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Merge branch 'master' into SWAP-4573-remove-default-values-in-dtos-to-prevent-overwriting
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‎.env.example

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@@ -48,8 +48,8 @@ DELETE_GROUPS=""
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CREATE_DATASET_GROUPS="all"
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CREATE_DATASET_WITH_PID_GROUPS=""
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CREATE_DATASET_PRIVILEGED_GROUPS=""
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CREATE_JOB_GROUPS=""
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UPDATE_JOB_GROUPS=""
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CREATE_JOB_PRIVILEGED_GROUPS=""
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UPDATE_JOB_PRIVILEGED_GROUPS=""
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SAMPLE_PRIVILEGED_GROUPS="sampleingestor"
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SAMPLE_GROUPS="group1"
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PROPOSAL_GROUPS=""

‎.github/workflows/deploy.yml

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@@ -39,7 +39,7 @@ jobs:
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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- uses: actions/create-github-app-token@v1
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- uses: actions/create-github-app-token@v2
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id: app-token
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with:
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app-id: ${{ secrets.WORKFLOW_DISPATCHER_APP_ID }}

‎.github/workflows/release-and-publish-sdk.yml

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@@ -92,7 +92,7 @@ jobs:
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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- uses: actions/create-github-app-token@v1
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- uses: actions/create-github-app-token@v2
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id: app-token
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with:
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app-id: ${{ secrets.WORKFLOW_DISPATCHER_APP_ID }}

‎.github/workflows/test.yml

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@@ -153,8 +153,8 @@ jobs:
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CREATE_DATASET_WITH_PID_GROUPS: "group2"
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CREATE_DATASET_PRIVILEGED_GROUPS: "datasetIngestor,group3"
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ACCESS_GROUPS_STATIC_VALUES: "ess"
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CREATE_JOB_GROUPS: group1,group2
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UPDATE_JOB_GROUPS: group1
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CREATE_JOB_PRIVILEGED_GROUPS: group1,group2
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UPDATE_JOB_PRIVILEGED_GROUPS: group3
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DELETE_JOB_GROUPS: "archivemanager,admin"
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PROPOSAL_GROUPS: "proposalingestor"
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SAMPLE_PRIVILEGED_GROUPS: "sampleingestor"

‎docs/frontend-config-guide/dynamic-dataset-detail-component.md

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@@ -23,6 +23,8 @@ Below you can find the example configuration, but for more advanced customizatio
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"type": "regular",
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"label": "General Information",
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"order": 0,
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"row": 1,
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"col": 4,
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"fields": [
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{
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"element": "text",
@@ -34,29 +36,45 @@ Below you can find the example configuration, but for more advanced customizatio
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"source": "pid",
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"order": 1
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},
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{
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"element": "internalLink",
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"source": "proposalIds",
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"order": 2
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},
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{
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"element": "text",
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"source": "description",
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"order": 2
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"order": 3
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}
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{
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"element": "text",
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"source": "scientificMetadata.start_time.value",
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"order": 4
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},
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]
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},
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{
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"type": "attachments",
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"label": "Scientific Metadata",
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"order": 1,
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"row": 1,
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"col": 6,
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"options": { "limit": 10, "size": "large" }
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},
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{
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"type": "scientificMetadata",
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"label": "Scientific Metadata",
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"viewMode": "table",
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"order": 2
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"order": 2,
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"row": 1,
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"col": 10,
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},
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{
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"type": "datasetJsonView",
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"label": "Metadata JSON view",
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"order": 3
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"order": 3,
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"row": 1,
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"col": 10,
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}
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]
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}
@@ -69,7 +87,7 @@ Below you can find the example configuration, but for more advanced customizatio
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| **regular** | **label** | Title for the section that can be customized. | - `label`: Custom label for the section (e.g., "General Information") | `"label": "General Information"` |
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| | **order** | Controls the display order of the Regular section in the UI | - `order`: Integer, determines position in the UI | `"order": 0` |
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| | **fields** | List of fields to display within the section. It should contain an array of objects, each with `element`, `source`, and `order` fields. | | `{"fields": [{"element": "text", "source": "datasetName", "order": 0}]}` |
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| | - **element** | Defines the type of data to display in the row (e.g., text, copy, tag, linky, date). | - `element`: Field type (e.g., `text`, `copy`, `tag`, `linky`, `date`) | `"element": "text" ` |
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| | - **element** | Defines the type of data to display in the row (e.g., text, copy, tag, linky, date, internalLink). | - `element`: Field type (e.g., `text`, `copy`, `tag`, `linky`, `date`, `internalLink`) | `"element": "text" ` |
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| | - **source** | Specifies the dataset property to display, and it must match a field in the `OutputDatasetDto` . | - `source`: Dataset property name | `"source": "datasetName"` |
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| | - **order** | Controls the display order of the field in the fields. | - `order`: Integer, defines the sequence of fields in the UI. Lower values appear first. | `"order": 1` |
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| **attachments** | **label** | Custom label for the section that can be configured. | - `label`: Custom title for the attachments section (e.g., "Gallery") | `"label": "Scientific Metadata"` |
@@ -110,6 +128,10 @@ Below you can find the example configuration, but for more advanced customizatio
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![alt text](./screenshots/regular-tag.png)
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- internalLink: Converts the value into a clickable link for internal navigation. Supported fields: `instrumentIds`, `proposalIds`, `sampleIds`, and `inputDatasets`.
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![alt text](./screenshots/regular-internalLink.png)
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- **scientificMetadata:** Displays metadata in different views:
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- table

‎docs/frontend-config-guide/screenshots/regular-internalLink.png

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‎migrations/20250318101300-migrate-attachment-id-field-to-aid.js

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module.exports = {
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async up(db, client) {
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await db.collection("Attachment").updateMany(
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{
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$or: [
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{ datasetId: { $exists: true } },
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{ sampleId: { $exists: true } },
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{ proposalId: { $exists: true } },
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{ id: { $exists: true } },
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{ aid: { $exists: false } },
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],
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},
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[
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{
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$set: {
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relationships: {
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// Build relationships array by checking ALL IDs
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$cond: [
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{
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$or: [
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{ $ifNull: ["$datasetId", false] },
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{ $ifNull: ["$sampleId", false] },
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{ $ifNull: ["$proposalId", false] },
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],
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},
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{
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$concatArrays: [
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// Add dataset relationship if datasetId exists
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{
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$cond: [
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{ $ifNull: ["$datasetId", false] },
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[
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{
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targetId: "$datasetId",
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targetType: "dataset",
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relationType: "is attached to",
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},
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],
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[],
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],
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},
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// Add sample relationship if sampleId exists
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{
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$cond: [
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{ $ifNull: ["$sampleId", false] },
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[
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{
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targetId: "$sampleId",
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targetType: "sample",
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relationType: "is attached to",
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},
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],
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[],
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],
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},
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// Add proposal relationship if proposalId exists
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{
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$cond: [
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{ $ifNull: ["$proposalId", false] },
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[
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{
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targetId: "$proposalId",
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targetType: "proposal",
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relationType: "is attached to",
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},
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],
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[],
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],
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},
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],
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},
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// Fallback to existing relationships if no IDs
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"$relationships",
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],
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},
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aid: { $ifNull: ["$id", "$_id"] },
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},
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},
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{ $unset: ["datasetId", "sampleId", "proposalId", "id"] },
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],
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);
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},
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async down(db, client) {
85+
await db
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.collection("Attachment")
87+
.updateMany({ relationships: { $exists: true } }, [
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{
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$set: {
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datasetId: {
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$let: {
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vars: {
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datasetRel: {
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$arrayElemAt: [
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{
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$filter: {
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input: "$relationships",
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as: "rel",
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cond: { $eq: ["$$rel.targetType", "dataset"] },
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},
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},
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0,
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],
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},
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},
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in: {
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$ifNull: ["$$datasetRel.targetId", "$$REMOVE"],
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},
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},
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},
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sampleId: {
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$let: {
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vars: {
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sampleRel: {
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$arrayElemAt: [
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{
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$filter: {
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input: "$relationships",
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as: "rel",
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cond: { $eq: ["$$rel.targetType", "sample"] },
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},
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},
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0,
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],
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},
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},
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in: {
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$ifNull: ["$$sampleRel.targetId", "$$REMOVE"],
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},
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},
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},
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proposalId: {
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$let: {
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vars: {
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proposalRel: {
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$arrayElemAt: [
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{
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$filter: {
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input: "$relationships",
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as: "rel",
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cond: { $eq: ["$$rel.targetType", "proposal"] },
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},
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},
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0,
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],
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},
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},
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in: {
149+
$ifNull: ["$$proposalRel.targetId", "$$REMOVE"],
150+
},
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},
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},
153+
// Revert aid back to id.
154+
id: "$aid",
155+
},
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},
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{ $unset: ["relationships", "aid"] },
158+
]);
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},
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};

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