Endpoint to return submission summary

[Buwujiu]

Description

The current get submission endpoint returns all raw data, making it very hard to see the data structure and submission status. Create a new endpoint to return submission summary.
Must return:

• number of entries
• entities names
• submission status - valid or errors
• summary of errors
  the endpoint will indicate whether the submission is successful or not, it's not meant to return raw data.

[Buwujiu]

Leo will attach PR to ticket.

[leoraba]

See PR # 133 for more specific implementation details.

[leoraba]

deployed in https://submission.pcgl-dev.cumulus.genomeinformatics.org/api-docs/

[hknahal]

Tested in staging using this endpoint: https://submission.ingress.staging.k8s.pcgl.dev-sd4h.ca/api-docs/#/Submission/get_submission__submissionId__details

In this example, I tested using submission ID 75:

curl -X 'GET' \
  'https://submission.ingress.staging.k8s.pcgl.dev-sd4h.ca/submission/75/details' \
  -H 'accept: application/json'

This returns the following:

{
  "data": [
    {
      "type": "INSERTS",
      "entity": "diagnosis",
      "value": {
        "age_at_diagnosis": 68,
        "submitter_diagnosis_id": "diagnosis-80",
        "submitter_participant_id": "DONOR_780"
      },
      "index": 0
    },
    {
      "type": "INSERTS",
      "entity": "diagnosis",
      "value": {
        "disease_code": "MONDO:0004994",
        "disease_term": "cardiomyopathy",
        "age_at_diagnosis": 74,
        "submitter_diagnosis_id": "diagnosis-81",
        "submitter_participant_id": "DONOR_781"
      },
      "index": 1
    },
    {
      "type": "INSERTS",
      "entity": "diagnosis",
      "value": {
        "disease_code": "MONDO:0004976",
        "disease_term": "amyotrophic lateral sclerosis",
        "age_at_diagnosis": 52,
        "submitter_diagnosis_id": "diagnosis-82",
        "submitter_participant_id": "DONOR_782"
      },
      "index": 2
    },
    {
      "type": "INSERTS",
      "entity": "treatment",
      "value": {
        "treatment_type": "Medication",
        "age_at_treatment": 68,
        "treatment_intent": "Curative",
        "treatment_status": "Treatment ongoing",
        "treatment_duration": 120,
        "treatment_response": "Stable Disease",
        "submitter_diagnosis_id": "diagnosis-80",
        "submitter_treatment_id": "treatment_a1",
        "submitter_participant_id": "DONOR_780"
      },
      "index": 0
    },
    {
      "type": "INSERTS",
      "entity": "treatment",
      "value": {
        "treatment_type": "Procedure",
        "age_at_treatment": 75,
        "treatment_intent": "Curative",
        "treatment_status": "Treatment ongoing",
        "treatment_duration": 90,
        "treatment_response": "Stable Disease",
        "submitter_diagnosis_id": "diagnosis-81",
        "submitter_treatment_id": "treatment_a2",
        "submitter_participant_id": "DONOR_781"
      },
      "index": 1
    },
    {
      "type": "INSERTS",
      "entity": "treatment",
      "value": {
        "treatment_type": "Medication",
        "age_at_treatment": 52,
        "treatment_intent": "Palliative",
        "treatment_status": "Treatment stopped due to acute toxicity",
        "treatment_duration": 110,
        "treatment_response": "Clinical remission",
        "submitter_diagnosis_id": "diagnosis-82",
        "submitter_treatment_id": "treatment_a3",
        "submitter_participant_id": "DONOR_782"
      },
      "index": 2
    },
    {
      "type": "INSERTS",
      "entity": "demographic",
      "value": {
        "vital_status": "Alive",
        "age_at_enrollment": 67,
        "submitter_participant_id": "DONOR_780"
      },
      "index": 0
    },
    {
      "type": "INSERTS",
      "entity": "demographic",
      "value": {
        "vital_status": "Alive",
        "age_at_enrollment": 74,
        "submitter_participant_id": "DONOR_781"
      },
      "index": 1
    },
    {
      "type": "INSERTS",
      "entity": "demographic",
      "value": {
        "age_at_death": 57,
        "vital_status": "Deceased",
        "cause_of_death": "Died of other reasons",
        "age_at_enrollment": 52,
        "submitter_participant_id": "DONOR_782"
      },
      "index": 2
    },
    {
      "type": "INSERTS",
      "entity": "participant",
      "value": {
        "study_id": "TEST-CA",
        "duo_modifier": [],
        "duo_permission": "DUO:0000007 (disease specific research)",
        "submitter_participant_id": "DONOR_780",
        "disease_specific_modifier": [
          "MONDO:0011429"
        ]
      },
      "index": 0
    },
    {
      "type": "INSERTS",
      "entity": "participant",
      "value": {
        "study_id": "TEST-CA",
        "duo_modifier": [],
        "duo_permission": "DUO:0000042 (general research use)",
        "submitter_participant_id": "DONOR_781",
        "disease_specific_modifier": []
      },
      "index": 1
    },
    {
      "type": "INSERTS",
      "entity": "participant",
      "value": {
        "study_id": "TEST-CA",
        "duo_modifier": [],
        "duo_permission": "DUO:0000042 (general research use)",
        "submitter_participant_id": "DONOR_782",
        "disease_specific_modifier": []
      },
      "index": 2
    }
  ],
  "errors": [
    {
      "index": 0,
      "errors": [
        {
          "message": "A value is required for this field.",
          "restriction": {
            "rule": true,
            "type": "required"
          }
        }
      ],
      "reason": "INVALID_BY_RESTRICTION",
      "fieldName": "disease_code"
    }
  ]
}

The endpoint returns the following:

• entity names
• action type (ie. INSERT, DELETE or UPDATE)
• summary of errors (in the "errors" array near the bottom)

But is missing the following:

• number of entries
• overall submission status (ie. INVALID or VALID)