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feat: CLIN-5494 Safe parse OMIM phenotypes attributes #284

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Merged
emmanuelnau merged 4 commits into from
Jan 22, 2026
Merged

feat: CLIN-5494 Safe parse OMIM phenotypes attributes #284

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779172c
feat: CLIN-5494 Safe parse OMIM phenotypes attributes
emmanuelnau Jan 16, 2026
bf2032c
feat: CLIN-5494 Add doc for local publish
emmanuelnau Jan 21, 2026
1066a5b
feat: CLIN-5494 Revert regex changes to use a dedicated regex + test
emmanuelnau Jan 21, 2026
d572279
feat: CLIN-5494 Update regex, to match genemap2-parser parsing
emmanuelnau Jan 22, 2026
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8 changes: 6 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,11 @@ The following table lists the versions supported of the main dependencies
| datalake-spark3 | `3.2.2` | `1.2.0` | `1.2.1` | `2.12` `2.13` | `1.0.6` |

## release

```
```shell
sbt "publishSigned; sonatypeRelease"
```

## local release
```shell
sbt VERSION=14.14.2-SNAPSHOT sbt publishLocal
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@creativeyann17 creativeyann17 Jan 21, 2026

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👍

```
8 changes: 5 additions & 3 deletions ...rc/main/scala/bio/ferlab/datalake/spark3/publictables/normalized/omim/OmimPhenotype.scala
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Expand Up @@ -51,12 +51,14 @@ object OmimPhenotype {
val parse_pheno: UserDefinedFunction = udf { raw: String =>
raw match {
case pheno_regexp(name, omim_id, inheritance) =>
val omimIdValue: Option[String] = Option(omim_id)
val inheritanceValue: Option[String] = Option(inheritance)
Some(
OmimPhenotype(
name.replace("{", "").replace("}", "").trim,
omim_id.trim,
mapInheritance(inheritance),
mapInheritanceCode(inheritance)
omimIdValue.map(_.trim).getOrElse(""),
mapInheritance(inheritanceValue.map(_.trim).orNull),
mapInheritanceCode(inheritanceValue.map(_.trim).orNull)
)
)
case _ => None
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