Skip to content

Commit

Permalink
Whole Data Contributors using the API was completed
Browse files Browse the repository at this point in the history
  • Loading branch information
MikhailAf committed Aug 5, 2024
1 parent 06d02ca commit dab9562
Show file tree
Hide file tree
Showing 10 changed files with 35 additions and 45 deletions.
80 changes: 35 additions & 45 deletions docs/user-guide/quick-start/contributor-api.md
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,6 @@ An access token is required to work with the API endpoints. Follow these steps t
![Authorize access](quick-start-images/authorize-access.png)

4. Click on **Try it out** to activate it. The **Try it out** step is required for every single endpoint.

![Try it out](quick-start-images/try-it-out.png)

## The ODM Data Model
Expand Down Expand Up @@ -192,76 +191,67 @@ Use the ID to track the status of the import
## Linking your entities

1. **Redirect to the Integration Curator Page**: To link entities (e.g., samples and data) with the study,
provide your token and authorize the execution of the selected endpoint. Identify the ID accession from the uploaded study.
Note the Genestack accession values shown in the response (e.g., for sample metadata, the accession number is GSF1147034).

For this particular example, these are the accession IDs:

* **Study Accession ID: GSF1147033**
* **Samples Accession ID: GSF1147034**
* **Experimental Data Accession ID: GSF1147049**

1. **Integration Endpoints**: Click on the integration endpoints, shown as integrationCurator. These endpoints will
provide your token and authorize the execution of the selected endpoint. Identify the ID accession from
the uploaded study. Note the Genestack accession values shown in the response (e.g., for sample metadata,
the accession number is GSF1147034).
For this particular example, these are the accession IDs:
* **Study Accession ID: GSF1147033**
* **Samples Accession ID: GSF1147034**
* **Experimental Data Accession ID: GSF1147049**

2. **Integration Endpoints**: Click on the integration endpoints, shown as integrationCurator. These endpoints will
allow you to link data and metadata to samples and samples to studies.

![API Main](quick-start-images/api-main-page.png)
![Integration Endpoints](quick-start-images/integration-endpoints.png)

### Link Samples and Study

1. **Link Samples to Study**: Once the samples and study are uploaded to the ODM, the next step is to link the
samples to the study. Important: At least one parameter has to match with the Study file, e.g., **Sample Source ID**.

1. **Identify the GroupId** from the response obtained after uploading the samples (e.g., **GSF1147034**)
2. **Identify the GroupId** from the response obtained after uploading the samples (e.g., **GSF1147034**)

1. Select the section **Sample Integration as a Curator** to link samples with a study. Select the endpoint
3. Select the section **Sample Integration as a Curator** to link samples with a study. Select the endpoint
**Create a Link Between a Group of Sample Objects and a Study**
/api/v1/as-curator/integration/link/sample/group/{sourceId}/to/study/{targetId}

![API Main](quick-start-images/api-main-page.png)

1. **Enter Accession Details:** Add the required values (ID accession) for the study and samples, and click **Execute**.

* **Study Accession ID: GSF1147033**
* **Samples Accession ID: GSF1147034**
`/api/v1/as-curator/integration/link/sample/group/{sourceId}/to/study/{targetId}`.
![Sample Integration](quick-start-images/post-sample-integration.png)

![API Main](quick-start-images/api-main-page.png)
4. **Enter Accession Details:** Add the required values (ID accession) for the study and samples, and click **Execute**.
* **Study Accession ID: GSF1147033**
* **Samples Accession ID: GSF1147034**
![Accession](quick-start-images/sample-integration-accession.png)

1. **Check the Response**: A response will show that the link was successful.
![API Main](quick-start-images/api-main-page.png)

1. **Confirm in ODM**: You can open the study in the ODM interface to see that the data is now linked.
5. **Check the Response**: A response will show that the link was successful.
![Response](quick-start-images/sample-integration-response.png)

![API Main](quick-start-images/api-main-page.png)
6. **Confirm in ODM**: You can open the study in the ODM interface to see that the data is now linked.
![Confirmation](quick-start-images/sample-integration-confirm.png)

### Link Experimental Data and Samples

1. Identify the **groupID** number for the Data. For this particular example, the Data accession number is **GSF1147049**
* **Samples Accession ID: GSF1147034**
* **Experimental Data Accession ID: GSF1147049**

* **Samples Accession ID: GSF1147034**
* **Experimental Data Accession ID: GSF1147049**

1. To link experimental data with samples (and the study), click on the "Expression integration as Curator" endpoints.
2. To link experimental data with samples (and the study), click on the "Expression integration as Curator" endpoints.
1. Select the endpoint to create a link between data (for this specific example expression in GCT format
previously uploaded) with a group of samples.
1. Click on the endpoint to **Create a link between a group of expression objects and a group of
samples objects**: /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId}

![API Main](quick-start-images/api-main-page.png)
2. Click on the endpoint to **Create a link between a group of expression objects and a group of
samples objects**:
`/api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId}`
![Data Integration](quick-start-images/post-data-integration.png)

1. **Enter Accession Details:** Add the relevant information, including the data accession number and samples accession
3. **Enter Accession Details:** Add the relevant information, including the data accession number and samples accession
number, and click **Execute.**
![Accession](quick-start-images/post-data-accession.png)

![API Main](quick-start-images/api-main-page.png)

1. **Check the Response**: The response will show that the link has been created between the group of samples and
4. **Check the Response**: The response will show that the link has been created between the group of samples and
the experimental data
![Response](quick-start-images/post-data-response.png)

![API Main](quick-start-images/api-main-page.png)

1. **Confirm in ODM**: You can open the ODM interface to confirm that samples and experimental data are now
5. **Confirm in ODM**: You can open the ODM interface to confirm that samples and experimental data are now
linked to the study.

![API Main](quick-start-images/api-main-page.png)
![Confirmation](quick-start-images/post-data-confirm.png)

By following these steps, you can efficiently interact with the API endpoints via the Swagger interface,
tailored to your role and permissions.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

0 comments on commit dab9562

Please sign in to comment.