Skip to content

add multi submitter id validation - #67

Open
edsu7 wants to merge 2 commits into
developfrom
song_submitter_array
Open

add multi submitter id validation#67
edsu7 wants to merge 2 commits into
developfrom
song_submitter_array

Conversation

@edsu7

@edsu7 edsu7 commented Aug 14, 2026

Copy link
Copy Markdown
Contributor
  • edit options.json to reflect new variable
  • change IDs from string to array
  • example for multi array

Using endpoint:
https://file-manager.submission.ingress.dev.k8s.pcgl.dev-sd4h.ca/submit/PCGLST0003?allowDuplicates=true

1. String instead of array

"submitter_experiment_ids": "EXP001",

Result:

"message": "[SubmitService::schema.violation] - #/submitter_experiment_ids: expected type: JSONArray, found: String",

2. Duplicate items

"submitter_experiment_ids": ["EXP_001","EXP_001"],

Result:

"message": "[SubmitService::schema.violation] - #/submitter_experiment_ids: array items are not unique",

3. Non-existent record

"submitter_experiment_ids": ["EXP_001","EXP_111"],

Result:

"message": "[SubmitService::schema.violation] - #: Value 'EXP_111' from path 'submitter_experiment_ids' is not permitted as it failed to validate with external validation source.",

- edit options.json to reflect new variable
- change IDs from string to array
- example for multi array
@edsu7
edsu7 requested a review from lindaxiang August 14, 2026 21:47
Comment thread base/base.yaml
range: string
required: true
pattern: ^[A-Za-z0-9\-\._]{1,64}
submitter_participant_ids:

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Any reason we fully duplicated slot definitions rather than using is_a slot inheritance feature, e.g,

  submitter_participant_ids:
    is_a: submitter_participant_id
    name: submitter_participant_ids
    description: A list of unique identifiers (min 1) for participants within the study, assigned by the data provider.
    multivalued: true
    minimum_cardinality: 1
    list_elements_unique: true

Comment thread base/base.yaml
- variant_calling_strategy
- variant_class
slot_usage:
submitter_analysis_id:

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

change to submitter_analysis_ids?

Comment thread base/base.yaml
rank: 1
slot_group: Database Identifiers
submitter_experiment_id:
name: submitter_experiment_id

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

submitter_experiment_ids?

Comment thread base/base.yaml
rank: 2
slot_group: Database Identifiers
submitter_participant_id:
name: submitter_participant_id

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

submitter_participant_ids

Comment thread base/base.yaml
rank: 3
slot_group: Database Identifiers
submitter_sample_id:
name: submitter_sample_id

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

submitter_sample_ids

Comment thread base/base.yaml
rank: 4
slot_group: Database Identifiers
submitter_specimen_id:
name: submitter_specimen_id

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

submitter_specimen_ids

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants