Import SATF Library Sequence

src/components/modals/LibrarySequenceModal.svelte

@@ -0,0 +1,67 @@
+<svelte:options immutable={true} />
+
+<script lang="ts">
+  import { createEventDispatcher } from 'svelte';
+  import { parcels } from '../../stores/sequencing';
+  import Modal from './Modal.svelte';
+  import ModalContent from './ModalContent.svelte';
+  import ModalFooter from './ModalFooter.svelte';
+  import ModalHeader from './ModalHeader.svelte';
+
+  export let height: number = 200;
+  export let width: number = 380;
+
+  const dispatch = createEventDispatcher<{
+    close: void;
+    save: { library: FileList; parcel: number };
+  }>();
+
+  let saveButtonDisabled: boolean = true;
+  let modalTitle: string;
+  let libraryName: FileList;
+  let parcelId: number;
+
+  $: saveButtonDisabled = parcelId === null || libraryName === undefined;
+  $: modalTitle = 'Import Library';
+
+  function save() {
+    if (!saveButtonDisabled) {
+      dispatch('save', { library: libraryName, parcel: parcelId });
+    }
+  }
+
+  function onKeydown(event: KeyboardEvent) {
+    const { key } = event;
+    if (key === 'Enter') {
+      event.preventDefault();
+      save();
+    }
+  }
+</script>
+
+<svelte:window on:keydown={onKeydown} />
+
+<Modal {height} {width}>
+  <ModalHeader on:close>{modalTitle}</ModalHeader>
+
+  <ModalContent>
+    <div class="st-typography-body">Parcel (required)</div>
+    <select bind:value={parcelId} class="st-select w-100" name="parcel">
+      <option value={null} />
+      {#each $parcels as parcel}
+        <option value={parcel.id}>
+          {parcel.name}
+        </option>
+      {/each}
+    </select>
+    <fieldset>
+      <label for="name">Imported Library</label>
+      <input bind:files={libraryName} class="w-100" name="libraryFile" type="file" />
+    </fieldset>
+  </ModalContent>
+
+  <ModalFooter>
+    <button class="st-button secondary" on:click={() => dispatch('close')}> Cancel </button>
+    <button class="st-button" disabled={saveButtonDisabled} on:click={save}> Import </button>
+  </ModalFooter>
+</Modal>

src/components/sequencing/Sequences.svelte

@@ -9,9 +9,13 @@
   import { parcels, userSequences, userSequencesColumns, workspaces } from '../../stores/sequencing';
   import type { User } from '../../types/app';
   import type { Parcel, UserSequence, Workspace } from '../../types/sequencing';
+  import { satfToSequence } from '../../utilities/codemirror/satf/satf-sasf-utils';
+  import effects from '../../utilities/effects';
   import { getSearchParameterNumber, setQueryParam } from '../../utilities/generic';
+  import { showLibrarySequenceModel } from '../../utilities/modal';
   import { permissionHandler } from '../../utilities/permissionHandler';
   import { featurePermissions } from '../../utilities/permissions';
+  import { showFailureToast } from '../../utilities/toast';
   import Input from '../form/Input.svelte';
   import CssGrid from '../ui/CssGrid.svelte';
   import CssGridGutter from '../ui/CssGridGutter.svelte';
@@ -59,6 +63,41 @@
     const workspaceId = getSearchParameterNumber(SearchParameters.WORKSPACE_ID);
     goto(`${base}/sequencing/new${workspaceId ? `?${SearchParameters.WORKSPACE_ID}=${workspaceId}` : ''}`);
   }
+
+  async function importLibarySequences(): Promise<void> {
+    const workspaceId = getSearchParameterNumber(SearchParameters.WORKSPACE_ID);
+    if (workspaceId === null) {
+      console.log("Workspace doesn't exist");
+      showFailureToast("Library Import: Workspace doesn't exist");
+      return;
+    }
+    const { confirm, value } = await showLibrarySequenceModel();
+
+    if (confirm && value) {
+      const fileName = await value.libraryFile.name;
+      const type = fileName.slice(fileName.lastIndexOf('.') + 1);
+      if (type !== 'satf') {
+        console.log(`Unsupported file type ${type}`);
+        showFailureToast('Library Import: Unsupported file type');
+        return;
+      }
+      const contents = await value.libraryFile.text();
+      const parcel = await value.parcel;
+      const sequences = (await satfToSequence(contents)).sequences;
+      sequences.forEach(async seqN => {
+        await effects.createUserSequence(
+          {
+            definition: seqN.sequence,
+            name: seqN.name,
+            parcel_id: parcel,
+            seq_json: '',
+            workspace_id: workspaceId,
+          },
+          user,
+        );
+      });
+    }
+  }
 </script>
 
 <CssGrid bind:columns={$userSequencesColumns}>
@@ -86,6 +125,18 @@
         >
           New Sequence
         </button>
+
+        <button
+          class="st-button secondary ellipsis"
+          use:permissionHandler={{
+            hasPermission: featurePermissions.sequences.canCreate(user),
+            permissionError: 'You do not have permission to upload library sequences',
+          }}
+          disabled={workspace === undefined}
+          on:click|stopPropagation={importLibarySequences}
+        >
+          Import Library
+        </button>
       </div>
     </svelte:fragment>
 

src/utilities/codemirror/codemirror-utils.ts

@@ -120,10 +120,11 @@ export function getDefaultVariableArgs(parameters: VariableDeclaration[]): strin
         return parameter.allowable_values && parameter.allowable_values.length > 0
           ? `"${parameter.allowable_values[0]}"`
           : parameter.enum_name
-            ? `${parameter.enum_name}`
+            ? `"${parameter.enum_name}"`
             : 'UNKNOWN';
       default:
-        throw Error(`unknown argument type ${parameter.type}`);
+        console.log(`Unknown argument type ${parameter.type}`);
+        return `ERROR:"${parameter.name}"`;
     }
   }) as string[];
 }

src/utilities/codemirror/satf/satf-sasf-utils.test.ts

@@ -91,9 +91,9 @@ describe('satfToSequence', () => {
     expect(result.sequences[0].name).toStrictEqual('test');
     expect(result.sequences[0].sequence).toStrictEqual(`## test
 R00:01:00  01VV param6 10 false "abc" # This command turns, to correct position.
-@MODEL(x,1,"00:00:00")
-@MODEL(z,1.1,"00:00:00")
-@MODEL(y,"abc","00:00:00")`);
+@MODEL "x" 1 "00:00:00"
+@MODEL "z" 1.1 "00:00:00"
+@MODEL "y" "abc" "00:00:00"`);
   });
 
   it('should return multiple sequence with models', async () => {
@@ -127,9 +127,9 @@ R00:01:00  01VV param6 10 false "abc" # This command turns, to correct position.
     expect(result.sequences[0].name).toStrictEqual('test');
     expect(result.sequences[0].sequence).toStrictEqual(`## test
 R00:01:00  01VV param6 10 false "abc" # This command turns, to correct position.
-@MODEL(x,1,"00:00:00")
-@MODEL(z,1.1,"00:00:00")
-@MODEL(y,"abc","00:00:00")`);
+@MODEL "x" 1 "00:00:00"
+@MODEL "z" 1.1 "00:00:00"
+@MODEL "y" "abc" "00:00:00"`);
   });
 });
 

src/utilities/codemirror/satf/satf-sasf-utils.ts

@@ -881,7 +881,7 @@ function parseModel(modelNode: SyntaxNode | null, text: string): string {
       if (!keyNode || !valueNode) {
         return null;
       }
-      return `@MODEL(${text.slice(keyNode.from, keyNode.to)},${text.slice(valueNode.from, valueNode.to)},"00:00:00")`;
+      return `@MODEL "${text.slice(keyNode.from, keyNode.to)}" ${text.slice(valueNode.from, valueNode.to)} "00:00:00"`;
     })
     .filter(model => model !== null)
     .join('\n');

src/utilities/codemirror/satf/satf-sasf.grammar

@@ -26,7 +26,7 @@
   HeaderPairs { HeaderPair* }
   HeaderPair {Key"="Value ";" newLine}
   Key { (identifier | ":")* }
-  Value { headerValue+ }
+  Value { (headerValue | "/")+ }
   SfduHeader { headerMarker newLine HeaderPairs headerMarker}
 
   Start { "$$"identifier identifier* newLine}

src/utilities/modal.ts

@@ -12,6 +12,7 @@ import DeleteExternalEventSourceTypeModal from '../components/modals/DeleteExter
 import DeleteExternalSourceModal from '../components/modals/DeleteExternalSourceModal.svelte';
 import EditViewModal from '../components/modals/EditViewModal.svelte';
 import ExpansionSequenceModal from '../components/modals/ExpansionSequenceModal.svelte';
+import LibrarySequenceModal from '../components/modals/LibrarySequenceModal.svelte';
 import ManageGroupsAndTypesModal from '../components/modals/ManageGroupsAndTypesModal.svelte';
 import ManagePlanConstraintsModal from '../components/modals/ManagePlanConstraintsModal.svelte';
 import ManagePlanDerivationGroupsModal from '../components/modals/ManagePlanDerivationGroupsModal.svelte';
@@ -556,6 +557,39 @@ export async function showWorkspaceModal(
   });
 }
 
+export async function showLibrarySequenceModel(): Promise<ModalElementValue<{ libraryFile: File; parcel: number }>> {
+  return new Promise(resolve => {
+    if (browser) {
+      const target: ModalElement | null = document.querySelector('#svelte-modal');
+
+      if (target) {
+        const workspaceModal = new LibrarySequenceModal({
+          target,
+        });
+        target.resolve = resolve;
+
+        workspaceModal.$on('close', () => {
+          target.replaceChildren();
+          target.resolve = null;
+          resolve({ confirm: false });
+          workspaceModal.$destroy();
+        });
+
+        workspaceModal.$on('save', (e: CustomEvent<{ library: FileList; parcel: number }>) => {
+          const library = e.detail.library[0];
+          const parcel = e.detail.parcel;
+          target.replaceChildren();
+          target.resolve = null;
+          resolve({ confirm: true, value: { libraryFile: library, parcel } });
+          workspaceModal.$destroy();
+        });
+      }
+    } else {
+      resolve({ confirm: false });
+    }
+  });
+}
+
 /**
  * Shows a CreatePlanBranchModal with the supplied arguments.
  */

src/utilities/sequence-editor/sequence-linter.ts

@@ -566,16 +566,24 @@ function validateActivateLoad(
               } else {
                 value = parseInt(num);
               }
-              parameter.allowable_ranges?.forEach(range => {
-                if (value < range.min || value > range.max) {
+
+              if (parameter.allowable_ranges) {
+                const invalidRanges = parameter.allowable_ranges.filter(range => {
+                  return value < range.min || value > range.max;
+                });
+                if (invalidRanges.length === parameter.allowable_ranges.length) {
                   diagnostics.push({
                     from: arg.from,
-                    message: `Value must be between ${range.min} and ${range.max}`,
+                    message: `Value must be between ${parameter.allowable_ranges
+                      .map(range => {
+                        return `[${range.min} and ${range.max}]`;
+                      })
+                      .join(' or ')}`,
                     severity: 'error',
                     to: arg.to,
                   });
                 }
-              });
+              }
 
               if (parameter.type === 'UINT') {
                 if (value < 0) {
@@ -1237,7 +1245,7 @@ function validateCommandStructure(
   addDefault: (view: any) => any,
 ): Diagnostic | undefined {
   if (arguments.length > 0) {
-    if (!argsNode || argsNode.length === 0) {
+    if (!argsNode || (argsNode.length === 0 && exactArgSize > 0)) {
       return {
         actions: [],
         from: stemNode.from,