[Backend] Update the importer to include adding a discussion section in each new analysis

[JmScherer]

Checklist before requesting a review

• I have performed a self-review of my code.
• My code follows the style guidelines enforced by static analysis tools.
• If it is a core feature, I have added thorough tests.
• My changes generate no new warnings.
• New and existing unit tests pass locally with my changes.

Pull Request Details

https://www.wrike.com/open.htm?id=1206943181

Changes made:

This pull request is intended to create consistency with how Analysis documents are created

• Updates the PhenotipsImporter.py to add both the discussions and supporting_evidence_files keys to every uploaded analysis.
  • Assigns to empty arrays
• Updates the existing fixtures to include the keys
  • Consistent fixture data to have empty arrays if no entries

To Review:

• Static Analysis by Reviewer
• Deploy and upload a new analysis for local Rosalution
  To check this run the following commands:

  # from the root of Rosalution
  docker compose down
  docker system prune -a --volumes
  
  docker compose up --build -d

  • Go to http://local.rosalution.cgds/rosalution
  • Login with developer
  • Click on the card with the +
  • Upload a new analysis from: ./etc/fixtures/import
    • e.g. C-PAM0042.json
• Does the Analysis have the new fields upon upload?

  # Find the container name running mongo
  docker ps
  
  docker exec -it <mongo_container_name> mongosh rosalution_db
  
  Example:
  
  docker exec -it rosalution-rosalution-db-1 mongosh rosalution_db
  
  # Ensure the fields were created on upload
  
  db.analyses.find({"name": "CPAM0042"})

• All Github Actions checks have passed.

---

[SeriousHorncat]

Imported case and it successfully added and it included both of the attributes as expected.

rosalution_db> db.analyses.find({"name": "CPAM0042"})
[
  {
    _id: ObjectId("657cb1d57f0888d94a655ef6"),
    name: 'CPAM0042',
    description: '',
    nominated_by: '',
    genomic_units: [
      {
        gene: 'JAK2',
        transcripts: [ { transcript: 'NM_004972.3' } ],
        variants: [
          {
            hgvs_variant: 'NM_004972.3:c.1694G>C',
            c_dot: 'c.1694G>C',
            p_dot: 'p.Arg565Thr',
            build: 'GRCh37',
            case: [ [Object], [Object] ]
          }
        ]
      }
    ],
    sections: [
      {
        header: 'Brief',
        content: [
          { type: 'section-text', field: 'Nominator', value: [] },
          { type: 'section-text', field: 'Participant', value: [] },
          { type: 'section-text', field: 'Phenotype', value: [] },
          {
            type: 'section-text',
            field: 'ACMG Classification',
            value: []
          },
          {
            type: 'section-text',
            field: 'ACMG Classification Criteria',
            value: []
          },
          {
            type: 'section-text',
            field: 'ACMG Criteria To Add',
            value: []
          },
          { type: 'section-text', field: 'Decision', value: [] }
        ]
      },
      {
        header: 'Clinical History',
        content: [
          {
            type: 'section-text',
            field: 'Clinical Diagnosis',
            value: []
          },
          {
            type: 'section-text',
            field: 'Affected Individuals Identified',
            value: []
          },
          { type: 'section-text', field: 'Sequencing', value: [] },
          { type: 'section-text', field: 'Testing', value: [] },
          { type: 'section-text', field: 'Systems', value: [] },
          {
            type: 'section-text',
            field: 'Additional Details',
            value: []
          }
        ]
      },
      {
        header: 'Pedigree',
        attachment_field: 'Pedigree',
        content: [ { type: 'images-dataset', field: 'Pedigree', value: [] } ]
      },
      {
        header: 'JAK2 Gene To Phenotype',
        attachment_field: 'JAK2 Gene To Phenotype',
        content: [
          {
            type: 'images-dataset',
            field: 'JAK2 Gene To Phenotype',
            value: []
          },
          {
            type: 'section-text',
            field: 'HPO Terms',
            value: [
              'HP:0000155: Oral ulcer; HP:0000217: Xerostomia; HP:0000365: Hearing impairment; HP:0000508: Ptosis; HP:0000716: Depressivity; HP:0000872: Hashimoto thyroiditis; HP:0000988: Skin rash; HP:0000992: Cutaneous photosensitivity; HP:0001097: Keratoconjunctivitis sicca; HP:0001337: Tremor; HP:0001369: Arthritis; HP:0001370: Rheumatoid arthritis; HP:0001596: Alopecia; HP:0001701: Pericarditis; HP:0001882: Leukopenia; HP:0001903: Anemia; HP:0002035: Rectal prolapse; HP:0002102: Pleuritis; HP:0002315: Headache; HP:0002583: Colitis; HP:0003401: Paresthesia; HP:0005681: Juvenile rheumatoid arthritis; HP:0030880: Raynaud phenomenon; HP:0100543: Cognitive impairment; HP:0100654: Retrobulbar optic neuritis'
            ]
          }
        ]
      },
      {
        header: 'JAK2 Molecular Mechanism',
        content: [
          {
            type: 'section-text',
            field: 'JAK2 Molecular Mechanism',
            value: []
          }
        ]
      },
      {
        header: 'JAK2 Function',
        attachment_field: 'JAK2 Function',
        content: [
          { type: 'images-dataset', field: 'JAK2 Function', value: [] }
        ]
      },
      {
        header: 'Model Goals',
        content: [
          {
            type: 'section-text',
            field: 'Model of Interest',
            value: []
          },
          { type: 'section-text', field: 'Goals', value: [] },
          {
            type: 'section-text',
            field: 'Proposed Model/Project',
            value: []
          },
          {
            type: 'section-text',
            field: 'Existing Collaborations',
            value: []
          },
          {
            type: 'section-text',
            field: 'Existing Funding',
            value: []
          }
        ]
      }
    ],
    discussions: [],
    supporting_evidence_files: [],
    timeline: [
      {
        event: 'create',
        timestamp: ISODate("2023-12-15T20:06:45.667Z"),
        username: '3bghhsmnyqi6uxovazy07ryn9q1tqbnt'
      }
    ]
  }
]