Import SATF Library Sequence (#1592)

* Bugfix allow for paths in Headers

* Library Sequence Modal

This modal allows you to select a parcel and import a library sequence file

* Hook up the library modal to workspaces

* Fixed incorrect linting errors when multiple ranges are defined.

The linter incorrectly reported errors for values within a valid range when multiple ranges were defined. For example, if the ranges were 5-10 and 11-20, the linter would erroneously flag the value 8 as invalid because it falls outside the 11-20 range, even though it is valid within the 5-10 range.

* Improved autocomplete functionality by allowing completion even with invalid variable types.

Allow autocomplete to succeed and show the ERROR parameter value. The user will see this error in the editor and manually have to fix it.

* Fix @model generation.

There shouldn't be any parenthesis and commas in the SeqN generation

* fix buttons wrapping

---------

Co-authored-by: bduran <[email protected]>

Author: goetzrrGit

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" accept=".satf" />
+    </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

@@ -9,6 +9,8 @@
   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 { permissionHandler } from '../../utilities/permissionHandler';
   import { featurePermissions } from '../../utilities/permissions';
@@ -59,6 +61,28 @@
     const workspaceId = getSearchParameterNumber(SearchParameters.WORKSPACE_ID);
     goto(`${base}/sequencing/new${workspaceId ? `?${SearchParameters.WORKSPACE_ID}=${workspaceId}` : ''}`);
   }
+
+  async function importLibrary(): Promise<void> {
+    const library = await effects.importLibrarySequences(workspaceId);
+    if (!library) {
+      return;
+    }
+
+    const parcel = library.parcel;
+    const sequences = (await satfToSequence(library.fileContents)).sequences;
+    sequences.forEach(async seqN => {
+      await effects.createUserSequence(
+        {
+          definition: seqN.sequence,
+          name: seqN.name,
+          parcel_id: parcel,
+          seq_json: '',
+          workspace_id: workspaceId !== null ? workspaceId : -1,
+        },
+        user,
+      );
+    });
+  }
 </script>
 
 <CssGrid bind:columns={$userSequencesColumns}>
@@ -86,6 +110,18 @@
         >
           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={importLibrary}
+        >
+          Import Library
+        </button>
       </div>
     </svelte:fragment>
 
@@ -108,3 +144,11 @@
     {user}
   />
 </CssGrid>
+
+<style>
+  .right {
+    column-gap: 5px;
+    display: flex;
+    flex-wrap: nowrap;
+  }
+</style>

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

@@ -356,10 +356,12 @@ describe('getDefaultVariableArgs', () => {
     { allowable_ranges: [{ min: 5 }], type: 'INT' },
     { allowable_ranges: [{ min: 7 }], type: 'UINT' },
     { allowable_values: ['VALUE1'], enum_name: 'ExampleEnum', type: 'ENUM' },
+    { enum_name: 'ExampleEnum2', type: 'ENUM' },
     { type: 'INT' },
+    { name: 'hexValue', type: 'HEX' },
   ] as VariableDeclaration[];
   it('should return default values for different types', () => {
     const result = getDefaultVariableArgs(mockParameters);
-    expect(result).toEqual(['"exampleString"', 1.2, 5, 7, '"VALUE1"', 0]);
+    expect(result).toEqual(['"exampleString"', 1.2, 5, 7, '"VALUE1"', '"ExampleEnum2"', 0, 'ERROR:"hexValue"']);
   });
 });

src/utilities/codemirror/codemirror-utils.ts

@@ -120,10 +120,10 @@ 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 ${parameter.type}`);
+        return `ERROR:"${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

@@ -475,7 +475,15 @@ export function generateSatfVariables(
       return (
         `\t${variable.name}` +
         `(\n\t\tTYPE,${variable.type}${variable.enum_name ? `\n\tENUM,${variable.enum_name}` : ''}` +
-        `${variable.allowable_ranges ? `\n\t\tRANGES,${variable.allowable_ranges}` : ''}` +
+        `${
+          variable.allowable_ranges
+            ? variable.allowable_ranges
+                .map(range => {
+                  return `\n\t\tRANGES,\\${range.min}...${range.max}\\`;
+                })
+                .join(',')
+            : ''
+        }` +
         `${variable.allowable_values ? `\n\t\tVALUES,${variable.allowable_values}` : ''}` +
         `${variable.sc_name ? `\n\t\tSC_NAME,${variable.sc_name}` : ''}\n\t)`
       );
@@ -881,7 +889,7 @@ function parseModel(modelNode: SyntaxNode | null, text: string): string {
       if (!keyNode || !valueNode) {
         return null;
       }
-      return `@MODEL(${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/effects.ts

@@ -226,6 +226,7 @@ import {
   showDeleteActivitiesModal,
   showDeleteExternalSourceModal,
   showEditViewModal,
+  showLibrarySequenceModel,
   showManageGroupsAndTypes,
   showManagePlanConstraintsModal,
   showManagePlanDerivationGroups,
@@ -4791,6 +4792,28 @@ const effects = {
     }
   },
 
+  async importLibrarySequences(
+    workspaceId: number | null,
+  ): Promise<{ fileContents: string; parcel: number } | undefined> {
+    if (workspaceId === null) {
+      showFailureToast("Library Import: Workspace doesn't exist");
+      return undefined;
+    }
+    const { confirm, value } = await showLibrarySequenceModel();
+
+    if (!confirm || !value) {
+      return undefined;
+    }
+
+    try {
+      const contents = await value.libraryFile.text();
+      return { fileContents: contents, parcel: value.parcel };
+    } catch (e) {
+      showFailureToast('Library Import: Unable to open file');
+      return undefined;
+    }
+  },
+
   async importPlan(
     name: string,
     modelId: number,

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

@@ -567,16 +567,24 @@ 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) {