UPD feedback

client/src/components/home/HomeRoadmap.vue

@@ -146,7 +146,14 @@
                   <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: 25%"></div>
+                    <div class="border-2 border-solid border-gb-2 rounded" style="width: 45%"></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>
+                  <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>
                 </div>
               </div>

client/src/presets/windscm/radiobutton/index.js

@@ -36,21 +36,32 @@ export default {
       {
         'text-surface-700 dark:text-white/80':
           props.value !== props.modelValue && props.value !== undefined,
-        'bg-surface-0 dark:bg-surface-900':
-          props.value !== props.modelValue && props.value !== undefined,
+        // 'bg-surface-0 dark:bg-surface-900':
+        //   props.value !== props.modelValue && props.value !== undefined,
         'border-surface-300 dark:border-surface-700':
           props.value !== props.modelValue && props.value !== undefined,
-        'border-primary-500 dark:border-primary-400':
+        'bg-primary-500 border-primary-500 dark:bg-primary-400 dark:border-primary-400':
           props.value == props.modelValue && props.value !== undefined
       },
-
       // States
       {
-        'outline-none outline-offset-0': !props.disabled,
-        'peer-focus-visible:ring-2 peer-focus-visible:ring-offset-2 peer-focus-visible:ring-offset-surface-0 dark:focus-visible:ring-offset-surface-800 peer-focus-visible:ring-primary-500 dark:peer-focus-visible:ring-primary-400':
+        'peer-hover:border-surface-400 dark:peer-hover:border-surface-400':
+          !props.disabled && !props.invalid && props.value !== props.modelValue,
+        'peer-hover:border-primary-hover':
+          !props.disabled && props.value == props.modelValue && props.value !== void 0,
+        'peer-hover:[&>*:first-child]:bg-primary-600 dark:peer-hover:[&>*:first-child]:bg-primary-300':
+          !props.disabled && props.value == props.modelValue && props.value !== void 0,
+        'peer-focus-visible:ring-1 peer-focus-visible:ring-primary-500 dark:peer-focus-visible:ring-primary-400':
           !props.disabled,
-        'opacity-60 cursor-default': props.disabled
+        'bg-surface-200 [&>*:first-child]:bg-surface-600 dark:bg-surface-700 dark:[&>*:first-child]:bg-surface-400 border-surface-300 dark:border-surface-700 select-none pointer-events-none cursor-default':
+          props.disabled
       }
+      // {
+      //   'outline-none outline-offset-0': !props.disabled,
+      //   'peer-focus-visible:ring-2 peer-focus-visible:ring-offset-2 peer-focus-visible:ring-offset-surface-0 dark:focus-visible:ring-offset-surface-800 peer-focus-visible:ring-primary-500 dark:peer-focus-visible:ring-primary-400':
+      //     !props.disabled,
+      //   'opacity-60 cursor-default': props.disabled
+      // }
     ]
   }),
   input: {

client/src/utils/selection.js

@@ -5,7 +5,7 @@ import { toTree, toCascade, nestedSort, toIds } from '@/utils/index.js'
 export const updModification = (selection) => {
   // update modification
   // grouped Dropdown works with one child tree
-  let tree = toTree(selection, ['rna', 'modomics_sname'], 'modification_id')
+  let tree = toTree(selection, ['rna_name', 'modomics_sname'], 'modification_id')
   nestedSort(tree, ['children'])
   return tree
 }
@@ -58,6 +58,7 @@ export const updSelectionFromAll = (selection, slctMod, slctOrg, slctTech) => {
   )
   let selection_id = opts.map((item) => item.selection_id)
   let taxid = [...new Set(opts.map((item) => item.taxa_id))]
+  // there should be only one RNA type, bt we don't check...
   let rna = [...new Set(opts.map((item) => item.rna))]
   return { selection: selection_id, technology: idsTech, taxid: taxid[0], rna: rna[0] }
 }

client/src/views/BrowseView.vue

@@ -33,23 +33,18 @@ const initFilters = (defaultGlobal) => {
     },
     modomics_sname: {
       operator: FilterOperator.AND,
-      constraints: [{ value: null, matchMode: FilterMatchMode.CONTAINS }]
+      constraints: [{ value: null, matchMode: FilterMatchMode.EQUALS }]
     },
     tech: {
       operator: FilterOperator.AND,
-      constraints: [{ value: null, matchMode: FilterMatchMode.CONTAINS }]
+      constraints: [{ value: null, matchMode: FilterMatchMode.EQUALS }]
     },
     taxa_sname: {
       operator: FilterOperator.AND,
       constraints: [{ value: null, matchMode: FilterMatchMode.EQUALS }]
     },
     cto: {
       operator: FilterOperator.AND,
-      constraints: [{ value: null, matchMode: FilterMatchMode.CONTAINS }]
-    },
-    // access: { value: null, matchMode: FilterMatchMode.IN },
-    access: {
-      operator: FilterOperator.OR,
       constraints: [{ value: null, matchMode: FilterMatchMode.EQUALS }]
     }
   }
@@ -108,8 +103,7 @@ onMounted(() => {
               'modomics_sname',
               'tech',
               'taxa_sname',
-              'cto',
-              'access'
+              'cto'
             ]"
             paginatorTemplate="FirstPageLink PrevPageLink CurrentPageReport NextPageLink LastPageLink  RowsPerPageDropdown"
             :rowsPerPageOptions="[5, 10, 25]"

client/src/views/CompareView.vue

@@ -201,7 +201,7 @@ const tablePt = {
           <Button
             @click="active = 0"
             rounded
-            label="A"
+            label="1"
             severity="secondary"
             :outlined="active !== 0"
             :pt="buttonPt"
@@ -210,7 +210,7 @@ const tablePt = {
           <Button
             @click="active = 1"
             rounded
-            label="B"
+            label="2"
             severity="secondary"
             :outlined="active !== 1"
             :pt="buttonPt"
@@ -219,7 +219,7 @@ const tablePt = {
           <Button
             @click="active = 2"
             rounded
-            label="C"
+            label="3"
             severity="secondary"
             :outlined="active !== 2"
             :pt="buttonPt"
@@ -228,7 +228,7 @@ const tablePt = {
         </div>
 
         <TabView v-model:activeIndex="active">
-          <TabPanel header="Select reference dataset">
+          <TabPanel header="1. Select reference dataset">
             <div class="h-52">
               <div class="mb-4">
                 Select one organism and choose up to three reference dataset. Use the dataset search
@@ -237,7 +237,7 @@ const tablePt = {
               <CompareStepA v-model="selectedDatasetA" @dataset-updated="datasetUpdated = $event" />
             </div>
           </TabPanel>
-          <TabPanel header="Select dataset for comparison">
+          <TabPanel header="2. Select dataset for comparison">
             <div class="h-52">
               <div class="mb-4">
                 At least one reference dataset must be selected. Upload your own data or select up
@@ -254,7 +254,7 @@ const tablePt = {
               />
             </div>
           </TabPanel>
-          <TabPanel header="Select query criteria">
+          <TabPanel header="3. Select query criteria">
             <div>
               <form @submit="onSubmit">
                 <div class="h-52">

client/src/views/DocumentationView.vue

@@ -58,39 +58,7 @@ import SubTitle from '@/components/ui/SubTitle.vue'
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           Simply put, a dataset consists of per-site records of RNA modifications stored in a given
-          bedRMod file. The bedRMod or EU (epitranscriptome unified data exchange) format is similar
-          to the
-          <a
-            class="text-primary-500 hover:text-secondary-500"
-            href="https://www.encodeproject.org/data-standards/wgbs/"
-            target="_blank"
-            rel="noopener noreferrer"
-            >ENCODE bedMethyl</a
-          >
-          format (BED9+2), but includes a header. The name (4th column) must conform to the
-          <a
-            class="text-primary-500 hover:text-secondary-500"
-            href="https://www.genesilico.pl/modomics/modifications"
-            target="_blank"
-            rel="noopener noreferrer"
-            >MODOMICS</a
-          >
-          nomenclature for the modification short name, and the score (5th column) is a
-          site-specific measure of confidence.
-        </p>
-        <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          The bedRMod file is a tabulated count of base modifications from every sequencing read
-          over each reference genomic position. It is a convenient representation of the information
-          stored in the
-          <a
-            class="text-primary-500 hover:text-secondary-500"
-            href="http://samtools.github.io/hts-specs/SAMtags.pdf"
-            target="_blank"
-            rel="noopener noreferrer"
-            >MM/ML tags</a
-          >
-          in BAM alignment files. When aligning or basecalling, most recent software should output
-          these tags. For more information, consult the
+          bedRMod file. For more information, consult the
           <a
             class="text-primary-500 hover:text-secondary-500"
             href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
@@ -135,7 +103,8 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           available technologies. Sci-ModoM contains a large amount of records; selecting a
           particular gene or 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.
+          exported to CSV. To download all records for a given dataset, use
+          <span class="italic">Browse</span>.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           Columns with arrow signs can be sorted. Multiple columns can be sorted, this requires a
@@ -164,11 +133,11 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           compare dataset with your own data.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          <span class="font-bold">A</span> First select a given organism, then select up to 3
+          <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.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          <span class="font-bold">B</span> Select up to 3 dataset for comparison. You can also use
+          <span class="font-bold">2.</span> Select up to 3 dataset 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"
@@ -179,9 +148,9 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           </span>
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          <span class="font-bold">C</span> Select the operation you want to perform on the dataset
-          selected in A and B. The more dataset you select or the larger the dataset, the longer the
-          query time. Records can be exported to CSV.
+          <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
+          longer the query time. Records can be exported to CSV.
         </p>
       </div>
       <!-- DATA MANAGEMENT -->
@@ -190,17 +159,18 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           <span>Data management</span>
         </h1>
         <p class="indent-4 text-xl leading-relaxed mt-4 mb-2">
-          Sci-ModoM is freely available, and does not require login or registration. Interested
-          users can however register to propose new projects, and eventually upload dataset and
-          attachments that are made publicly available to all users.
+          <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
+          dataset and attachments that are made publicly available to all users.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Project template
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           To create a new project, fill the template request form, accessible for logged-in users
-          through User menu > Data > Project template. Add a new metadata sheet for each dataset
-          that belongs to this project.
+          through <span class="italic">User menu > Data > Project template</span>. Add a new
+          metadata sheet for each dataset that belongs to this project.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">For example:</p>
         <div class="pl-8">
@@ -231,9 +201,9 @@ import SubTitle from '@/components/ui/SubTitle.vue'
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           To add dataset to an existing project, fill the upload form (Upload bedRMod), accessible
-          for logged-in users through User menu > Data > Dataset upload. Use the Attach BAM files
-          form to upload attachments. Attaching BAM files to a given dataset allow users to access
-          read-level information.
+          for logged-in users through <span class="italic">User menu > Data > Dataset upload</span>.
+          Use the Attach BAM files form to upload attachments. Attaching BAM files to a given
+          dataset allow users to access read-level information.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Dataset upload errors
@@ -247,7 +217,7 @@ import SubTitle from '@/components/ui/SubTitle.vue'
             rel="noopener noreferrer"
             >bedRMod format specification</a
           >. Pay particular attention to the header, which must meet strict requirements. Most
-          errors are due to a badly formatted header, or a mismatch between a header tag, value pair
+          errors are due to a badly formatted header, or a mismatch between a header tag-value pair
           and a corresponding value that you entered when filling the upload form. Most of these
           errors can be resolved quickly without the need to contact us.
         </p>
@@ -262,18 +232,17 @@ import SubTitle from '@/components/ui/SubTitle.vue'
             <li>too many contigs/scaffolds (only chromosomes are used)</li>
             <li>wrong modification name (4th column)</li>
             <li>mismatch between the modification name (4th column) and that chosen at upload</li>
-            <li>too many rows with undefined strand (6th column)</li>
             <li>
-              too many rows with out-of-range values for score (5th column) or frequency (11th
-              column)
+              too many rows with out-of-range values <span class="italic">e.g.</span> score (5th
+              column) or frequency (11th column)
             </li>
           </ul>
         </div>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           If you get a <span class="italic">Liftover failed</span> error, it is likely that your
           data could not be lifted over (too many unmapped records). Since your data has by then
           been validated for organism, assembly, missing records, <span class="italic">etc.</span>,
-          this is unlikely to happen. Please contact us.
+          this is unlikely to happen. Please contact us in such cases.
         </p>
       </div>
     </SectionLayout>

server/docs/source/bedrmod.rst

@@ -13,14 +13,14 @@ The bedRMod format specification
 
 The bedRMod, previously known as the EU (epitranscriptome unified data exchange) format is similar to the `ENCODE bedMethyl <https://www.encodeproject.org/data-standards/wgbs/>`_ format (BED9+2), but includes a header. The name (4th column) must conform to the `MODOMICS <https://www.genesilico.pl/modomics/modifications>`_ nomenclature for the modification short name, and the score (5th column) is a site-specific measure of confidence.
 
-The bedRMod file is a tabulated count of base modifications from every sequencing read over each reference genomic position or modification site. It is a convenient representation of the information stored in the MM/ML tags in BAM alignment files.
+The bedRMod file is a tabulated count of base modifications from every sequencing read over each reference genomic position or modification site. It is a convenient representation of the information stored in the `MM/ML tags <http://samtools.github.io/hts-specs/SAMtags.pdf>`_ in BAM alignment files.
 
 .. note::
 
   Sci-ModoM requirements
 
   A given dataset or bedRMod file can contain more than one modification, as reported in column 4 (MODOMICS short name), but this should
-  be for the same RNA type. Supported RNA types are *WTS* or *whole transcriptome sequencing* and *tRNA* or *transfer RNA*. A dataset or bedRMod
+  be for the same RNA type. Currently, supported RNA types are *WTS* or *whole transcriptome sequencing*. A dataset or bedRMod
   file can only contain ONE RNA type, ONE technology, ONE organism (incl. cell type, tissue, or organ), and records from the same assembly.
   The best way to handle treatment and/or conditions is to have as many bedRMod files as required to describe the experimental protocol, and
   provide a meaningful title and metadata for each file.
@@ -102,12 +102,11 @@ The first nine columns generally follow the standard `BED specification <https:/
 
     For data upload to Sci-ModoM, chromosomes (1st column) must be formatted following the Ensembl short format *e.g.* 1 and not chr1, or MT and not chrM.
     Only chromosomes are considered, records from contigs/scaffolds are discarded. The modification name (4th column) must match exactly the chosen
-    modifications, according to the `MODOMICS <https://www.genesilico.pl/modomics/modifications>`_ nomenclature for the modification short name. Rows with
-    undefined strand (6th column) are discarded. Rows with out-of-range values for score (5th column) or frequency (11th column) are discarded.
+    modifications, according to the `MODOMICS <https://www.genesilico.pl/modomics/modifications>`_ nomenclature for the modification short name. Rows with out-of-range values for score (5th column) or frequency (11th column) are discarded.
 
 .. warning::
 
-    File upload will fail if there are too many skipped records.
+    File upload will fail if there are too many skipped records, *e.g.* due to wrong chromosome formatting, too many contigs, out-of-range values, *etc.*
 
 
 Additional columns