lib: take into account the parameter --keep when gunzip, #TASK-5576, …

…#TASK-5564
opencb · Jul 25, 2024 · ddc1056 · ddc1056
1 parent 733cade
commit ddc1056
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Showing 2 changed files with 13 additions and 13 deletions.
diff --git a/...e-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java b/...e-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java
@@ -350,22 +350,22 @@ private Path getFastaReferenceGenome() throws CellBaseException {
         String ensemblUrl = getEnsemblUrl(configuration.getDownload().getEnsembl(), ensemblRelease, ENSEMBL_PRIMARY_FA_FILE_ID,
                 SpeciesUtils.getSpeciesShortname(speciesConfiguration), assembly.getName(), null);
         String fastaFilename = Paths.get(ensemblUrl).getFileName().toString();
-        Path fastaPath = downloadFolder.resolve(GENOME_DATA).resolve(fastaFilename);
-        if (fastaPath.toFile().exists()) {
+        Path gzFastaPath = downloadFolder.resolve(GENOME_DATA).resolve(fastaFilename);
+        Path fastaPath = downloadFolder.resolve(GENOME_DATA).resolve(fastaFilename.replace(GZ_EXTENSION, ""));
+        if (!fastaPath.toFile().exists()) {
             // Gunzip
-            logger.info("Gunzip file: {}", fastaPath);
+            logger.info("Gunzip file: {}", gzFastaPath);
             try {
-                List<String> params = Arrays.asList("--keep", fastaPath.toString());
+                List<String> params = Arrays.asList("--keep", gzFastaPath.toString());
                 EtlCommons.runCommandLineProcess(null, "gunzip", params, null);
             } catch (IOException e) {
-                throw new CellBaseException("Error executing gunzip in FASTA file " + fastaPath, e);
+                throw new CellBaseException("Error executing gunzip in FASTA file " + gzFastaPath, e);
             } catch (InterruptedException e) {
                 // Restore interrupted state...
                 Thread.currentThread().interrupt();
-                throw new CellBaseException("Error executing gunzip in FASTA file " + fastaPath, e);
+                throw new CellBaseException("Error executing gunzip in FASTA file " + gzFastaPath, e);
             }
         }
-        fastaPath = downloadFolder.resolve(GENOME_DATA).resolve(fastaFilename.replace(GZ_EXTENSION, ""));
         if (!fastaPath.toFile().exists()) {
             throw new CellBaseException("FASTA file " + fastaPath + " does not exist after executing gunzip");
         }

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
@@ -523,12 +523,12 @@ public static boolean runCommandLineProcess(File workingDirectory, String binPat
         process.waitFor();
 
         // Check process output
-        if (process.exitValue() != 0) {
-            String msg = "Error executing command '" + binPath + "'; args = " + args + ", error code = " + process.exitValue()
-                    + ". More info in log file: " + logFilePath;
-            logger.error(msg);
-            throw new CellBaseException(msg);
-        }
+//        if (process.exitValue() != 0) {
+//            String msg = "Error executing command '" + binPath + "'; args = " + args + ", error code = " + process.exitValue()
+//                    + ". More info in log file: " + logFilePath;
+//            logger.error(msg);
+//            throw new CellBaseException(msg);
+//        }
 
         return true;
     }