Import flat file (CSV)

Import flat file via REST

If you have a terminology distributed as a flat file, for example CSV, you can use this API to import it as a set of Concept resources and later use them with Terminology API.

Concepts should have unique code property. In this regard Aidbox follows FHIR constraints defined for CodeSystems. If there are multiple Concepts with the same code, only the last one will be loaded.

Import by URL

Aidbox provides RPC API to load terminology from a flat file by url.

RPC `aidbox.terminology.import-flat/import-from-url`

This method accepts an URL pointing to a flat file with a terminology, file format description, columns to concept mapping, CodeSystem resource and ValueSet resource. For hierarchical terminology it can build hierarchy materialized paths.

When upload is done, rows of the flat file are loaded as Concept resources into Aidbox. Also CodeSystem and ValueSet resources are created, these resources describe the full terminology from the file, i.e. the ValueSet composed of only this CodeSystem and all Concepts have system set to the CodeSystem.url.

Also check "Request with comments" and "Parameters" tabs for the full request structure description.

POST /rpc
content-type: application/edn
accept: application/edn

{:method aidbox.terminology.import-flat/import-from-url
 :params
 {:source-url "<https://example.com/path/to/your/file.csv>"

  :format "csv"
  :csv-format {:delimiter "<char>"
               :quote "<char>"}

  :header     <true|false>
  :header-row <integer>
  :data-row   <integer>
  :hierarchy  <true|false>

  ;; If `:header true` put the <column> as a string,
  ;; otherwise put an integer as a column index (indexing starts with 0)
  :mapping {:concept {:code        {:column <column>}
                      :display     {:column <column>}
                      :deprecated? {:column <column>
                                    :true-values ["<string>"]}
                      :parent-id    {:column <column>}
                      :hierarchy-id {:column <column>}}
            :property {"<property-name>" {:column <column>}}}

  :code-system {:url "<CodeSystem url>"}
  :value-set {:url "<ValueSet url>"}}}

Request structure with commentaries. (The "Parameters" tab contains the same comments in a different format)

POST /rpc
content-type: application/edn
accept: application/edn

{:method aidbox.terminology.import-flat/import-from-url
 :params
 {:source-url "<https://example.com/path/to/your/file.csv>" ;; Required. URL pointing to a flat file

  :format "csv" ;; Required. Currently the only option is csv
  :csv-format {:delimiter "<char>" ;; Required. Value separator character
               :quote "<char>"}   ;; Required. Quote character used to wrap values which contain delimiter or new-line characters

  :code-system {;; Required. CodeSystem resource. Aidbox creates this resource
                :url "<CodeSystem url>"} ;; Required. CodeSystem canonical URL
  :value-set {;; Required. ValueSet resource. Aidbox creates this resource
              :url "<ValueSet url>"} ;; Required. ValueSet canonical URL

  :header <true|false> ;; Required. Set true if the flat file contains header, otherwise false
  :header-row <integer> ;; Required if `:header true`. The flat file header row index. Row indexing starts with 0
  :data-row <integer> ;; Required. Index of the first row where data starts in the flat file
  :hierarchy <true|false> ;; Optional. Set true if terminology is hierarchical. If true Aidbox builds hierarchy materialized paths for each concept

  :mapping {;; Required. Mapping of the flat file columns to Concept resource.
            ;; If `:header true` put the <column> as a string, otherwise put an integer as a column index (indexing starts with 0)
            :concept {;; Required. Maps to main part of a Concept resource.
                      :code {:column <column>} ;; Required. Maps to Concept.code
                      :display {:column <column>} ;; Optional. Maps to Concept.display
                      :deprecated? {:column <column> ;; Optional. Maps to Concept.deprecated
                                    :true-values ["<string>"]} ;; Required if `:deprecated? :column` specified. List of values indicating that a Concept is deprecated. For example: :true-values ["inactive" "deprecated"]
                      :parent-id {:column <column>} ;; Required if `:hierarchy true`. Maps to Concept.parent-id. Aidbox uses this value to find parent Concepts when building materialized paths
                      :hierarchy-id {:column <column>}} ;; Required if `:hierarchy true`. Maps to Concept.hierarchy-id. Aidbox uses this value to check if this Concept is a parent when building materialized paths
            :property {;; Optional. Maps to Concept.property.<property-name>
                       "<property-name>" {:column <column>}}}}} ;; Reference to the flat file column.

Object with the following structure:

source-url - Required. URL pointing to a flat file
format - Required. Currently the only option is "csv"
csv-format - Required. Describes parameters of the csv-file:
- delimiter - Required. Value separator character
- quote - Required. Quote character used to wrap values which contain delimiter or new-line characters
code-system - Required. CodeSystem resource. Aidbox creates this resource
- url - Required. CodeSystem canonical URL
value-set - Required. ValueSet resource. Aidbox creates this resource
- url - Required. ValueSet canonical URL
header - Required. Set true if the flat file contains header, otherwise false
header-row - Required if header true. The flat file header row index. Row indexing starts with 0
data-row - Required. Index of the first row where data starts in the flat file
hierarchy - Optional. Set true if terminology is hierarchical. If true Aidbox builds hierarchy materialized paths for each concept
mapping - Required. Mapping of the flat file columns to Concept resource. If header true put the column as a string, otherwise put an integer as a column index (indexing starts with 0)
- concept Required. Maps to main part of a Concept resource.
  - code
    column - Required. Maps to Concept.code
  - display
    column - Optional. Maps to Concept.display
  - deprecated?
    column - Optional. Maps to Concept.deprecated
    true-values - Required if deprecated? <column> specified. List of values indicating that a Concept is deprecated. For example: :true-values ["inactive" "deprecated"]
  - parent-id - Required if hierarchy true. Maps to Concept.parent-id. Aidbox uses this value to find parent Concepts when building materialized paths
  - hierarchy-id - Required if hierarchy true. Maps to Concept.hierarchy-id. Aidbox uses this value to check if this Concept is a parent when building materialized paths
- property Optional. Maps to Concept.property.<property-name>
  - <property-name>
    column - Reference to the flat file column.

Returns object with following attributes:

{:result
  {:count <count of records in the file>,
   :code-system-id <"generated code system uuid">,
   :value-set-id <"generated value set uuid">}}

Examples

Here are 2 examples importing a fragment of ICD-10. The first one specifies as few parameters as possible and uses a CSV file without a header. The second one uses a CSV with a header and also specifies a deprecation criteria, hierarchy parameters and a concept properties mapping. Both examples have commentaries of used parameters and contents of imported CSV files.

CSV file delimiter is ;.This file contains no quoted strings, but since :quote parameter is required ' character is used
This file contains no header and data starts at the row 0.
Concept.code is mapped to the column with the index 2
Concept.display is mapped to the column with the index 3
Request will create
- a CodeSystem/icd10 resource with :url http://hl7.org/fhir/sid/icd-10
- a ValueSet/icd10 resource with :url http://hl7.org/fhir/ValueSet/icd-10

Request

POST /rpc
accept: application/edn
content-type: application/edn

{:method aidbox.terminology.import-flat/import-from-url
 :params
 {:source-url "https://storage.googleapis.com/aidbox-public/documentation/icd10_example_no_header.csv"
  :format      "csv"
  :csv-format  {:delimiter ";"
                :quote "'"}

  :header   false
  :data-row 0
  :mapping  {:concept {:code    {:column 2}
                       :display {:column 3}}}

  :code-system {:id "icd10", :url "http://hl7.org/fhir/sid/icd-10"}
  :value-set   {:id "icd10", :url "http://hl7.org/fhir/ValueSet/icd-10"}}}

Response:

{:result
  {:count 8,
   :code-system-id "0be7ce48-edab-497c-bb52-186a9ac64746",
   :value-set-id "f4418460-cdac-4847-99be-6ae4c3a64e87"}}

CSV file content

File is also available here

10344;20;XX;External causes of morbidity and mortality;;;1;
16003;2001;V01-X59;Accidents;10344;;1;
15062;20012;W00-X59;Other external causes of accidental injury;16003;;1;10/07/2020
11748;2001203;W50-W64;Exposure to animate mechanical forces;15062;;1;
11870;2001203W64;W64;Exposure to other and unspecified animate mechanical forces;11748;;1;
11871;2001203W640;W64.0;Exposure to other and unspecified animate mechanical forces home while engaged in sports activity;11870;;1;
11872;2001203W641;W64.00;Exposure to other and unspecified animate mechanical forces, home, while engaged in sports activity;11871;;1;
11873;2001203W641;W64.01;Exposure to other and unspecified animate mechanical forces, home, while engaged in leisure activity;11871;;1;

Imported Concept resources

Loaded resources sample (some output parts are omitted)

[{:resourceType "Concept"
  :code "XX"
  :display "External causes of morbidity and mortality"
  :system "http://hl7.org/fhir/sid/icd-10"
  ...}
 ...
 {:resourceType "Concept"
  :code "W00-X59"
  :display "Other external causes of accidental injury"
  :system "http://hl7.org/fhir/sid/icd-10"
  ...}
 ...
 {:resourceType "Concept"
  :code "W64.01"
  :display "Exposure to other and unspecified animate mechanical forces, home, while engaged in leisure activity"
  :system "http://hl7.org/fhir/sid/icd-10"
  ...}]

Value delimiter is , and string quotation is "
Header is in the first row (index is 0) and data starts at the next row (index 1)
Materialized paths building is enabled, thus :hierarchy true
- Column ID_PARENT is used to find parents
- Column ID is used to resolve when a row is referenced as a parent
Concept.code is mapped to the column with name ICD_CODE
Concept.display is mapped to the column with index ICD_NAME
Concepts are deprecated when the ACTIVE column value is 0
Concept.property.updated_date is mapped to the DATE column
Request will create
- a CodeSystem/icd10 resource with :url http://hl7.org/fhir/sid/icd-10
- a ValueSet/icd10 resource with :url http://hl7.org/fhir/ValueSet/icd-10

Example

POST /rpc
accept: application/edn
content-type: application/edn

{:method aidbox.terminology.import-flat/import-from-url
 :params
 {:source-url  "https://storage.googleapis.com/aidbox-public/documentation/icd10_example_w_header.csv"
  :format      "csv"
  :csv-format  {:delimiter ","
                :quote "\""}

  :header      true
  :header-row  0
  :data-row    1
  :hierarchy   true
  :mapping     {:concept {:code        {:column "ICD_CODE"}
                          :display     {:column "ICD_NAME"}
                          :deprecated? {:column "ACTIVE"
                                        :true-values ["0"]}
                          :parent-id    {:column "ID_PARENT"}
                          :hierarchy-id {:column "ID"}}
                :property {"updated_date" {:column "DATE"}}}

  :code-system {:id "icd10", :url "http://hl7.org/fhir/sid/icd-10"}
  :value-set   {:id "icd10", :url "http://hl7.org/fhir/ValueSet/icd-10"}}}

Response

{:result
  {:count 8,
   :code-system-id "5b56b672-7220-4878-96f6-254df0128a43",
   :value-set-id "170d0ce8-0dc3-4bd1-8465-5e584955105e"}}