Refactoring of all SequenceAnnotation web services

[jabaws.git] / engine / compbio / engine / client / EnvVariableProcessor.java

diff --git a/engine/compbio/engine/client/EnvVariableProcessor.java b/engine/compbio/engine/client/EnvVariableProcessor.java
index b968857..3423c8f 100644 (file)
--- a/engine/compbio/engine/client/EnvVariableProcessor.java
+++ b/engine/compbio/engine/client/EnvVariableProcessor.java
@@ -49,7 +49,7 @@ public class EnvVariableProcessor {
                if (containsMultipleVariables(property)) {\r
                        return property.split(NEXT_ENV_PROPERTY_DELIMITER);\r
                }\r
-               return new String[] { property };\r
+               return new String[]{property};\r
        }\r
 \r
        static String getEnvVariableName(String property) {\r
@@ -92,6 +92,7 @@ public class EnvVariableProcessor {
         */\r
        private final static String mafft_binaries = "MAFFT_BINARIES";\r
        private final static String fasta4mafft = "FASTA_4_MAFFT";\r
+       private final static String iupred_path = "IUPred_PATH";\r
 \r
        public static Map<String, String> getEnvVariables(String property,\r
                        Class<?> clazz) {\r
@@ -101,12 +102,11 @@ public class EnvVariableProcessor {
                }\r
                for (String evar : getEnvVariableList(property)) {\r
                        if (!isValidEnvVariableProperty(evar)) {\r
-                               log\r
-                                               .error(clazz.getName()\r
-                                                               + " environment variable is specified by is NOT VALID! Skipping. "\r
-                                                               + "Valid format is propertyName"\r
-                                                               + PROP_NAME_VALUE_SEPARATOR + "propertyValue. "\r
-                                                               + "Given values is: " + evar);\r
+                               log.error(clazz.getName()\r
+                                               + " environment variable is specified by is NOT VALID! Skipping. "\r
+                                               + "Valid format is propertyName"\r
+                                               + PROP_NAME_VALUE_SEPARATOR + "propertyValue. "\r
+                                               + "Given values is: " + evar);\r
                        }\r
                        String varName = getEnvVariableName(evar);\r
                        String varValue = getEnvVariableValue(evar);\r
@@ -114,7 +114,8 @@ public class EnvVariableProcessor {
                        if (!PathValidator.isAbsolutePath(varValue)) {\r
                                varName = varName.trim();\r
                                if (varName.equalsIgnoreCase(mafft_binaries)\r
-                                               || varName.equalsIgnoreCase(fasta4mafft)) {\r
+                                               || varName.equalsIgnoreCase(fasta4mafft)\r
+                                               || varName.equalsIgnoreCase(iupred_path)) {\r
                                        varValue = compbio.engine.client.Util\r
                                                        .convertToAbsolute(varValue);\r
                                }\r