 additions & 0 deletions database/migrations/2022_11_04_135000_add_primer_column.php
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@@ -0,0 +1,32 @@
<?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::table('users', function (Blueprint $table) {
$table->boolean('primed')->default(false);
});
}

/**
* Reverse the migrations.
*
* @return void
*/
public function down()
{
Schema::table('users', function($table) {
$table->dropColumn('primed');
});
}
};
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5 changes: 5 additions & 0 deletions resources/js/Pages/Public/Project/Dataset.vue
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Expand Up @@ -298,6 +298,11 @@
class="mt-2 text-2xl font-bold break-words text-gray-900"
>
{{ dataset.data.name }}
<span v-if="dataset.data.type"
>- ({{
dataset.data.type.replace(/,\s*$/, "")
}})</span
>
</h1>
<div class="my-7">
<SpectraViewer
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5 changes: 5 additions & 0 deletions resources/js/Pages/Public/Project/Study.vue
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Expand Up @@ -314,6 +314,11 @@
:value="dataset"
>
{{ dataset.name }}
<span v-if="dataset.type"
>({{
dataset.type.replace(/,\s*$/, "")
}})</span
>
<span class="text-gray-200"
>- #{{ dataset.identifier }}</span
>
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13 changes: 10 additions & 3 deletions resources/js/Pages/Study/Datasets.vue
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Expand Up @@ -126,9 +126,16 @@
:key="dataset.slug"
:value="dataset"
>
{{ dataset.name }} - #{{
dataset.id
}}
{{ dataset.name }}
<span v-if="dataset.type"
>({{
dataset.type.replace(
/,\s*$/,
""
)
}})</span
>
- #{{ dataset.id }}
</option>
</select>
</div>
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4 changes: 2 additions & 2 deletions resources/js/Shared/DatasetCard.vue
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Expand Up @@ -41,7 +41,7 @@
{{ dataset.name }}
</p>
<p
class="mt-0 text-sm capitalize text-gray-800 line-clamp-4"
class="mt-0 text-sm text-gray-800 line-clamp-4"
>
<small class="text-gray-400">Project:</small
><br />
Expand Down Expand Up @@ -195,7 +195,7 @@
</Link>
</p>
<p
class="mt-0 text-sm capitalize text-gray-800 line-clamp-4"
class="mt-0 text-sm text-gray-800 line-clamp-4"
>
<small class="text-gray-400">Project:</small
><br />
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140 changes: 77 additions & 63 deletions resources/js/Shared/FileSystemBrowser.vue
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Expand Up @@ -9,72 +9,84 @@
]"
>
<div>
<div :class="[fullScreen ? 'px-6 py-4' : '', 'flex justify-end']">
<span
class="float-right text-xs cursor-pointer hover:text-blue-700 mt-2 mr-2"
>
<a
href="https://docs.nmrxiv.org/docs/submission-guides/submission/folder-structure"
target="_blank"
>Learn more about folder structuring</a
<div :class="[fullScreen ? 'px-6 py-4' : '', 'flex']">
<div class="w-full">
<div
class="float-left text-sm cursor-pointer hover:text-blue-700 mt-2 mr-10"
>
</span>
<button class="right" @click="toggleFullScreen">
<span v-if="fullScreen">
<svg
width="24"
height="24"
viewBox="0 0 24 24"
fill="none"
xmlns="http://www.w3.org/2000/svg"
<i
><a
href="https://docs.nmrxiv.org/docs/submission-guides/submission/folder-structure"
target="_blank"
class="mb-4"
>
<ToolTip
class="w-3.5 h-3.5"
text="To submit data you will need an account with nmrXiv, so you will be redirected to our register page and once registered you can then go ahead and submit data. For more information please checkout our <a target='_blank' href='//docs.nmrxiv.org' class='text-gray-400' target='_blank'>documentation</a>."
></ToolTip>
<span class="ml-4">
Learn more about folder structuring
</span>
</a></i
>
<path
d="M9 19V15M9 15H5M9 15L4 20"
stroke="black"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
<path
d="M15 5V9M15 9H19M15 9L20 4"
stroke="black"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
<path
d="M9 5V9M9 9H5M9 9L4 4"
stroke="black"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
<path
d="M15 19V15M15 15H19M15 15L20 20"
stroke="black"
</div>
<button class="float-right" @click="toggleFullScreen">
<span v-if="fullScreen">
<svg
width="24"
height="24"
viewBox="0 0 24 24"
fill="none"
xmlns="http://www.w3.org/2000/svg"
>
<path
d="M9 19V15M9 15H5M9 15L4 20"
stroke="black"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
<path
d="M15 5V9M15 9H19M15 9L20 4"
stroke="black"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
<path
d="M9 5V9M9 9H5M9 9L4 4"
stroke="black"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
<path
d="M15 19V15M15 15H19M15 15L20 20"
stroke="black"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
</svg>
</span>
<span v-else>
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-6 w-6"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
/>
</svg>
</span>
<span v-else>
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-6 w-6"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
stroke-width="2"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
d="M4 8V4m0 0h4M4 4l5 5m11-1V4m0 0h-4m4 0l-5 5M4 16v4m0 0h4m-4 0l5-5m11 5l-5-5m5 5v-4m0 4h-4"
/>
</svg>
</span>
</button>
>
<path
stroke-linecap="round"
stroke-linejoin="round"
d="M4 8V4m0 0h4M4 4l5 5m11-1V4m0 0h-4m4 0l-5 5M4 16v4m0 0h4m-4 0l5-5m11 5l-5-5m5 5v-4m0 4h-4"
/>
</svg>
</span>
</button>
</div>
</div>
<div v-if="!readonly" :class="[fullScreen ? 'px-6 py-4' : '', '']">
<form class="py-2 mb-3">
Expand Down Expand Up @@ -392,6 +404,7 @@ import { Dropzone } from "dropzone";
import axiosRetry from "axios-retry";
import FileDetails from "@/Shared/FileDetails.vue";
import SelectInput from "@/Shared/SelectInput.vue";
import ToolTip from "@/Shared/ToolTip.vue";
import {
FolderIcon,
Expand Down Expand Up @@ -424,6 +437,7 @@ export default {
CheckIcon,
SelectInput,
TrashIcon,
ToolTip,
},
props: ["draft", "readonly"],
data() {
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6 changes: 3 additions & 3 deletions resources/js/Shared/SpectraEditor.vue
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Expand Up @@ -483,7 +483,7 @@ export default {
} else {
let nmriumVersion = 3;
if (nmrium_info && nmrium_info["version"]) {
nmriumVersion = nmrium_info["version"]
nmriumVersion = nmrium_info["version"];
}
let mols = [];
if (this.isString(nmrium_info.molecules)) {
Expand All @@ -502,7 +502,7 @@ export default {
data: {
spectra: spectra,
molecules: mols,
version: nmriumVersion
version: nmriumVersion,
},
type: "nmrium",
};
Expand Down Expand Up @@ -554,7 +554,7 @@ export default {
{
spectra: this.selectedSpectraData,
molecules: this.currentMolecules,
version: this.version ? this.version : 3
version: this.version ? this.version : 3,
}
)
.catch((err) => {
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4 changes: 2 additions & 2 deletions resources/js/Shared/SpectraViewer.vue
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Expand Up @@ -353,7 +353,7 @@ export default {
);
let nmriumVersion = 3;
if (nmrium_info && nmrium_info["version"]) {
nmriumVersion = nmrium_info["version"]
nmriumVersion = nmrium_info["version"];
}
if (nmrium_info && nmrium_info["spectra"]) {
if (this.isString(nmrium_info["spectra"])) {
Expand Down Expand Up @@ -386,7 +386,7 @@ export default {
data: {
spectra: spectra,
molecules: mols,
version: nmriumVersion
version: nmriumVersion,
},
type: "nmrium",
};
Expand Down
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