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[ALS-7437] Switch study to dataset for concept node detail
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Luke Sikina
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Oct 10, 2024
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18 changes: 18 additions & 0 deletions
18
src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/Dataset.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| package edu.harvard.dbmi.avillach.dictionary.dataset; | ||
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| import jakarta.annotation.Nullable; | ||
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| import java.util.Map; | ||
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| public record Dataset( | ||
| String ref, String fullName, String abbreviation, String description, @Nullable Map<String, String> meta | ||
| ) { | ||
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| public Dataset(String ref, String fullName, String abbreviation, String description) { | ||
| this(ref, fullName, abbreviation, description, null); | ||
| } | ||
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| public Dataset withMeta(Map<String, String> meta) { | ||
| return new Dataset(ref, fullName, abbreviation, description, meta); | ||
| } | ||
| } |
18 changes: 18 additions & 0 deletions
18
src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetMapper.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| package edu.harvard.dbmi.avillach.dictionary.dataset; | ||
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| import org.springframework.jdbc.core.RowMapper; | ||
| import org.springframework.stereotype.Component; | ||
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| import java.sql.ResultSet; | ||
| import java.sql.SQLException; | ||
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| @Component | ||
| public class DatasetMapper implements RowMapper<Dataset> { | ||
| @Override | ||
| public Dataset mapRow(ResultSet rs, int rowNum) throws SQLException { | ||
| return new Dataset( | ||
| rs.getString("ref"), rs.getString("full_name"), | ||
| rs.getString("abbreviation"), rs.getString("description") | ||
| ); | ||
| } | ||
| } |
53 changes: 53 additions & 0 deletions
53
src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetRepository.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| package edu.harvard.dbmi.avillach.dictionary.dataset; | ||
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| import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; | ||
| import edu.harvard.dbmi.avillach.dictionary.util.MapExtractor; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; | ||
| import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; | ||
| import org.springframework.stereotype.Repository; | ||
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| import java.util.Map; | ||
| import java.util.Optional; | ||
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| @Repository | ||
| public class DatasetRepository { | ||
| private final NamedParameterJdbcTemplate template; | ||
| private final DatasetMapper mapper; | ||
| private final MapExtractor metaExtractor = new MapExtractor("key", "value"); | ||
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| @Autowired | ||
| public DatasetRepository(NamedParameterJdbcTemplate template, DatasetMapper mapper) { | ||
| this.template = template; | ||
| this.mapper = mapper; | ||
| } | ||
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| public Optional<Dataset> getDataset(String ref) { | ||
| String sql = """ | ||
| SELECT | ||
| ref, full_name, abbreviation, description | ||
| FROM | ||
| dataset | ||
| WHERE | ||
| dataset.REF = :ref | ||
| """; | ||
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| MapSqlParameterSource params = new MapSqlParameterSource().addValue("ref", ref); | ||
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| return template.query(sql, params, mapper).stream().findAny(); | ||
| } | ||
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| public Map<String, String> getDatasetMeta(String ref) { | ||
| String sql = """ | ||
| SELECT | ||
| key, value | ||
| FROM | ||
| dataset_meta | ||
| LEFT JOIN dataset ON dataset_meta.dataset_id = dataset.dataset_id | ||
| WHERE | ||
| dataset.REF = :ref | ||
| """; | ||
| MapSqlParameterSource params = new MapSqlParameterSource().addValue("ref", ref); | ||
| return template.query(sql, params, metaExtractor); | ||
| } | ||
| } |
24 changes: 24 additions & 0 deletions
24
src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetService.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| package edu.harvard.dbmi.avillach.dictionary.dataset; | ||
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| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.stereotype.Service; | ||
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| import java.util.Map; | ||
| import java.util.Optional; | ||
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| @Service | ||
| public class DatasetService { | ||
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| private final DatasetRepository repository; | ||
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| @Autowired | ||
| public DatasetService(DatasetRepository repository) { | ||
| this.repository = repository; | ||
| } | ||
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| public Optional<Dataset> getDataset(String ref) { | ||
| Map<String, String> meta = repository.getDatasetMeta(ref); | ||
| return repository.getDataset(ref).map(ds -> ds.withMeta(meta)); | ||
| } | ||
| } |
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