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Merge pull request #33 from genestack/srz11d-patch-1_AdminUI
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‎docs/release-notes/v1.50-v1.59.md‎

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@@ -449,30 +449,31 @@ The vxQuery parameter has been enhanced to support variant filtering based on `f
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along with their logical combinations using `not (!)`, `and (&&)`, and `or (||)` operators, respecting standard
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Boolean precedence.
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* ??? abstract "vxQuery Parameter abilities"
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??? abstract "vxQuery Parameter abilities"
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* `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals
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to `PASS` : `filter = PASS` or `filter != PASS`.
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* `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma.
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Expression `id = rs3214,rg1234` is equivalent to `id = rs3214 or id = rg1234`.
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Expression `id = rs3214,rg1234` is equivalent to `id = rs3214 or id = rg1234`.
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* `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1`,
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by interval within a chromosome `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by
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indefinite ranges like `region = x:3456789-*` . Multiple regions could be separated via comma,
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e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.
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* ??? danger "Affected endpoints (for both as-curator and as-users) that include vxQuery parameter"
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* GET `/api/v1/as-curator/omics/expression/data`
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* GET `/api/v1/as-curator/omics/expression/group`
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* GET `/api/v1/as-curator/omics/flow-cytometry/data`
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* GET `/api/v1/as-curator/omics/flow-cytometry/group`
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* GET `/api/v1/as-curator/omics/samples`
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* GET `/api/v1/as-curator/omics/variant/data`
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* GET `/api/v1/as-curator/omics/variant/group`
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??? danger "Affected endpoints (for both as-curator and as-users) that include vxQuery parameter"
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* GET `/api/v1/as-curator/omics/expression/data`
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* GET `/api/v1/as-curator/omics/expression/group`
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* GET `/api/v1/as-curator/omics/flow-cytometry/data`
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* GET `/api/v1/as-curator/omics/flow-cytometry/group`
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* GET `/api/v1/as-curator/omics/samples`
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* GET `/api/v1/as-curator/omics/variant/data`
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* GET `/api/v1/as-curator/omics/variant/group`
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3. **Retrieving Original VCF Annotation Data**
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When a new VCF file is uploaded, the format and descriptions from the VCF header are stored and available for query.
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This allows users to understand available fields for filtering. Annotation details are added under the “metadata”
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section in the response for relevant endpoints.
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* ??? danger "Affected endpoints (for both as-curator and as-users)"
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??? danger "Affected endpoints (for both as-curator and as-users)"
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* GET `/api/v1/as-user/variants/group`
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* GET `/api/v1/as-user/variants/group/by/run/{id}`
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* GET `/api/v1/as-user/variants/group/{id}`
@@ -499,19 +500,19 @@ Please review the documentation, as these changes may impact your integrations.
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1. **Common changes for all data types**
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* ??? abstract "Introduced changes to all data types"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------|
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| New “**itemOrigin**” section in the response format | A new section **“itemOrigin”** is introduced in the response body to store information regarding the origin of the data item: **runSourceId** - run id from the original file, **runId** - Genestack run id generated upon import, **groupId** - id of the original file. |
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||“**Run Source ID**” is moved from the metadata section to “itemOrigin” and renamed to “runSourceId”. In the OMICS Endpoints (integrationCurator, integrationUser) **sampleFilter**, **libraryFilter** or **preparationFilter** can be used for retrieving an individual run.|
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| New “**runSourceFilter**” parameter | A new parameter allows filtering data by the Run IDs from the original files. |
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| “**runFilter**” parameter takes list of strings | “**runFilter**” parameter which is taking the auto generated internal id for runs takes list of strings |
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| Deprecated filter option | FIltering by “**Run Source ID**” in the metadata filter is not available. |
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??? abstract "Introduced changes to all data types"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------|
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| New “**itemOrigin**” section in the response format | A new section **“itemOrigin”** is introduced in the response body to store information regarding the origin of the data item: **runSourceId** - run id from the original file, **runId** - Genestack run id generated upon import, **groupId** - id of the original file. |
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||“**Run Source ID**” is moved from the metadata section to “itemOrigin” and renamed to “runSourceId”. In the OMICS Endpoints (integrationCurator, integrationUser) **sampleFilter**, **libraryFilter** or **preparationFilter** can be used for retrieving an individual run.|
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| New “**runSourceFilter**” parameter | A new parameter allows filtering data by the Run IDs from the original files. |
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| “**runFilter**” parameter takes list of strings | “**runFilter**” parameter which is taking the auto generated internal id for runs takes list of strings |
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| Deprecated filter option | FIltering by “**Run Source ID**” in the metadata filter is not available. |
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* ??? example "Response example"
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??? example "Response example"
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![RN](1.58/1-58-1.png)
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* ??? danger "Affected endpoints (for both as-curator and as-users)"
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??? danger "Affected endpoints (for both as-curator and as-users)"
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| Endpoint Group | Endpoints Affected |
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|:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------|
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| expressionUser | GET `/api/v1/as-user/expressions` GET `/api/v1/as-user/expressions/{id}` |
@@ -525,18 +526,16 @@ Please review the documentation, as these changes may impact your integrations.
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1. **Tabular Data Endpoint Changes**
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* ??? abstract "Introduced changes to Tabular Data"
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??? abstract "Introduced changes to Tabular Data"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Deprecating old response format | The old response format for tabular data will be deprecated. The **"multi_value"** response format (introduced in July 2023) will be the default option. It allows retrieval of data with one or more features and suits any type of tabular data, including **.gct** files. |
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| Changing field name | The **“gene”** field is renamed to **“feature”** and incorporates all the feature attributes. The **“expression”** field with the measurement value for the **“feature”** was renamed to **“value”** and placed in the new **“value”** section. |
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* ??? example "Response example"
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??? example "Response example"
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![RN](1.58/1-58-2.png)
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* ??? danger "Affected endpoints (for both as-curator and as-users)"
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??? danger "Affected endpoints (for both as-curator and as-users)"
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| Endpoint Group | Endpoints Affected |
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|:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------|
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| expressionUser | GET `/api/v1/as-user/expressions` GET `/api/v1/as-user/expressions/{id}` |
@@ -546,17 +545,15 @@ Please review the documentation, as these changes may impact your integrations.
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2. **Variants Endpoint Changes**
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* ??? abstract "Introduced changes to Variants"
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??? abstract "Introduced changes to Variants"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Introducing **“variant”** section | A new section **“variant”** contains all fields related to a specific variation from the original VCF file: CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO. |
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* ??? example "Response example"
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??? example "Response example"
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![RN](1.58/1-58-3.png)
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* ??? danger "Affected endpoints (for both as-curator and as-users)"
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??? danger "Affected endpoints (for both as-curator and as-users)"
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| Endpoint Group | Endpoints Affected |
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|:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------|
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| variantUser | GET `/api/v1/as-user/variants` GET `/api/v1/as-user/variants/{id}` |
@@ -566,18 +563,16 @@ Please review the documentation, as these changes may impact your integrations.
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3. **Flow Cytometry Endpoint Changes**
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* ??? abstract "Introduced changes to Flow Cytometry"
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??? abstract "Introduced changes to Flow Cytometry"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Introducing **“feature”** and **“value”** sections | Flow-cytometry data response now has section **“feature”** including **"readoutType"**, **"cellPopulation"** and **"marker"** fields. **“Value”** section contains the expression field which is renamed to **“value”**.|
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| Changing field name | The old **“expression”** field with the measurement for the **“feature”** was renamed to **“value”** and placed into the new “value” section. |
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* ??? example "Response example"
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??? example "Response example"
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![RN](1.58/1-58-4.png)
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* ??? danger "Affected endpoints (for both as-curator and as-users)"
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??? danger "Affected endpoints (for both as-curator and as-users)"
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| Endpoint Group | Endpoints Affected |
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|:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------|
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| flowCytometryUser | GET `/api/v1/as-user/flow-cytometries` GET `/api/v1/as-user/flow-cytometries/{id}` |
@@ -590,7 +585,8 @@ Please review the documentation, as these changes may impact your integrations.
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1. **User Guide Update**: A revised user guide is now available, featuring a series of new quick start guide articles.
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* [Quick Start Guide](../user-guide/quick-start/index.md) - introduction to User Interface and API documentation.
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* [Advanced User Interface Guide](../user-guide/index.md)
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* !!! note "We are working on making our guide better. Please reach us in case of any inconsistency."
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!!! note "We are working on making our guide better. Please reach us in case of any inconsistency."
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2. **Lipidomics Data Class**: A new **Lipidomics** data class is available for selection during the upload of tabular data files.
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This new class is integrated within the metadata editor and study browser.

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