Updating metadata

Using Swagger

An individual analysis can be updated through the Patch PatchUpdateAnalysis endpoint located in the Analysis dropdown on the Swagger UI.

The PatchUpdateAnalysis endpoint requires the following inputs:

Your Authorization token
An analysisID
The updated Analysis content
A StudyId

Programmatic Updates

Here, we provide some examples of updating analyses using the Song API programmatically. If you have any questions or require technical support for your specific use case, please contact us on our Slack channel.

Updating an analysis

The following script shows how to update a specific analysis in a given study by making a PATCH request to Song’s API:

python

### Define variables
analysis_id="ANALYSIS-ABC123-SAMPLEA"
url="https://song.virusseq-dataportal.ca"
study="ABC123"
api_token="PASSWORD"
    
### PATCH endpoint
endpoint="%s/studies/%s/analysis/%s" % (url,study,analysis_id)
headers={"accept":"*/*","Authorization":"Bearer %s" % (api_token),"Content-Type": "application/json"}
payload = {'experiment':{'sequencing_instrument':new_value}}

patch_response=requests.patch(endpoint,json=payload,headers=headers)
if patch_response.status_code!=200:
   print("error calling patch endpoint",endpoint,patch_response.status_code)
   break

Updating multiple analyses

The following script demonstrates how to update multiple analyses associated with specific samples within a study. This is achieved by iterating over a list of sample IDs, retrieving the corresponding analyses, and modifying a specific attribute of each analysis. The script utilizes the PATCH request method to update the analyses in the data portal's API.

python

### Define variables
samples_to_mod=["SAMPLE_A","SAMPLE_B","SAMPLE_C","SAMPLE_D","SAMPLE_E","SAMPLE_F"]
url="https://song.virusseq-dataportal.ca"
study="ABC123"
api_token="PASSWORD"

for sample in samples_to_mod:
    ### Retrieve analyses associated to samples
    endpoint="%s/studies/%s/analysis/search/id?submitterDonorId=%s" % (url,study,sample)
    headers={"accept":"*/*"}

    get_response=requests.get(endpoint,headers=headers)
    
    ### Catch endpoint call fail
    if get_response.status_code!=200:
        print("Error :%s" % (endpoint))
        break
    ### We only expect 1 analysis
    if len([analysis for analysis in get_response.json() if analysis['analysisState']=='PUBLISHED'])==0:
        print("No published detected :%s" % (endpoint))
        break
    if len([analysis for analysis in get_response.json() if analysis['analysisState']=='PUBLISHED'])>1:
        print("Multiple analsyes detected :%s" % (endpoint))
        break
        
    analysis=get_response.json()[0]
    analysis_id=analysis['analysisId']
    old_value=get_response.json()[0]['experiment']['sequencing_instrument']
    new_value="Illumina MiSeq"
    
    ### PATCH endpoint
    endpoint="%s/studies/%s/analysis/%s" % (url,study,analysis_id)
    headers={"accept":"*/*","Authorization":"Bearer %s" % (api_token),"Content-Type": "application/json"}
    payload = {'experiment':{'sequencing_instrument':new_value}}

    patch_response=requests.patch(endpoint, json=payload,headers=headers)
    if patch_response.status_code!=200:
        print("error calling patch endpoint",endpoint,patch_response.status_code)
        break

Song-assigned IDs

Song-assigned IDs (donor, sample, specimen, analysis and object IDs) and those specified in the base schema are immutable and cannot be altered. In the event you need to change any of these values, it is suggested to UNPUBLISH and SUPPRESS the analysis and resubmit the analysis.

Retrieving Metadata

Submitting Data

Song github