Fix conda channels ordering for gpt client

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
seqeralabs · May 19, 2024 · ed3c0be · ed3c0be
1 parent 08f3f56
commit ed3c0be
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/app/src/main/java/io/seqera/wave/cli/App.java b/app/src/main/java/io/seqera/wave/cli/App.java
@@ -82,6 +82,8 @@
         usageHelpAutoWidth = true)
 public class App implements Runnable {
 
+    static public final String DEFAULT_CONDA_CHANNELS = "conda-forge,bioconda";
+
     private static final org.slf4j.Logger log = LoggerFactory.getLogger(App.class);
 
     private static final boolean isWindows = System.getProperty("os.name").toLowerCase().contains("windows");
@@ -158,7 +160,7 @@ public class App implements Runnable {
     private List<String> condaRunCommands;
 
     @Option(names = {"--conda-channels"}, paramLabel = "''", description = "Conda channels used to build the container (default: ${DEFAULT-VALUE}).")
-    private String condaChannels = "conda-forge,bioconda";
+    private String condaChannels = DEFAULT_CONDA_CHANNELS;
 
     @Option(names = {"--spack-file"}, paramLabel = "''",  description = "A Spack file used to build the container e.g. /some/path/spack.yaml.")
     private String spackFile;

diff --git a/app/src/main/java/io/seqera/wave/cli/util/GptHelper.java b/app/src/main/java/io/seqera/wave/cli/util/GptHelper.java
@@ -18,6 +18,7 @@
 package io.seqera.wave.cli.util;
 
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
@@ -29,6 +30,7 @@
 import dev.langchain4j.model.openai.OpenAiChatModel;
 import dev.langchain4j.model.output.Response;
 import io.seqera.wave.api.PackagesSpec;
+import io.seqera.wave.cli.App;
 import io.seqera.wave.cli.exception.BadClientResponseException;
 import io.seqera.wave.cli.json.JsonHelper;
 import org.apache.commons.lang3.StringUtils;
@@ -117,7 +119,7 @@ static protected PackagesSpec jsonToPackageSpec(String json) {
                 throw new IllegalArgumentException("Unable to resolve packages from json response: " + json);
             List<String> channels = (List<String>) object.get("channels");
             if( Checkers.isEmpty(channels) )
-                channels = List.of("bioconda","conda-forge");
+                channels = Arrays.asList(App.DEFAULT_CONDA_CHANNELS.split(","));
             return new PackagesSpec()
                     .withType(PackagesSpec.Type.CONDA)
                     .withEntries(packages)