Feature/release notes 1.62

docs/release-notes/v1.60-v1.69.md

@@ -16,6 +16,142 @@
     **Admins** - users who manage the organization in ODM, including overseeing users, groups, and permissions. 
     They are also responsible for creating, defining, and editing metadata templates as needed.
 
+## 1.62
+
+### Single-Cell functionality
+
+* **New `Cell` entity**: ODM now supports storing and managing **per-cell metadata and expression** for single-cell datasets.
+* **Cell Groups**: Each Cell record belongs to a **Cell Group**, representing a single-cell table/group.
+* **Cell metadata import (TSV only)**: Import cell metadata via **Jobs API** (`/api/v1/jobs/import/cells` or `/api/v1/jobs/import/cells/multipart`) or the **`odm-import-data` script** (`--cells/-c`) and link to Samples/Libraries/Preparations.
+* **Cell expression import**: Import expression via **Jobs API** (`/api/v1/jobs/import/expression` or `/api/v1/jobs/import/expression/multipart`); `.br` / `.lz4` archives recommended. Link expression to a Cell metadata group (1:1).
+* **Validation**: Enforces required fields (e.g., `barcode`, `batch`) and rejects duplicate barcodes within a group; invalid types are ignored with warnings.
+* **[BETA] Analytics**: New endpoints for **Cell Ratio**, **Gene Summary**, and **Differential Expression** calculations over filtered single-cell populations.
+* **Deletion**: Remove Cell metadata or expression groups via the **manage-data/data** endpoint.
+
+    Read more on **[Working with Single Cell Data page](../user-guide/doc-odm-user-guide/single-cell.md)**.
+
+    ![Data Model](../assets/data_model.svg)
+
+### Multipart/form-data job endpoints
+
+We have added **multipart form-data upload endpoints** to the `jobs` import API, enabling **direct file uploads** (no `dataLink` required) for common ODM import flows:
+
+* `POST /api/v1/jobs/import/samples/multipart` — upload **Sample metadata** (TSV)
+* `POST /api/v1/jobs/import/libraries/multipart` — upload **Library metadata** (TSV)
+* `POST /api/v1/jobs/import/preparations/multipart` — upload **Preparation metadata** (TSV)
+* `POST /api/v1/jobs/import/cells/multipart` — upload **Cell metadata** (TSV)
+* `POST /api/v1/jobs/import/expression/multipart` — upload **tabular expression** data (TSV, GCT)
+* `POST /api/v1/jobs/import/variant/multipart` — upload **variation data/metadata** (VCF, TSV)
+* `POST /api/v1/jobs/import/flow-cytometry/multipart` — upload **flow cytometry data/metadata** (FACS, TSV)
+* `POST /api/v1/jobs/import/file/multipart` — upload a **file attachment** via Jobs import
+
+### Attachments transformation
+
+ODM now supports an **attachment transformation workflow** that converts uploaded attachments into **ODM-indexable formats** and can automatically kick off the relevant **jobs import** flow.
+
+* **Transform attachments into supported formats**
+
+    Use transformations to convert files ODM can’t ingest directly (e.g., **CSV**) into formats it can index (e.g., **TSV** for metadata imports).
+
+* **Image + configuration model**
+
+    Each transformation uses:
+
+    * a **transformation image** (script) defining how to convert input → output, and
+    * a **configuration** defining the **destination** (e.g., Samples, Libraries, Preparations, Cells, Expression, Variants).
+
+* **Discover available transformation images**
+
+    New API to list available images via **Processors Controller**:
+  `GET /transformations/images`.
+
+* **Create and manage transformation configurations**
+
+    Define reusable configs via:
+  `POST /transformations/configurations` (and retrieve via `GET /transformations/configurations`)
+  Example: config to route **csv → samples**.
+
+* **Run transformations as jobs**
+
+    Trigger a transformation run using an **attachment accession**, **configuration**, and **image reference**:
+  `POST /transformations/jobs`
+  Track progress via: `GET /transformations/jobs/{id}`.
+
+* **Automatic import after conversion**
+
+    On successful transformation, ODM **automatically uploads the converted file** and triggers the corresponding **Jobs import multipart endpoint** (e.g., CSV → TSV → `POST /api/v1/jobs/import/samples/multipart`), creating a new metadata group in the same Study where the original attachment was stored.
+
+    Read more on **[Attachments transformation page](../user-guide/doc-odm-user-guide/attachment-transformation.md)**.
+
+    ![AT Diagram](../user-guide/doc-odm-user-guide/doc-odm-user-guide/images/attachments-transformation-diagram.png)
+
+### API search by latest committed (published) data
+
+* **Updated search behavior across all endpoints**: Metadata search endpoints now query against the **latest committed metadata**, ensuring results reflect the most up-to-date committed changes.
+* **Filters and queries remain supported**: All existing **filter and query parameters** continue to work as before, but are now applied to the **latest committed dataset**.
+
+### New Data Classes
+
+New Data classes were introduced:
+
+* Spatial transcriptomics `SPT`
+* Phenomics `PHE`
+* Copy number alterations `CNA`
+* Microbiome / Metagenomics `MIC`
+* Immune repertoire `IMR`
+* Genetic screens (CRISPR / RNAi) `GSC`
+* Cell imaging `CIM`
+* Nanopore data class was renamed to Long-read sequencing (Nanopore, PacBio) `LRS`
+* `MTX` label for Metabolomics was renamed to `MTB`
+
+### Samples
+
+* Starting with this release, creating a Study no longer automatically creates four empty Sample entries. Instead, use the **Add Samples** button to upload a Samples metadata file.
+
+![Add Samples](../user-guide/doc-odm-user-guide/doc-odm-user-guide/images/add-samples-button.png)
+
+* Sample deletion is no longer available via the GUI. Instead, a new option is available to delete a single Sample object via the **manageData** endpoint.
+
+![Single Sample deletion](../user-guide/doc-odm-user-guide/doc-odm-user-guide/images/sample-object-deletion.png)
+
+### Templates
+
+Starting with this release, the Template Editor includes a new feature to view the list of Studies that use the template you’re viewing. In the new Study Browser window, you’ll see the list of Studies available to you.
+
+![Template applied](../user-guide/doc-odm-user-guide/doc-odm-user-guide/images/template-applied-to-studies.png)
+
+### Preview PDF attachments
+
+* **Preview PDFs directly from ME**: Attachments with filenames ending in **`.pdf`** can now be previewed from the attachment list.
+* **One-click preview**: A **Preview** action/button is available for PDF attachments.
+* **Opens in a new browser tab**: Clicking **Preview** opens the file in a **new tab** using the browser’s built-in PDF viewer.
+
+![PDF Preview](../user-guide/doc-odm-user-guide/doc-odm-user-guide/images/pdf-preview.png)
+
+### Permanent tokens
+
+* **Instant token display**: When creating an ODM personal access token from the Profile page, the **token value is now shown immediately** after the user confirms creation (and enters their password, if prompted).
+* **Email step removed**: Token creation no longer requires an email with a secure link/code exchange.
+
+![New token](../user-guide/doc-odm-user-guide/doc-odm-user-guide/images/token.png)
+
+### Access (Bearer) tokens
+
+1. The user identifier for Azure token authentication was changed from `subject` to `oid`, enabling login without defining an Azure app scope.
+2. As a result, all users registered in ODM via Azure SSO will need to log in via the UI once again to have their records updated in the database.
+
+### Metadata validity facet
+
+A new default facet has been added to filter Studies by **valid** or **invalid** metadata, validated against the applied template. Metadata is considered **invalid** if at least one field is invalid in any Study entity.
+
+![Validity Facet](../user-guide/doc-odm-user-guide/doc-odm-user-guide/images/validity-facet.png)
+
+### Key security improvements
+
+1. Removing the email-based token delivery flow to eliminate a potential attack vector.
+2. Spring Boot upgrade to v4 with updated transitive dependencies resolved plenty of security vulnerabilities.
+3. Three vulnerabilities (SQL injection, path traversal, log injection) identified and fixed by code analysis tools.
+
 ## 1.61
 
 Release 1.61 introduces powerful enhancements focused on improving data governance and preventing common user errors.

docs/user-guide/doc-odm-user-guide/single-cell.md

@@ -93,7 +93,7 @@ Learn more about [uploading data to ODM via API here](../doc-odm-user-guide/impo
 
 ### Uploading via script
 
-Curators can upload and link Cell metadata groups to ODM using the [import_ODM_data script](../../tools/odm-sdk/terminal/study/uploading-study.md).
+Curators can upload and link Cell metadata groups to ODM using the [odm_import_data script](../../tools/odm-sdk/terminal/study/uploading-study.md).
 This extension allows you to include Cell groups in the same import workflow as other metadata entities (Studies, 
 Samples, Libraries, and Preparations), ensuring a consistent and automated data-loading process.