Refactor Base Schema to not require Donor/Specimen/Sample #878
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| # Custom Analysis Schemas | ||
|
|
||
| ## Minimal Example | ||
|
|
||
| ```json | ||
| { | ||
| "name": "minimalExample", | ||
| "options":{}, | ||
| "schema":{ | ||
| "type": "object", | ||
| "required":[ | ||
| "experiment" | ||
| ], | ||
| "properties":{ | ||
| "experiment":{} | ||
| } | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ## Options | ||
|
|
||
| The `options` property defines extra validations for this analysis schema, such as restrictions on file types and checks on the data with an external service. The `options` property is not required. Similarly, each property in `options` is also optional. If no value is provided for one of the `options` properties, a default configuration will be used for the analysis. If this is an update to an existing analysis type, you can omit any option and its value will be maintained from the previous version. | ||
|
|
||
| ```json | ||
| { | ||
| "fileTypes":["bam", "cram"], | ||
| "externalValidations":[ | ||
| { | ||
| "url": "http://localhost:8099/", | ||
| "jsonPath": "experiment.someId" | ||
| } | ||
| ] | ||
| }, | ||
| ``` | ||
|
|
||
| If you want to remove the previous value of an option so that this validation is no longer required, for instance removing the restriction on file types so that any file type could be provided, you should provide an empty list for that option. | ||
|
|
||
| In the example below, both `fileTypes` and `externalValidations` properties are set to empty arrays, which means that these validations will not be applied to submitted analysis: | ||
|
|
||
| ```json | ||
| { | ||
| "options": { | ||
| "fileTypes": [], | ||
| "externalValidations": [] | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ### File Types | ||
|
|
||
| `options.fileTypes` can be provided an array of strings. These represent the file types (file extensions) that are allowed to be uploaded for this type of analysis. | ||
|
|
||
| If an empty array is provided, then any file type will be allowed. If an array of file types is provided, then an analysis will be invalid if it contains files of a type not listed. | ||
|
|
||
| ```json | ||
| { | ||
| "options": { | ||
| "fileTypes": ["bam","cram"] | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ### External Validation | ||
|
|
||
| External validations configure Song to check a value in the analysis against an external service by sending an HTTP GET request to a configurable URL. The service should respond with a 2XX status message to indicate the value "is valid". | ||
|
|
||
| As an example, if the project clinical data is being managed in a separate service, we can add an external validation to the donor id field of our custom scheme. This will send the donor id to the external service which can confirm that we have previously registered that donor. | ||
|
|
||
| This might look like the following: | ||
|
|
||
| ```json | ||
| { | ||
| "url": "http://example.com/{study}/donor/{value}", | ||
| "jsonPath": "experiment.donorId" | ||
| } | ||
| ``` | ||
|
|
||
| The URL provided is a template, with two variables that will be replaced during validation. Song will replace the token `{value}` with the value read from the analysis at the property as defined in the `jsonPath`. Song will also replace the token `{study}` with the study ID for the Analysis. | ||
|
|
||
| Continuing the above example, if the following analysis was submitted: | ||
|
|
||
| ```json | ||
| { | ||
| "studyId": "ABC123", | ||
| "analysisType": { | ||
| "name": "minimalExample" | ||
| }, | ||
| "files": [ | ||
| { | ||
| "dataType": "text", | ||
| "fileName": "file1.txt", | ||
| "fileSize": 123, | ||
| "fileType": "txt", | ||
| "fileAccess": "open", | ||
| "fileMd5sum": "595f44fec1e92a71d3e9e77456ba80d1" | ||
| } | ||
| ], | ||
| "experiment": { | ||
| "donorId": "id01" | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| Song would attempt to validate the donorId by sending a validation request to `http://example.com/ABC123/donor/id01`. | ||
|
|
||
| The URL parsing allows using either the `{study}` or `{value}` placeholders multiple times (e.g. `http://example.com/{study}-{value}/{value}`), each instance will be interpolated accordingly. | ||
|
|
||
| > [!Warning] | ||
| > The URL may cause errors in Song if it contains any tokens matching the `{word}` format other than `{study}` and `{value}` | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,16 @@ | ||
| package bio.overture.song.core.model; | ||
|
|
||
| import java.util.List; | ||
| import lombok.AllArgsConstructor; | ||
| import lombok.Builder; | ||
| import lombok.Data; | ||
| import lombok.NoArgsConstructor; | ||
|
|
||
| @Data | ||
| @Builder | ||
| @NoArgsConstructor | ||
| @AllArgsConstructor | ||
| public class AnalysisTypeOptions { | ||
| private List<String> fileTypes; | ||
| private List<ExternalValidation> externalValidations; | ||
| } |
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
love it. very helpful description 👍