Merge pull request #36 from jhourani/experimental

Fixes issue #34, implements --no-preserve.

README.rst

@@ -23,6 +23,8 @@ set of computable networks and APIs.
 
 .. contents::
 
+**For a more complete guide to using the BEL Framework, we encourage you to check out our** `wiki pages`_.
+
 The OpenBEL Ecosystem
 ---------------------
 
@@ -86,6 +88,7 @@ intended on serving a particular purpose.
 .. _freenode IRC network: http://www.freenode.net/
 .. _XChat: http://xchat.org/
 .. _Xirc: http://www.aquaticx.com/
+.. _wiki pages: http://wiki.openbel.org
 
 Distribution
 ------------
@@ -151,13 +154,17 @@ contractual assumptions directly impose on those licensors and authors.
 Further Reference
 -----------------
 
+**For Users:**
+ * Ohloh: https://www.ohloh.net/p/openbel-framework
+ * BEL Portal: http://openbel.org
+ * Selventa: http://www.selventa.com/
+ * API documentation: http://openbel.github.com/openbel-framework
+ * Freecode: http://freecode.com/projects/openbel-framework
+
+**For Developers:**
  * API documentation: http://openbel.github.com/openbel-framework
  * User documentation: http://openbel-framework.readthedocs.org/en/master/
  * Nightly builds: http://ci.selventa.com/browse/FWMASTER-NIGHTLY/latest/artifact
  * OpenBEL build server: http://ci.selventa.com
  * GitHub: https://github.com/OpenBEL
- * BEL Portal: http://openbel.org
- * Selventa: http://www.selventa.com/
- * Ohloh: https://www.ohloh.net/p/openbel-framework
  * Freecode: http://freecode.com/projects/openbel-framework
-

docs/examples/belscript/test_7.bel

@@ -5,19 +5,9 @@
 # add a redundant extra hasMember relationship.                                  #
 #                                                                                #
 #   No compiler arguments
-#       13 nodes, 12 edges:
-#           p(HGNC:AKT1) -> p(PFH:"AKT Family")
-#           p(HGNC:AKT1) >> r(HGNC:AKT1)
-#           r(HGNC:AKT1) :> g(HGNC:AKT1)
-#           p(PFH:"AKT Family") hasMember p(HGNC:FOXO1)
-#           p(HGNC:FOXO1) >> r(HGNC:FOXO1)
-#           r(HGNC:FOXO1) :> g(HGNC:FOXO1)
-#           p(PFH:"AKT Family") hasMember p(HGNC:FOXO3)
-#           p(HGNC:FOXO3) >> r(HGNC:FOXO3)
-#           r(HGNC:FOXO3) :> g(HGNC:FOXO3)
-#           p(PFH:"AKT Family") hasMember p(HGNC:FOXO4)
-#           p(HGNC:FOXO4) >> r(HGNC:FOXO4)
-#           r(HGNC:FOXO4) :> g(HGNC:FOXO4)
+#       16 nodes, 15 edges:
+#
+#   //TODO
 ##################################################################################
 # Document Properties Section
 

org.openbel.framework.common/src/main/java/org/openbel/framework/common/Strings.java

@@ -461,7 +461,12 @@ public class Strings {
      * {@value}
      */
     public static final String KAM_NAME = "KAM Store name";
-
+
+    /*
+     * {@value}
+     */
+    public static final String KAM_NAME_ALREADY_EXISTS = "KAM name already exists.\n";
+
     /**
      * {@value}
      */
@@ -567,6 +572,16 @@ public class Strings {
      * {@value}
      */
     public static final String MICRO_RNA_ABUNDANCE = "microRNAAbundance";
+
+    /*
+     * {@value}
+     */
+    public final static String LONG_OPT_KAM_NAME = "kam-name";
+
+    /**
+     * {@value}
+     */
+    public final static String LONG_OPT_NO_PRESERVE = "no-preserve";
 
     /**
      * {@value}
@@ -1141,6 +1156,11 @@ public class Strings {
      * {@value}
      */
     public final static String SHA_256 = "SHA-256";
+
+    /*
+     * {@value}
+     */
+    public final static String SHORT_OPT_KAM_NAME = "k";
 
     /**
      * {@value}

org.openbel.framework.common/src/main/java/org/openbel/framework/common/enums/ExitCode.java

@@ -54,145 +54,151 @@
 public enum ExitCode {
 
     /**
-     * Success.
+     * Success. ExitCode(0)
      */
     SUCCESS(0, Strings.SUCCESS),
 
     /**
-     * General failure.
+     * General failure. ExitCode(1) 
      */
     GENERAL_FAILURE(1, Strings.GENERAL_FAILURE),
 
     /**
-     * Unrecoverable error.
+     * Unrecoverable error. ExitCode(2) 
      */
     UNRECOVERABLE_ERROR(2, Strings.UNRECOVERABLE_ERROR_MSG),
 
     /**
-     * All documents failed validation.
+     * All documents failed validation. ExitCode(3) 
      */
     NO_VALID_DOCUMENTS(3, ALL_DOCUMENTS_FAILED_VALIDATION),
 
     /**
-     * All documents failed conversion.
+     * All documents failed conversion. ExitCode(4) 
      */
     NO_CONVERTED_DOCUMENTS(4, ALL_DOCUMENTS_FAILED_CONVERSION),
 
     /**
-     * No proto-networks saved.
+     * No proto-networks saved. ExitCode(5) 
      */
     NO_PROTO_NETWORKS_SAVED(5, NO_NETWORKS_SAVED),
 
     /**
-     * No XBEL documents.
+     * No XBEL documents. ExitCode(6) 
      */
     NO_XBEL_DOCUMENTS(6, Strings.NO_XBEL_DOCUMENTS),
 
     /**
-     * Bad output directory.
+     * Bad output directory. ExitCode(7) 
      */
     BAD_OUTPUT_DIRECTORY(7, BAD_OUTPUT_DIR),
 
     /**
-     * Invalid namespace resource location.
+     * Invalid namespace resource location. ExitCode(8) 
      */
     INVALID_NAMESPACE_RESOURCE_LOCATION(8,
             Strings.INVALID_NAMESPACE_RESOURCE_LOCATION),
 
     /**
-     * Parse error.
+     * Parse error. ExitCode(9) 
      */
     PARSE_ERROR(9, Strings.PARSE_ERROR),
 
     /**
-     * KAM connection failure.
+     * KAM connection failure. ExitCode(10) 
      */
     KAM_CONNECTION_FAILURE(10, Strings.KAM_CONNECTION_FAILURE),
 
     /**
-     * No global proto network.
+     * No global proto network. ExitCode(11) 
      */
     NO_GLOBAL_PROTO_NETWORK(11, Strings.NO_GLOBAL_PROTO_NETWORK),
 
     /**
-     * Failed to merge proto-networks.
+     * Failed to merge proto-networks. ExitCode(12) 
      */
     FAILED_TO_MERGE_PROTO_NETWORKS(12, Strings.NETWORK_MERGE_FAILURE),
 
     /**
-     * Missing system configuration.
+     * Missing system configuration. ExitCode(13) 
      */
     MISSING_SYSTEM_CONFIGURATION(13, Strings.MISSING_SYSCFG),
 
     /**
-     * Failure loading into the KAM catalog.
+     * Failure loading into the KAM catalog. ExitCode(14) 
      */
     KAM_CATALOG_LOAD_FAILED(14, Strings.KAM_CATALOG_LOAD_FAILED),
 
     /**
-     * Failure deleting a directory.
+     * Failure deleting a directory. ExitCode(15) 
      */
     DIRECTORY_DELETION_FAILED(15, Strings.DIRECTORY_DELETION_FAILED),
 
     /**
-     * Failed creating a directory.
+     * Failed creating a directory. ExitCode(16) 
      */
     DIRECTORY_CREATION_FAILED(16, Strings.DIRECTORY_CREATION_FAILED),
-
+
+    /*
+     * Duplicate KAM name. ExitCode(23) 
+     */
+    DUPLICATE_KAM_NAME(23, Strings.KAM_NAME_ALREADY_EXISTS),
+
     /**
-     * Failed loading the KAM.
+     * Failed loading the KAM. ExitCode(17) 
      */
     KAM_LOAD_FAILURE(17, Strings.KAM_LOAD_FAILURE),
 
+
     /**
-     * Out of memory.
+     * Out of memory. ExitCode(42) 
      */
     OOM_ERROR(42, Strings.OOM),
 
     // PEDANTIC RETURN CODES BEYOND HERE
 
     /**
-     * Pedantic validation failure.
+     * Pedantic validation failure. ExitCode(101) 
      */
     VALIDATION_FAILURE(101, PEDANTIC_VALIDATION_FAILURE),
 
     /**
-     * Pedantic conversion failure.
+     * Pedantic conversion failure. ExitCode(102) 
      */
     CONVERSION_FAILURE(102, PEDANTIC_CONVERSION_FAILURE),
 
     /**
-     * Pedantic namespace resolution failure.
+     * Pedantic namespace resolution failure. ExitCode(103) 
      */
     NAMESPACE_RESOLUTION_FAILURE(103, PEDANTIC_NAMESPACE_RESOLUTION_FAILURE),
 
     /**
-     * Pedantic namespace indexing failure.
+     * Pedantic namespace indexing failure. ExitCode(104) 
      */
     NAMESPACE_INDEXING_FAILURE(104, PEDANTIC_NAMESPACE_INDEXING_FAILURE),
 
     /**
-     * Pedantic semantic verification failure.
+     * Pedantic semantic verification failure. ExitCode(105) 
      */
     SEMANTIC_VERIFICATION_FAILURE(105, PEDANTIC_SEMANTIC_VERIFICATION_FAILURE),
 
     /**
-     * Pedantic symbol verification failure.
+     * Pedantic symbol verification failure. ExitCode(106) 
      */
     SYMBOL_VERIFICATION_FAILURE(106, PEDANTIC_SYMBOL_VERIFICATION_FAILURE),
 
     /**
-     * Pedantic proto-network save failure.
+     * Pedantic proto-network save failure. ExitCode(107) 
      */
     PROTO_NETWORK_SAVE_FAILURE(107, PEDANTIC_PROTO_NETWORK_SAVE_FAILURE),
 
     /**
-     * Term expansion failure.
+     * Term expansion failure. ExitCode(108) 
      */
     TERM_EXPANSION_FAILURE(108, PEDANTIC_TERM_EXPANSION_FAILURE),
 
     /**
-     * Statement expansion failure.
+     * Statement expansion failure. ExitCode(109) 
      */
     STATEMENT_EXPANSION_FAILURE(109, PEDANTIC_STATEMENT_EXPANSION_FAILURE);
 

org.openbel.framework.core/src/main/java/org/openbel/framework/core/StandardOptions.java

@@ -126,6 +126,12 @@ public class StandardOptions {
      * For example:<br>{@code --help}
      */
     public final static String LONG_OPT_HELP = "help";
+
+    /*
+     * The long option to enable no-preserve.<br>
+     * For example:<br>{@code --no-preserve}
+     */
+    public final static String LONG_OPT_NO_PRESERVE= "no-preserve";
 
     /**
      * Default private constructor.

org.openbel.framework.tools/src/main/java/org/openbel/framework/tools/PhaseApplication.java

@@ -175,7 +175,7 @@ public List<Option> getCommandLineOptions() {
         Option o = new Option(SHRT_OPT_SYSCFG, LONG_OPT_SYSCFG, true, help);
         o.setArgName(ARG_SYSCFG);
         ret.add(o);
-
+        
         return ret;
     }
 

org.openbel.framework.tools/src/main/java/org/openbel/framework/tools/PhaseFourApplication.java

@@ -42,11 +42,8 @@
  * @author Anthony Bargnesi {@code <[email protected]>}
  */
 public final class PhaseFourApplication extends PhaseApplication {
-    private final static String SHORT_OPT_KAM_NAME = "k";
-    private final static String LONG_OPT_KAM_NAME = "kam-name";
     private final static String SHORT_OPT_KAM_DESCRIPTION = "d";
     private final static String LONG_OPT_KAM_DESCRIPTION = "kam-description";
-    private final static String LONG_OPT_NO_PRESERVE = "no-preserve";
     private final DefaultPhaseFour p4;
     private final SystemConfiguration sysconfig;
 
@@ -287,19 +284,15 @@ public List<Option> getCommandLineOptions() {
         String help;
         Option o;
 
-        help = KAM_NAME_HELP;
-        o = new Option(SHORT_OPT_KAM_NAME, LONG_OPT_KAM_NAME, true, help);
-        o.setArgName("kam");
-        options.add(o);
-
         help = KAM_DESCRIPTION_HELP;
         o = new Option(SHORT_OPT_KAM_DESCRIPTION, LONG_OPT_KAM_DESCRIPTION,
                 true, help);
         o.setArgName("description");
         options.add(o);
-
-        help = NO_PRESERVE_HELP;
-        o = new Option(null, LONG_OPT_NO_PRESERVE, false, help);
+
+        help = KAM_NAME_HELP;
+        o = new Option(SHORT_OPT_KAM_NAME, LONG_OPT_KAM_NAME, true, help);
+        o.setArgName("kam");
         options.add(o);
 
         return options;