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[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..5d161df 100644 (file)
--- a/engine/compbio/engine/client/EnvVariableProcessor.java
+++ b/engine/compbio/engine/client/EnvVariableProcessor.java
@@ -18,6 +18,7 @@
 \r
 package compbio.engine.client;\r
 \r
+import java.util.Arrays;\r
 import java.util.Collections;\r
 import java.util.Map;\r
 \r
@@ -46,10 +47,11 @@ public class EnvVariableProcessor {
        }\r
 \r
        static String[] getEnvVariableList(String property) {\r
+               property = property.trim(); \r
                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
@@ -63,7 +65,8 @@ public class EnvVariableProcessor {
                                        "Must be only one value per property! Make sure the property does not contain '"\r
                                                        + PROP_NAME_VALUE_SEPARATOR + "' symbol!");\r
                }\r
-               if (vars.length == 0) {\r
+               if (vars.length == 0 || vars.length==1) {\r
+                       log.warn("Environmental variable '"+property+"' does not have a value!");\r
                        return "";\r
                }\r
                return vars[1];\r
@@ -76,14 +79,7 @@ public class EnvVariableProcessor {
                return property.contains(PROP_NAME_VALUE_SEPARATOR);\r
        }\r
 \r
-       /**\r
-        * This method change relative paths to absolute for two environmental\r
-        * variables MAFFT-BINARIES and FASTA_4_MAFFT to avoid requesting every user\r
-        * to specify these path for every installation\r
-        */\r
-       void absolutiseMafftpaths() {\r
 \r
-       }\r
 \r
        /*\r
         * This is a horrible hack, but it only requires to simplify configuration\r
@@ -92,6 +88,7 @@ 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
@@ -101,20 +98,21 @@ 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
+                       evar=evar.trim(); \r
                        String varName = getEnvVariableName(evar);\r
                        String varValue = getEnvVariableValue(evar);\r
                        // absolutise local paths to mafft env variables\r
                        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