UPD prep #136

client/package.json

@@ -11,31 +11,31 @@
     "format": "prettier --write src/"
   },
   "dependencies": {
-    "axios": "^1.7.2",
+    "axios": "^1.7.3",
     "jwt-decode": "^4.0.0",
-    "pinia": "^2.1.7",
+    "pinia": "^2.2.1",
     "plotly.js-dist": "^2.34.0",
     "primeicons": "^7.0.0",
-    "primevue": "^3.52.0",
-    "vee-validate": "^4.13.1",
+    "primevue": "^3.53.0",
+    "vee-validate": "^4.13.2",
     "vite-svg-loader": "^4.0.0",
     "vue": "^3.2.47",
     "vue-cookies": "^1.8.4",
-    "vue-router": "^4.3.3",
+    "vue-router": "^4.4.3",
     "yup": "^1.4.0"
   },
   "devDependencies": {
-    "@rushstack/eslint-patch": "^1.10.3",
+    "@rushstack/eslint-patch": "^1.10.4",
     "@vitejs/plugin-vue": "^4.6.2",
     "@vue/eslint-config-prettier": "^7.1.0",
     "@vue/test-utils": "^2.4.6",
-    "autoprefixer": "^10.4.19",
+    "autoprefixer": "^10.4.20",
     "eslint": "^8.57.0",
-    "eslint-plugin-vue": "^9.26.0",
+    "eslint-plugin-vue": "^9.27.0",
     "jsdom": "^21.1.2",
-    "postcss": "^8.4.38",
+    "postcss": "^8.4.41",
     "prettier": "^2.8.8",
-    "tailwindcss": "^3.4.4",
+    "tailwindcss": "^3.4.9",
     "vite": "^4.5.3",
     "vitest": "^0.29.8"
   }

client/src/components/home/HomeBanner.vue

@@ -2,7 +2,10 @@
   <SectionLayout>
     <div class="text-center">
       <h1 class="font-ham text-7xl font-semibold m-auto dark:text-white/80">
-        <span>The database of transcriptome-wide high-throughput RNA modification sites</span>
+        <span
+          >The quantitative database of transcriptome-wide high-throughput RNA modification
+          sites</span
+        >
       </h1>
     </div>
   </SectionLayout>

client/src/components/home/HomeFeatures.vue

@@ -39,8 +39,8 @@
           </span>
           <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">Database</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Starting with m6A, m5C, and Ψ (whole-transcriptome), we continuously add new data
-            encompassing a wide range of modifications, RNA types, technologies, and species.
+            Starting with whole-transcriptome m6A, m5C, Ψ, 2'-O-Me, and m7G, we continuously add
+            data encompassing a wide range of modifications, technologies, and species.
           </span>
         </div>
         <div class="col-12 md:col-4 mb-4 px-5">
@@ -49,8 +49,7 @@
           </span>
           <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">Tools</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Search and compare modifications across datasets. More tools coming: genome browser,
-            visualization.
+            Search and compare modifications across datasets.
           </span>
         </div>
         <div class="col-12 md:col-4 mb-4 px-5">

client/src/components/home/HomeIntro.vue

@@ -5,7 +5,7 @@
         <span>Sci-ModoM</span>
       </h1>
       <p class="text-xl font-medium text-gray-600 pt-4 pb-2 dark:text-surface-400">
-        Data availability and usability remain a critical challenge in Life Sciences.
+        Data availability and usability remains a critical challenge in Life Sciences.
       </p>
       <p class="text-xl font-medium text-gray-600 pb-4 dark:text-surface-400">
         In coordination with the epitranscriptomics community, we aim to establish a pan-European

client/src/components/home/HomeRoadmap.vue

@@ -8,7 +8,7 @@
         <p class="text-xl font-medium text-gray-600 p-4 dark:text-surface-400">
           We are working hard to improve Sci-ModoM, and we want to share our ideas for 2024. These
           are planned to be implemented in parallel to any regular maintenance work involving review
-          of issues, PRs and support to RMaP members and the wider community.
+          of issues, PRs and support to the wider community.
         </p>
       </div>
       <!-- ROADMAP ---- -->
@@ -133,11 +133,12 @@
                 </div>
                 <div class="p-3 border-l-4 border-solid border-gb-2 rounded-l dark:text-white/80">
                   <h2 class="text-lg font-bold mt-0 mb-2">Data Download</h2>
-                  <p class="mt-0 mb-3 line-height-3">
-                    Provide DB dumps and customizable downloads.
-                  </p>
+                  <p class="mt-0 mb-3 line-height-3">Provide dataset download in bedRMod.</p>
                   <div class="border-2 border-solid border-gb-2 rounded">
-                    <div class="border-2 border-solid border-gb-2 rounded" style="width: 80%"></div>
+                    <div
+                      class="border-2 border-solid border-gb-2 rounded"
+                      style="width: 100%"
+                    ></div>
                   </div>
                 </div>
               </div>
@@ -146,14 +147,20 @@
                   <h2 class="text-lg font-bold mt-0 mb-2">First release</h2>
                   <p class="mt-0 mb-3 line-height-3">Add data, release version.</p>
                   <div class="border-2 border-solid border-gb-2 rounded">
-                    <div class="border-2 border-solid border-gb-2 rounded" style="width: 45%"></div>
+                    <div
+                      class="border-2 border-solid border-gb-2 rounded"
+                      style="width: 100%"
+                    ></div>
                   </div>
                 </div>
                 <div class="p-3 border-l-4 border-solid border-gb-2 rounded-l dark:text-white/80">
-                  <h2 class="text-lg font-bold mt-0 mb-2">RNA types</h2>
-                  <p class="mt-0 mb-3 line-height-3">Add tRNA.</p>
+                  <h2 class="text-lg font-bold mt-0 mb-2">Genome Browser</h2>
+                  <p class="mt-0 mb-3 line-height-3">Visualize data via Ensembl.</p>
                   <div class="border-2 border-solid border-gb-2 rounded">
-                    <div class="border-2 border-solid border-gb-2 rounded" style="width: 15%"></div>
+                    <div
+                      class="border-2 border-solid border-gb-2 rounded"
+                      style="width: 100%"
+                    ></div>
                   </div>
                 </div>
               </div>
@@ -162,7 +169,7 @@
                   <h2 class="text-lg font-bold mt-0 mb-2">Additional Annotation</h2>
                   <p class="mt-0 mb-3 line-height-3">Add RBPs, SNPs, miRNA targets, ...</p>
                   <div class="border-2 border-solid border-gb-2 rounded">
-                    <div class="border-2 border-solid border-gb-2 rounded" style="width: 0%"></div>
+                    <div class="border-2 border-solid border-gb-2 rounded" style="width: 75%"></div>
                   </div>
                 </div>
                 <div class="p-3 border-l-4 border-solid border-gb-2 rounded-l dark:text-white/80">
@@ -173,8 +180,8 @@
                   </div>
                 </div>
                 <div class="p-3 border-l-4 border-solid border-gb-2 rounded-l dark:text-white/80">
-                  <h2 class="text-lg font-bold mt-0 mb-2">Genome Browser</h2>
-                  <p class="mt-0 mb-3 line-height-3">Add a genome browser to visualize data.</p>
+                  <h2 class="text-lg font-bold mt-0 mb-2">RNA types</h2>
+                  <p class="mt-0 mb-3 line-height-3">Add tRNA and more, data annotation.</p>
                   <div class="border-2 border-solid border-gb-2 rounded">
                     <div class="border-2 border-solid border-gb-2 rounded" style="width: 0%"></div>
                   </div>
@@ -269,7 +276,7 @@
                     <div class="border-2 border-solid border-gg-2 rounded">
                       <div
                         class="border-2 border-solid border-gg-2 rounded"
-                        style="width: 75%"
+                        style="width: 85%"
                       ></div>
                     </div>
                   </div>
@@ -318,7 +325,7 @@
                     <div class="border-2 border-solid border-gg-1 rounded">
                       <div
                         class="border-2 border-solid border-gg-1 rounded"
-                        style="width: 75%"
+                        style="width: 100%"
                       ></div>
                     </div>
                   </div>
@@ -332,7 +339,7 @@
                     <div class="border-2 border-solid border-gg-1 rounded">
                       <div
                         class="border-2 border-solid border-gg-1 rounded"
-                        style="width: 25%"
+                        style="width: 100%"
                       ></div>
                     </div>
                   </div>
@@ -346,7 +353,7 @@
                     <div class="border-2 border-solid border-gg-1 rounded">
                       <div
                         class="border-2 border-solid border-gg-1 rounded"
-                        style="width: 10%"
+                        style="width: 75%"
                       ></div>
                     </div>
                   </div>

client/src/components/home/HomeViews.vue

@@ -17,7 +17,9 @@ import CardLink from '@/components/ui/CardLink.vue'
       <div>
         <CardLink icon="pi pi-list dark:text-white/80" route="browse">
           <template v-slot:title> Data repository </template>
-          <template v-slot:content> Browse through or search the available datasets. </template>
+          <template v-slot:content>
+            Browse through and download available datasets, access metadata and more.
+          </template>
           <template v-slot:link> Browse </template>
         </CardLink>
       </div>

client/src/stores/UploadManager.js

@@ -12,7 +12,7 @@ const UPLOAD_STATE = Object.freeze({
 const MAX_PARALLEL_UPLOADS = 1
 const WAIT_UNTIL_EXPIRING_SUCCESSFUL_JOB_MS = 10 * 60 * 1000
 
-const MAX_FILE_SIZE = 1024 * 1024 * 1024
+const MAX_FILE_SIZE = 2 * 1024 * 1024 * 1024
 const MAX_FILE_SIZE_ERROR = `File to large (max ${MAX_FILE_SIZE} bytes)`
 
 function sleep(ms) {

client/src/views/DocumentationView.vue

@@ -19,8 +19,8 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           high-throughput sequencing experiments. It is dedicated to novel assays that provide
           transcriptome-wide information at single-base resolution. An intuitive user–interface
           allows to <span class="italic">Search</span> and
-          <span class="italic">Compare</span> modifications site-wise or across whole datasets, and
-          to <span class="italic">Browse</span> through or download datasets and retrieve the
+          <span class="italic">Compare</span> modifications site-wise across datasets, and to
+          <span class="italic">Browse</span> through or download datasets and retrieve the
           associated metadata.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
@@ -37,17 +37,17 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           Project and dataset
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          Data is also accessible at the study- or dataset-level (<span class="italic">Browse</span
-          >). One or more dataset can belong to a study or project,
-          <span class="italic">e.g.</span> dataset "Wildtype HEK293T" and "Wildtype mESC" belong to
-          the "GLORI" project. Each dataset is assigned a
+          Data is also accessible at the project- or dataset-level (<span class="italic"
+            >Browse</span
+          >). One or more dataset can belong to a project, <span class="italic">e.g.</span> dataset
+          "Wildtype HEK293T" and "Wildtype mESC" belong to the "GLORI" project. Projects are
+          identified using a <span class="font-semibold">SMID</span> or
+          <span class="font-semibold">Sci-ModoM identifier</span>. Each dataset is assigned a
           <span class="font-semibold">EUFID</span> or
           <span class="font-semibold"
             >Epitranscriptome Unified exchange Format (EUF) identifier</span
-          >. Projects are identified using a <span class="font-semibold">SMID</span> or
-          <span class="font-semibold">Sci-ModoM identifier</span>. A dataset can include one or more
-          modification, but is uniquely associated with a given species (including cell type,
-          tissue, or organ) and technology.
+          >. A dataset can include one or more modification, but is uniquely associated with a given
+          species (including cell type, tissue, or organ) and technology.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           bedRMod format
@@ -72,13 +72,6 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           match the database assembly version are lifted over. Only chromosome-level information is
           considered; unassigned contigs or scaffolds are discarded.
         </p>
-        <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
-          Annotation
-        </p>
-        <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          Datasets are annotated with gene informations and genomic features (UTRs, CDS, ...) using
-          a fixed version of Ensembl.
-        </p>
         <p class="indent-4 text-xl leading-relaxed mt-4 mb-2">
           For detailed documentation and development notes, consult the
           <a
@@ -104,8 +97,8 @@ import SubTitle from '@/components/ui/SubTitle.vue'
         </h1>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           Search modifications site-wise across whole transcriptomes. To query the database, first
-          select a modification and species, then available technologies. Some dataset may contain a
-          large amount of records; selecting a particular gene of interest or a genomic region can
+          select a modification and species, then available technologies. Some datasets may contain
+          a large amount of records; selecting a particular gene of interest or a genomic region can
           significantly reduce the query time. The search can also be narrowed down by selecting a
           biotype or a genomic feature. Selected records can be exported to CSV. To download all
           records for a given dataset, use
@@ -122,9 +115,9 @@ import SubTitle from '@/components/ui/SubTitle.vue'
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           Query the database to find projects and/or datasets. You can refine your search using
           global filters (top left of table), or table filters (RNA type and modification, organism,
-          cell, tissue and/or organ, or technology). Click the
+          cell, tissue and/or organ, or technology). Use "Match Any" to combine filters. Click the
           <i class="pi pi-plus -ml-3 mr-1" /> button to see project-related information and
-          additional attachments. A dataset can be downloaded as a
+          additional attachments (BAM files). A dataset can be downloaded as a
           <a
             class="text-primary-500 hover:text-secondary-500"
             href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
@@ -148,22 +141,22 @@ import SubTitle from '@/components/ui/SubTitle.vue'
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           <span class="font-bold">1.</span> First select a given organism, then select up to 3
-          reference dataset. Use the search bar (dataset dropdown) to narrow down your selection.
+          reference datasets. Use the search bar (dataset dropdown) to narrow down your selection.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          <span class="font-bold">2.</span> Select up to 3 dataset for comparison. You can also use
+          <span class="font-bold">2.</span> Select up to 3 datasets for comparison. You can also use
           your own data (bedRMod or BED format). BED files with more than 6 columns are cut down to
           BED6.
           <span class="italic"
             >As of June 2024, the header information for the bedRMod format is ignored. Hence there
-            is no organism and/or assembly validation (this is always the case for BED). If your
-            data comes from a different assembly or an inconsistent choice of reference dataset will
-            lead to spurious comparison results.
+            is no organism and/or assembly validation (this is always the case for BED). Data coming
+            from a different assembly or an inconsistent choice of reference dataset will lead to
+            spurious comparison results.
           </span>
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          <span class="font-bold">3.</span> Select the operation you want to perform on the dataset
-          selected in previous steps. The more dataset you select or the larger the dataset, the
+          <span class="font-bold">3.</span> Select the operation you want to perform on the datasets
+          selected in previous steps. The more datasets you select or the larger the datasets, the
           longer the query time. Records can be exported to CSV.
         </p>
       </div>
@@ -176,7 +169,9 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           <span class="font-bold"
             >Sci-ModoM is freely available, and does not require login or registration</span
           >. Interested users can however register to propose new projects, and eventually upload
-          datasets and attachments that are made publicly available to all users.
+          datasets and attachments that are made publicly available to all users. Feel free to
+          contact us if you would like to suggest new data, but you do not want to create an
+          account.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Project template
@@ -220,14 +215,8 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           dataset allow users to access read-level information.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          <a
-            class="text-primary-500 hover:text-secondary-500"
-            href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
-            target="_blank"
-            rel="noopener noreferrer"
-            >bedRMod</a
-          >
-          uses a 0-based, half-open coordinate system. If you use a 1-based index, all your
+          <span class="font-semibold text-red-500">Attention: </span>
+          bedRMod uses a 0-based, half-open coordinate system. If you use a 1-based index, all your
           modification sites will be <span class="italic">off-by-one</span>!
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">