{
  "opencollection": "1.0.0",
  "info": {
    "name": "Girder REST API (Emory Digital Slide Archive) annotation tcga API",
    "version": "3.2.14"
  },
  "items": [
    {
      "info": {
        "name": "tcga",
        "type": "folder"
      },
      "items": [
        {
          "info": {
            "name": "Get the TCGA collection",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga"
          },
          "docs": "Get the TCGA collection"
        },
        {
          "info": {
            "name": "Set the TCGA collection",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga",
            "params": [
              {
                "name": "collectionId",
                "value": "",
                "type": "query",
                "description": "The id of the collection"
              }
            ]
          },
          "docs": "Set the TCGA collection"
        },
        {
          "info": {
            "name": "Remove the TCGA collection",
            "type": "http"
          },
          "http": {
            "method": "DELETE",
            "url": "https://computablebrain.emory.edu/api/v1/tcga"
          },
          "docs": "Remove the TCGA collection"
        },
        {
          "info": {
            "name": "Import an item as an Aperio annotation",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/aperio",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "query",
                "description": "The id of the item or root to import"
              },
              {
                "name": "tag",
                "value": "",
                "type": "query",
                "description": "Import annotations with this tag"
              },
              {
                "name": "recursive",
                "value": "",
                "type": "query",
                "description": "Perform a recursive search for annotations"
              }
            ]
          },
          "docs": "Import an item as an Aperio annotation"
        },
        {
          "info": {
            "name": "List cases in the TCGA dataset",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case",
            "params": [
              {
                "name": "cohort",
                "value": "",
                "type": "query",
                "description": "The id of the cohort document"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "List cases in the TCGA dataset"
        },
        {
          "info": {
            "name": "Import a folder as a TCGA case",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case",
            "params": [
              {
                "name": "folderId",
                "value": "",
                "type": "query",
                "description": "The id of the folder to import"
              }
            ]
          },
          "docs": "Import a folder as a TCGA case"
        },
        {
          "info": {
            "name": "Get a case document from a label",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/label/:label",
            "params": [
              {
                "name": "label",
                "value": "",
                "type": "path",
                "description": "The label of the case"
              }
            ]
          },
          "docs": "Get a case document from a label"
        },
        {
          "info": {
            "name": "Search for cases by clinical data",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/search",
            "params": [
              {
                "name": "table",
                "value": "",
                "type": "query",
                "description": "A table to search"
              },
              {
                "name": "key",
                "value": "",
                "type": "query",
                "description": "A key that should be present"
              },
              {
                "name": "value",
                "value": "",
                "type": "query",
                "description": "The value associated with the given key"
              },
              {
                "name": "substring",
                "value": "",
                "type": "query",
                "description": "Find values containing this substring"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "Only one of \"value\" or \"substring\" may be provided."
        },
        {
          "info": {
            "name": "Get a case document from an id",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              }
            ]
          },
          "docs": "Get a case document from an id"
        },
        {
          "info": {
            "name": "Remove a case document",
            "type": "http"
          },
          "http": {
            "method": "DELETE",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              }
            ]
          },
          "docs": "Remove a case document"
        },
        {
          "info": {
            "name": "List images under a case",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id/images",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "List images under a case"
        },
        {
          "info": {
            "name": "List tables present inside case metadata",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id/metadata/tables",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              }
            ]
          },
          "docs": "List tables present inside case metadata"
        },
        {
          "info": {
            "name": "Get case metadata",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id/metadata/:table",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              },
              {
                "name": "table",
                "value": "",
                "type": "path",
                "description": "The table name to get"
              }
            ]
          },
          "docs": "Get case metadata"
        },
        {
          "info": {
            "name": "Create or replace case metadata",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id/metadata/:table",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              },
              {
                "name": "table",
                "value": "",
                "type": "path",
                "description": "The table to update"
              }
            ],
            "body": {
              "type": "json",
              "data": "{}"
            }
          },
          "docs": "Create or replace case metadata"
        },
        {
          "info": {
            "name": "Update case metadata",
            "type": "http"
          },
          "http": {
            "method": "PUT",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id/metadata/:table",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              },
              {
                "name": "table",
                "value": "",
                "type": "path",
                "description": "The table to update"
              }
            ],
            "body": {
              "type": "json",
              "data": "{}"
            }
          },
          "docs": "Set metadata fields to null to delete them."
        },
        {
          "info": {
            "name": "Delete case metadata",
            "type": "http"
          },
          "http": {
            "method": "DELETE",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/case/:id/metadata/:table",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the case"
              },
              {
                "name": "table",
                "value": "",
                "type": "path",
                "description": "The table to remove"
              }
            ]
          },
          "docs": "Delete case metadata"
        },
        {
          "info": {
            "name": "List cohorts in the TCGA dataset",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/cohort",
            "params": [
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "List cohorts in the TCGA dataset"
        },
        {
          "info": {
            "name": "Import a folder as a TCGA cohort type",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/cohort",
            "params": [
              {
                "name": "folderId",
                "value": "",
                "type": "query",
                "description": "The id of the folder to import"
              }
            ]
          },
          "docs": "Import a folder as a TCGA cohort type"
        },
        {
          "info": {
            "name": "Get a cohort document from an id",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/cohort/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the cohort"
              }
            ]
          },
          "docs": "Get a cohort document from an id"
        },
        {
          "info": {
            "name": "Remove a cohort type",
            "type": "http"
          },
          "http": {
            "method": "DELETE",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/cohort/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the cohort"
              }
            ]
          },
          "docs": "Remove a cohort type"
        },
        {
          "info": {
            "name": "List slide images in a cohort",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/cohort/:id/images",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the cohort"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "List slide images in a cohort"
        },
        {
          "info": {
            "name": "List slides in a cohort",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/cohort/:id/slides",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the cohort"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "List slides in a cohort"
        },
        {
          "info": {
            "name": "Find images",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/image",
            "params": [
              {
                "name": "slide",
                "value": "",
                "type": "query",
                "description": "The id of slide document"
              },
              {
                "name": "caseName",
                "value": "",
                "type": "query",
                "description": "The name of the case"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "Find images"
        },
        {
          "info": {
            "name": "Import an item as a TCGA slide image",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/image",
            "params": [
              {
                "name": "itemId",
                "value": "",
                "type": "query",
                "description": "The id of the item to import"
              }
            ]
          },
          "docs": "Import an item as a TCGA slide image"
        },
        {
          "info": {
            "name": "Get an image document by id",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/image/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the image"
              }
            ]
          },
          "docs": "Get an image document by id"
        },
        {
          "info": {
            "name": "Remove an image",
            "type": "http"
          },
          "http": {
            "method": "DELETE",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/image/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the image"
              }
            ]
          },
          "docs": "Remove an image"
        },
        {
          "info": {
            "name": "Recursively import the TCGA collection",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/import"
          },
          "docs": "This will run as a local job that will execute asynchronously."
        },
        {
          "info": {
            "name": "Find pathologies for a case",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/pathology",
            "params": [
              {
                "name": "case",
                "value": "",
                "type": "query",
                "description": "The id of a case document"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "Find pathologies for a case"
        },
        {
          "info": {
            "name": "Import an item as a TCGA pathology",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/pathology",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "query",
                "description": "The id of the item to import"
              },
              {
                "name": "recursive",
                "value": "",
                "type": "query",
                "description": "Perform a recursive search for pathologies"
              }
            ]
          },
          "docs": "Import an item as a TCGA pathology"
        },
        {
          "info": {
            "name": "Get a pathology document by id",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/pathology/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the pathology"
              }
            ]
          },
          "docs": "Get a pathology document by id"
        },
        {
          "info": {
            "name": "Remove a pathology",
            "type": "http"
          },
          "http": {
            "method": "DELETE",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/pathology/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the pathology"
              }
            ]
          },
          "docs": "Remove a pathology"
        },
        {
          "info": {
            "name": "Find slides for a case",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/slide",
            "params": [
              {
                "name": "case",
                "value": "",
                "type": "query",
                "description": "The id of case document"
              },
              {
                "name": "limit",
                "value": "",
                "type": "query",
                "description": "Result set size limit."
              },
              {
                "name": "offset",
                "value": "",
                "type": "query",
                "description": "Offset into result set."
              },
              {
                "name": "sort",
                "value": "",
                "type": "query",
                "description": "Field to sort the result set by."
              },
              {
                "name": "sortdir",
                "value": "",
                "type": "query",
                "description": "Sort order: 1 for ascending, -1 for descending."
              }
            ]
          },
          "docs": "Find slides for a case"
        },
        {
          "info": {
            "name": "Import a folder as a TCGA slide",
            "type": "http"
          },
          "http": {
            "method": "POST",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/slide",
            "params": [
              {
                "name": "folderId",
                "value": "",
                "type": "query",
                "description": "The id of the folder to import"
              }
            ]
          },
          "docs": "Import a folder as a TCGA slide"
        },
        {
          "info": {
            "name": "Get a slide document by id",
            "type": "http"
          },
          "http": {
            "method": "GET",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/slide/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the slide"
              }
            ]
          },
          "docs": "Get a slide document by id"
        },
        {
          "info": {
            "name": "Remove a slide",
            "type": "http"
          },
          "http": {
            "method": "DELETE",
            "url": "https://computablebrain.emory.edu/api/v1/tcga/slide/:id",
            "params": [
              {
                "name": "id",
                "value": "",
                "type": "path",
                "description": "The id of the slide"
              }
            ]
          },
          "docs": "Remove a slide"
        }
      ]
    }
  ],
  "bundled": true
}