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124 changes: 124 additions & 0 deletions
124
gemma-core/src/main/java/ubic/gemma/core/analysis/service/AbstractFileService.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,124 @@ | ||
| package ubic.gemma.core.analysis.service; | ||
|
|
||
| import com.fasterxml.jackson.databind.ObjectMapper; | ||
| import org.apache.commons.csv.CSVFormat; | ||
| import org.apache.commons.lang3.ArrayUtils; | ||
|
|
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| import javax.annotation.Nullable; | ||
| import java.io.*; | ||
| import java.math.RoundingMode; | ||
| import java.text.DecimalFormat; | ||
| import java.text.DecimalFormatSymbols; | ||
| import java.util.Locale; | ||
|
|
||
| /** | ||
| * Provide base implementation for all sorts of file services that serialize data in tabular format. | ||
| */ | ||
| public abstract class AbstractFileService<T> implements TsvFileService<T>, JsonFileService<T> { | ||
|
|
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| private final ObjectMapper objectMapper = new ObjectMapper(); | ||
|
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| private static final DecimalFormat smallNumberFormat, midNumberFormat, largeNumberFormat; | ||
|
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| static { | ||
| DecimalFormatSymbols symbols = DecimalFormatSymbols.getInstance( Locale.ENGLISH ); | ||
| symbols.setNaN( "" ); | ||
| symbols.setInfinity( "inf" ); | ||
|
|
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| // show 4 significant digits | ||
| smallNumberFormat = new DecimalFormat( "0.###E0" ); | ||
| smallNumberFormat.setDecimalFormatSymbols( symbols ); | ||
| smallNumberFormat.setRoundingMode( RoundingMode.HALF_UP ); | ||
|
|
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| // show from one up to 4 decimal places | ||
| midNumberFormat = new DecimalFormat( "0.0###" ); | ||
| midNumberFormat.setDecimalFormatSymbols( symbols ); | ||
| midNumberFormat.setRoundingMode( RoundingMode.HALF_UP ); | ||
|
|
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| // only show leading digits and at least one decimal place | ||
| largeNumberFormat = new DecimalFormat( "0.0" ); | ||
| largeNumberFormat.setDecimalFormatSymbols( symbols ); | ||
| largeNumberFormat.setRoundingMode( RoundingMode.HALF_UP ); | ||
| } | ||
|
|
||
| /** | ||
| * Preconfigure a {@link CSVFormat.Builder} with desirable defaults. | ||
| * @param extraHeaderComments additional header comments that will be included at the top of the TSV file. | ||
| */ | ||
| protected CSVFormat.Builder getTsvFormatBuilder( String... extraHeaderComments ) { | ||
| return CSVFormat.Builder.create( CSVFormat.TDF ) | ||
| .setCommentMarker( '#' ) | ||
| .setHeaderComments( ArrayUtils.addAll( new String[] { | ||
| "If you use this file for your research, please cite:", | ||
| "Lim et al. (2021) Curation of over 10 000 transcriptomic studies to enable data reuse.", | ||
| "Database, baab006 (doi:10.1093/database/baab006)." }, extraHeaderComments ) ); | ||
| } | ||
|
|
||
| /** | ||
| * Get the delimiter used within column. | ||
| */ | ||
| protected String getSubDelimiter() { | ||
| return "|"; | ||
| } | ||
|
|
||
| /** | ||
| * Format a {@link Double} for TSV. | ||
| * @param d a double to format | ||
| * @return a formatted double, an empty string if d is null or NaN or inf/-inf if infinite | ||
| */ | ||
| protected String format( @Nullable Double d ) { | ||
| if ( d == null ) { | ||
| return ""; | ||
| } else if ( d < 1e-4 ) { | ||
| return smallNumberFormat.format( d ); | ||
| } else if ( d < 1e3 ) { | ||
| return midNumberFormat.format( d ); | ||
| } else { | ||
| return largeNumberFormat.format( d ); | ||
| } | ||
| } | ||
|
|
||
| protected String escapeTsv( String s ) { | ||
| return s.replace( "\\", "\\\\" ) | ||
| .replace( "\n", "\\n" ) | ||
| .replace( "\t", "\\t" ) | ||
| .replace( "\r", "\\r" ); | ||
| } | ||
|
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| @Override | ||
| public void writeTsv( T entity, File file ) throws IOException { | ||
| try ( Writer writer = new OutputStreamWriter( new FileOutputStream( file ) ) ) { | ||
| writeTsv( entity, writer ); | ||
| } | ||
| } | ||
|
|
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| @Override | ||
| public void writeJson( T entity, Writer writer ) throws IOException { | ||
| objectMapper.writeValue( writer, entity ); | ||
| } | ||
|
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| @Override | ||
| public void writeJson( T entity, File file ) throws IOException { | ||
| try ( Writer writer = new OutputStreamWriter( new FileOutputStream( file ) ) ) { | ||
| writeJson( entity, writer ); | ||
| } | ||
| } | ||
|
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| @Override | ||
| public void write( T entity, Writer writer, String contentType ) throws IOException { | ||
| if ( "application/json".equalsIgnoreCase( contentType ) ) { | ||
| writeJson( entity, writer ); | ||
| } else if ( "text/tab-separated-values".equalsIgnoreCase( contentType ) ) { | ||
| writeTsv( entity, writer ); | ||
| } else { | ||
| throw new IllegalArgumentException( "Unsupported content type: " + contentType ); | ||
| } | ||
| } | ||
|
|
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| @Override | ||
| public void write( T entity, File file, String contentType ) throws IOException { | ||
| try ( Writer writer = new OutputStreamWriter( new FileOutputStream( file ) ) ) { | ||
| write( entity, writer, contentType ); | ||
| } | ||
| } | ||
| } |
59 changes: 0 additions & 59 deletions
59
gemma-core/src/main/java/ubic/gemma/core/analysis/service/AbstractTsvFileService.java
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