EVA-3933 Add script to read variant ids from a file and do the annotation remediatioin#206
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nitin-ebi merged 3 commits intoEBIvariation:masterfrom Mar 31, 2026
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| for (Map.Entry<String, String> entry : orgIdNewIdMap.entrySet()) { | ||
| regexCriteria.add(Criteria.where("_id").regex("^" + Pattern.quote(entry.getKey()) + "_\\d")) | ||
| regexCriteria.add(Criteria.where("_id").regex("^" + Pattern.quote(entry.getValue()) + "_\\d")) | ||
| } |
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Why not make two query per batch so that you know which one is old and which one is new?
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| // Group fetched annotation documents by variant id prefix (both old and new ids) | ||
| Map<String, Set<Document>> variantIdToDocuments = new HashMap<>() | ||
| for (Document doc : annotationsList) { |
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I might missunderstand this but it seems that for each annotation you go through all the document which would be 1000 * 1000 operations
Wouldn't it be simpler to derive the oldVariantId and newVariantId from the id by removing the end and match with that?
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| void storeNotRemediatedVariant(String oldVariantId, String newVariantId, String reason) { | ||
| try (BufferedWriter writer = new BufferedWriter(new FileWriter(notRemediatedVariantsFilePath, true))) { |
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Do we need to open the file every time? If we have a lot of failure it could take a while.
apriltuesday
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