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metadatacenter / cedar-submission-server

CEDAR server to handle submissions to metadata repositories
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CEDAR Submission Server

The server will listen on port 9010.

To validation an example CEDAR BioSample instance:

curl -X POST \
  -H "Accept: application/json" \
  -H "Content-type: application/json" \
  -H "Authorization: apiKey <CedarUserApiKey>" \
  -d @${CEDAR_HOME}/cedar-docs/repositories/BioSample/AMIA2016DemoBioSampleInstance-Example.json \
  "http://localhost:9010/command/validate-biosample"

To validate an example CEDAR AIRR instance:

curl -X POST \
  -H "Accept: application/json" \
  -H "Content-type: application/json" \
  -H "Authorization: apiKey <CedarUserApiKey>" \
  -d @${CEDAR_HOME}/cedar-docs/repositories/AIRR/EAB2017DemoAIRRSampleInstance-Example.json \
  "http://localhost:9010/command/validate-airr"

To submit an example CEDAR AIRR instance (with no user-supplied files):

curl -X POST \
  -H "Accept: application/json" \
  -H "Content-Type: multipart/form-data" \
  -H "Authorization: apiKey <CedarUserApiKey>" \
  -F "instance=@${CEDAR_HOME}/cedar-docs/repositories/AIRR/EAB2017DemoAIRRSampleInstance-Example.json" \
  "http://localhost:9010/command/submit-airr"

Here is a success response from the server:

{ 
  "isValid": true,
  "messages": []
}

Here is an error response from the server:

{ 
  "isValid": false,
  "messages": [ 
                "Empty Sample Identifier.", 
                "Empty attribute value for attribute 'biomaterial provider'." 
              ]
}

To validate that an example XML submission works against the BioSample REST service use the included example as follows: 

curl -X POST \
  -d @${CEDAR_HOME}/cedar-docs/repositories/BioSample/Human.1.0-Example.xml \
  "https://www.ncbi.nlm.nih.gov/projects/biosample/validate/"