diff --git a/.github/agents/main-release.agent.md b/.github/agents/main-release.agent.md new file mode 100644 index 0000000..c3d89e9 --- /dev/null +++ b/.github/agents/main-release.agent.md @@ -0,0 +1,19 @@ +--- +# Fill in the fields below to create a basic custom agent for your repository. +# The Copilot CLI can be used for local testing: https://gh.io/customagents/cli +# To make this agent available, merge this file into the default repository branch. +# For format details, see: https://gh.io/customagents/config + +name: MainRelease +description: Updates the main NEWS.md looking at each vocabualy NEWS.md +--- + +# Main Release NEWS.md Update +1. Look at the diffs between the development branch and the main brach for all the NEWS.md files in each of the vocabularies' folders +2. Use this diffs to create a summary of the changes for each vocabulary since the last main release +3. Update the root NEWS.md file by + - Bumping the major version + - Indicate the project update reason given in the issue that triggered this agent + - For each vocabulary that has an update, a summary of the updates + - Follow the format in the previous releases in the NEWS.md file + diff --git a/.github/agents/my-agent.agent.md b/.github/agents/my-agent.agent.md new file mode 100644 index 0000000..1dbe84b --- /dev/null +++ b/.github/agents/my-agent.agent.md @@ -0,0 +1,50 @@ +--- +# Fill in the fields below to create a basic custom agent for your repository. +# The Copilot CLI can be used for local testing: https://gh.io/customagents/cli +# To make this agent available, merge this file into the default repository branch. +# For format details, see: https://gh.io/customagents/config + +name: Koodistopalvelu Update +description: Given a file from koodistopalvelu update the target vocabulary +--- + +# Koodistopalvelu Update +The aim of this agent is to find what codes in the source tables do not exists in the target vocabulary and then append them in the correct format. + +## Inputs +- **Source table**: The issue using this agent must have a .txt as an attachment file or a small table in markdown format in the issue. + If not other wise specify, the source .txt file is a table with semi-colon separated values and encoded as ISO-8859-1. +- **Target vocabulary**: The issue using this workflow must indicate what is target vocabulary. + The table for the target vocabulary must exists in the repository under the folder VOCABULARY//.usagi.csv. + This is a table in csv format with UTF-8 formating. + +## Steps +1. Validate that the target vocabulary exits. Stop and inform the user if this do not exists. +2. Validate that the source table has the following columns: CodeId, LongName, A:Long_name, BeginningDate, ExpiringDate, ParentId. +3. Find the rows from the source vocabulary with a CodeId that DO NOT exists in the target vocabulary table. +4. Take these codes found in previous step and append them to the target vocabulary table following this rules per each target column : + - sourceCode: CodeId + - sourceName: A:Long_name, If A:Long_name is empty, then take LongName, which is in Finnish and traslate it into English + - sourceFrequency: 0 + - matchScore: 0 + - mappingStatus: UNCHECKED + - equivalence: UNREVIEWED + - statusSetBy: column with the current issue number as #. + - statusSetOn: column with the current datetime in milliseconds as integer. + - conceptId: 0 + - conceptName: unmapped + - domainId: unmapped + - mappingType: MAPS_TO + - createdBy: Koodistopalvelu Update Agent + - createdOn: same as statusSetOn + - ADD_INFO:sourceConceptId: **this has to be a unic number, look at the larges ADD_INFO:sourceConceptId and increment it per each new row** + - ADD_INFO:sourceConceptClass: look as how this is encoded in the current target table and apply the same logic. + - ADD_INFO:sourceDomain: same as others in the target table. + - ADD_INFO:sourceValidStartDate: Date in BeginningDate formated as YYYY-MM-DD or empty if it isempty in the source table. + - ADD_INFO:sourceValidEndDate: Date in ExpiringDate formated as YYYY-MM-DD or empty if it is empty in the source table. + - ADD_INFO:sourceParents: ParentId +5. Make sure that for all the new rows the new sourceNames are in English and not if Finnish. If they are in Finnish translate them to English. +6. Update the NEWS.md file for the target vocabulary in VOCABULARY//NEWS.md. Increase the number in the .. version tag. Summaryse in one line the changens introduced, including, number of additions and date. + + + diff --git a/NEWS.md b/NEWS.md index 8078a09..a39666f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,19 @@ +# v4.0.0 +- Updated Athena vocabulary February 2026 +- Updated mappings for FGVisitType, ICD10fi, LABfi_ALL, NCSPfi, SPAT, UNITfi and VNRfi vocabularies +- FGVisitType: Added Spirometry visit and measurement codes with mappings; Source biobanks within Spirometry now have parent concept BIOBANK +- FGVisitType: Added seven drug registry source codes covering vaccination, rheuma, hospital administered and other drugs +- ICD10fi: Added 7 new codes from THL ICD-10 koodistopalvelu update +- LABfi_ALL: Major release for FinnGen DF14; source codes longer than 50 characters are now truncated +- NCSPfi: Added 362 new codes from NCSPfi 2026 March update; translated 305 Finnish sourceName values to English +- NCSPfi: Added 93 HUS imaging and 262 HUS heart operation codes mapped in PHEMS project +- NCSPfi: Fixed mapping of AA1AA from CT of head to Plain X-ray of head +- SPAT: Added 5 new SPAT codes (SPAT1416–SPAT1420) from koodistopalvelu update +- UNITfi: Minor fixes for FinnGen DF14 +- VNRfi: Added 239 new drugs, out of which 89 have been mapped; introduced dummy VNRs from 20 million range +- VNRfi: Dummy vaccination VNRs between 20000000 and 20000096 were mapped to ATC concept id + + # v3.0.0 - Updated Athena vocabulary August 2025 - Updated mappings for ICD8fi, ICD9fi, ICD10fi, NCSPfi, ICPC, LABfi, LABfi_ALL, MICROBEfi, MICROBEfi_TKU, SNOMED2fi and VNRfi vocabularies