v1.0.0 Implementation Tracking

[claymcleod]

This discussion represents the progress that each federation member is making in implementing v1.0.0 of the API specification. Members are expected to edit this post for their respective implementations to report progress.

Kids First (Children's Hospital of Philadelphia)

Subjects

• Getting all subjects (GET /subject).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for subjects for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all subjects under a particular namespace (GET /subject/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /subject/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for subjects (GET /subject/summary).

Samples

• Getting all samples (GET /sample).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for samples for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all samples under a particular namespace (GET /sample/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /sample/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for sample (GET /sample/summary).

Files

• Getting all files (GET /file).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for files for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all file under a particular namespace (GET /file/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /file/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for file (GET /file/summary).

Metadata

• Metadata for subject fields (GET /metadata/fields/subject).
  • All harmonized fields do the following:
    • Have harmonized: true.
    • Have the path pointing to the right location (e.g., disease_phase—not metadata.disease_phase).
    • Have the wiki_url pointing to the wiki (e.g., https://github.com/CBIIT/ccdi-federation-api/wiki/Sample-Metadata-Fields#disease_phase)
    • For fields that are backed by a CDE, standard has both the name of the standard (e.g., caDSR CDE 12217251 v1.00) and the backing URL for the standard (e.g., https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=12217251%20and%20ver_nr=1).
  • All unharmonized fields do the following:
    • Have harmonized: false.
    • Have a name.
    • Have the path pointing to the right location (e.g., unharmonized.foobar—not metadata.unharmonized.foobar).
    • Have either a url, description or both that describe the metadata field. Be as specific as possible, don't link to a general documentation page (linking within a particular documentation page where a metadata element's definition can be easily located is okay).

Namespaces

• Implements getting all namespaces (GET /namespace).
• Implements getting a particular namespace (GET /namespace/{organization}/{namespace}).

Organizations

• Implements getting all organizations (GET /organization).
• Implements getting a particular organization (GET /organization/{name}).

Information

• Implements the all information endpoint (GET /info).

Other

• Have production URL serving the API.
• Update URL to ensure it's v1 instead of v0.

PCDC (University of Chicago)

Subjects

• Getting all subjects (GET /subject).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for subjects for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all subjects under a particular namespace (GET /subject/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /subject/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for subjects (GET /subject/summary).

Samples - Not supported

• Getting all samples (GET /sample).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for samples for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all samples under a particular namespace (GET /sample/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /sample/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for sample (GET /sample/summary).

Files - Not Supported

• Getting all files (GET /file).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for files for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all file under a particular namespace (GET /file/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /file/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for file (GET /file/summary).

Metadata

• Metadata for subject fields (GET /metadata/fields/subject).
  • All harmonized fields do the following:
    • Have harmonized: true.
    • Have the path pointing to the right location (e.g., disease_phase—not metadata.disease_phase).
    • Have the wiki_url pointing to the wiki (e.g., https://github.com/CBIIT/ccdi-federation-api/wiki/Sample-Metadata-Fields#disease_phase)
    • For fields that are backed by a CDE, standard has both the name of the standard (e.g., caDSR CDE 12217251 v1.00) and the backing URL for the standard (e.g., https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=12217251%20and%20ver_nr=1).
  • All unharmonized fields do the following:
    • Have harmonized: false.
    • Have a name.
    • Have the path pointing to the right location (e.g., unharmonized.foobar—not metadata.unharmonized.foobar).
    • Have either a url, description or both that describe the metadata field. Be as specific as possible, don't link to a general documentation page (linking within a particular documentation page where a metadata element's definition can be easily located is okay).

Namespaces

• Implements getting all namespaces (GET /namespace).
• Implements getting a particular namespace (GET /namespace/{organization}/{namespace}).

Organizations

• Implements getting all organizations (GET /organization).
• Implements getting a particular organization (GET /organization/{name}).

Information

• Implements the all information endpoint (GET /info).

Other

• Have production URL serving the API.
• Update URL to ensure it's v1 instead of v0.

St. Jude Cloud (St. Jude Children's Research Hospital)

Subjects

• Getting all subjects (GET /subject).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for subjects for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all subjects under a particular namespace (GET /subject/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /subject/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for subjects (GET /subject/summary).

Samples

• Getting all samples (GET /sample).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for samples for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all samples under a particular namespace (GET /sample/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /sample/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for sample (GET /sample/summary).

Files

• Getting all files (GET /file).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for files for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all file under a particular namespace (GET /file/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /file/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for file (GET /file/summary).

Metadata

• Metadata for subject fields (GET /metadata/fields/subject).
  • All harmonized fields do the following:
    • Have harmonized: true.
    • Have the path pointing to the right location (e.g., disease_phase—not metadata.disease_phase).
    • Have the wiki_url pointing to the wiki (e.g., https://github.com/CBIIT/ccdi-federation-api/wiki/Sample-Metadata-Fields#disease_phase)
    • For fields that are backed by a CDE, standard has both the name of the standard (e.g., caDSR CDE 12217251 v1.00) and the backing URL for the standard (e.g., https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=12217251%20and%20ver_nr=1).
  • All unharmonized fields do the following:
    • Have harmonized: false.
    • Have a name.
    • Have the path pointing to the right location (e.g., unharmonized.foobar—not metadata.unharmonized.foobar).
    • Have either a url, description or both that describe the metadata field. Be as specific as possible, don't link to a general documentation page (linking within a particular documentation page where a metadata element's definition can be easily located is okay).

Namespaces

• Implements getting all namespaces (GET /namespace).
• Implements getting a particular namespace (GET /namespace/{organization}/{namespace}).

Organizations

• Implements getting all organizations (GET /organization).
• Implements getting a particular organization (GET /organization/{name}).

Information

• Implements the all information endpoint (GET /info).

Other

• Have production URL serving the API.
• Update URL to ensure it's v1 instead of v0.

Treehouse (UCSC)

Subjects

• Getting all subjects (GET /subject).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for subjects for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all subjects under a particular namespace (GET /subject/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /subject/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for subjects (GET /subject/summary).

Samples

• Getting all samples (GET /sample).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata).
  • Error responses for missing data (404, only if you can't share data for samples for some reason or if you don't have any).
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all samples under a particular namespace (GET /sample/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /sample/by/{field}/count).
  • Harmonized fields support.
  • Unharmonized fields support.
• Summary endpoint for sample (GET /sample/summary).

Files

• Getting all files (GET /file).
  • Pagination with per_page and page support.
  • With functional quick filtering parameters for all harmonized elements.
  • [ ] With functional quick filtering parameters for any unharmonized keys (only if you have unharmonized metadata). Treehouse has no unharmonized file metadata. -ETK 5/28
  • [ ] Error responses for missing data (404, only if you can't share data for files for some reason or if you don't have any). Treehouse has no missing files data. -ETK 5/28
  • Error responses for incorrect pagination parameters.
  • Error responses for missing quick filtering parameters.
• Getting all file under a particular namespace (GET /file/{organization}/{namespace}/{name}).
• Grouping by a metadata field and returning counts (GET /file/by/{field}/count).
  • Harmonized fields support.
  • [ ] Unharmonized fields support. Treehouse has no unharmonized file fields. -ETK 5/28
• Summary endpoint for file (GET /file/summary).

Metadata

• Metadata for subject fields (GET /metadata/fields/subject).
  • All harmonized fields do the following:
    • Have harmonized: true.
    • Have the path pointing to the right location (e.g., disease_phase—not metadata.disease_phase).
    • Have the wiki_url pointing to the wiki (e.g., https://github.com/CBIIT/ccdi-federation-api/wiki/Sample-Metadata-Fields#disease_phase)
    • For fields that are backed by a CDE, standard has both the name of the standard (e.g., caDSR CDE 12217251 v1.00) and the backing URL for the standard (e.g., https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=12217251%20and%20ver_nr=1).
  • All unharmonized fields do the following:
    • Have harmonized: false.
    • Have a name.
    • Have the path pointing to the right location (e.g., unharmonized.foobar—not metadata.unharmonized.foobar).
    • Have either a url, description or both that describe the metadata field. Be as specific as possible, don't link to a general documentation page (linking within a particular documentation page where a metadata element's definition can be easily located is okay).

Namespaces

• Implements getting all namespaces (GET /namespace).
• Implements getting a particular namespace (GET /namespace/{organization}/{namespace}).

Organizations

• Implements getting all organizations (GET /organization).
• Implements getting a particular organization (GET /organization/{name}).

Information

• Implements the all information endpoint (GET /info).

Other

• Have production URL serving the API.
• Update URL to ensure it's v1 instead of v0.