Merge collective geometries into cohort and store in transition (still unhandled at commit)

Author: fvilla

klab.core.api/src/main/java/org/integratedmodelling/klab/api/data/RepositoryState.java

@@ -70,10 +70,16 @@ public enum Operation {
     FETCH_COMMIT_AND_PUSH,
     /** Fetch remote changes and merge them if no conflicts arise */
     FETCH_AND_MERGE,
+    /** Commit current local changes without contacting the remote repository */
+    SAVE_CHANGES,
+    /** Push committed local changes to the remote repository */
+    PUBLISH_CHANGES,
     /** Switch to another branch (possibly new) after locally committing any pending changes */
     COMMIT_AND_SWITCH,
     /** Hard reset head deleting all uncommitted changes */
     HARD_RESET,
+    /** Friendlier alias for HARD_RESET */
+    DISCARD_LOCAL_CHANGES,
 
     MERGE_CHANGES_FROM;
 
@@ -82,8 +88,11 @@ public String description() {
         case FETCH_COMMIT_AND_PUSH ->
             "Fetch remote changes, merge if no conflicts, commit and push";
         case FETCH_AND_MERGE -> "Fetch remote changes, merge if no conflicts";
+        case SAVE_CHANGES -> "Save current local changes";
+        case PUBLISH_CHANGES -> "Publish committed changes";
         case COMMIT_AND_SWITCH -> "Commit changes and switch to another branch";
         case HARD_RESET -> "Hard reset, deleting all uncommitted changes";
+        case DISCARD_LOCAL_CHANGES -> "Discard local uncommitted changes";
         case MERGE_CHANGES_FROM -> "Merge changes from another branch";
       };
     }

klab.core.api/src/main/java/org/integratedmodelling/klab/api/knowledge/organization/ProjectStorage.java

@@ -47,7 +47,7 @@ public static ResourceType forExtension(String extension) {
         case "kwv" -> ONTOLOGY;
         case "kim" -> MODEL_NAMESPACE;
         case "obs" -> STRATEGY;
-        case "kactor" -> BEHAVIOR;
+        case "kactor", "kactors" -> BEHAVIOR;
         default -> null;
       };
     }
@@ -57,7 +57,7 @@ public String getFileExtension() {
         case ONTOLOGY -> "kwv";
         case MODEL_NAMESPACE -> "kim";
         case STRATEGY -> "obs";
-        case BEHAVIOR, TESTCASE, SCRIPT -> "kactor";
+        case BEHAVIOR, TESTCASE, SCRIPT, APPLICATION -> "kactors";
         default ->
             throw new KlabUnimplementedException("file extension for document of class " + this);
       };
@@ -142,23 +142,32 @@ static Pair<ResourceType, String> getDocumentData(String relativeFilePath, Strin
     ResourceType type = null;
     String urn = null;
 
+    if (relativeFilePath == null || !relativeFilePath.contains(".")) {
+      return null;
+    }
+
     var extension = relativeFilePath.substring(relativeFilePath.lastIndexOf(".") + 1);
     var path = relativeFilePath.substring(0, relativeFilePath.lastIndexOf("."));
+    boolean behaviorExtension = "kactor".equals(extension) || "kactors".equals(extension);
 
     if ("json".equals(extension)) {
       // TODO manifest, docs, resource.
       if (relativeFilePath.startsWith("resources" + separator)) {
-        throw new KlabUnimplementedException("KAAAAAAAAKKKKKKKKKKKKKKKKKKK");
+        return null;
       }
     } else {
       if (relativeFilePath.startsWith("src" + separator)) {
         type = ResourceType.forExtension(extension);
         urn = path.substring("src".length() + 1).replace(separator, ".");
-      } else if (relativeFilePath.startsWith("scripts" + separator)) {
-        throw new KlabUnimplementedException("POOOOOO");
-      } else if (relativeFilePath.startsWith("tests" + separator)) {
-        throw new KlabUnimplementedException("PAAAAAAA");
-      } else if (relativeFilePath.startsWith("apps" + separator) && "apps".equals(extension)) {
+      } else if (relativeFilePath.startsWith("scripts" + separator) && behaviorExtension) {
+        type = ResourceType.SCRIPT;
+        urn = path.substring("scripts".length() + 1);
+      } else if ((relativeFilePath.startsWith("tests" + separator)
+              || relativeFilePath.startsWith("testcases" + separator))
+          && behaviorExtension) {
+        type = ResourceType.TESTCASE;
+        urn = path.substring(relativeFilePath.indexOf(separator) + separator.length());
+      } else if (relativeFilePath.startsWith("apps" + separator) && behaviorExtension) {
         type = ResourceType.APPLICATION;
         urn = path.substring("apps".length() + 1);
       } else if (relativeFilePath.startsWith("strategies" + separator) && "obs".equals(extension)) {
@@ -191,7 +200,7 @@ static String getRelativeFilePath(String urn, ResourceType type) {
   static String getRelativeFilePath(String urn, ResourceType type, String separator) {
     return switch (type) {
       case SCRIPT -> "scripts" + separator + urn + "." + type.getFileExtension();
-      case TESTCASE -> "tests" + separator + urn + "." + type.getFileExtension();
+      case TESTCASE -> "testcases" + separator + urn + "." + type.getFileExtension();
       case APPLICATION -> "apps" + separator + urn + "." + type.getFileExtension();
       case ONTOLOGY, MODEL_NAMESPACE, BEHAVIOR ->
           "src" + separator + urn.replace('.', separator.charAt(0)) + "." + type.getFileExtension();

klab.core.services/src/main/java/org/integratedmodelling/klab/resources/FileProjectStorage.java

@@ -233,17 +233,17 @@ public RepositoryState getRepositoryState() {
 
   public String getDocumentUrn(ResourceType type, URL url) {
 
-    File file = new File(url.getFile());
-    if (file.exists()) {
+    try {
+      File file = Path.of(url.toURI()).toFile();
       /*
       relative path
        */
       var relativePath = rootFolder.toPath().relativize(file.toPath());
       var data = ProjectStorage.getDocumentData(relativePath.toString(), File.separator);
       return data != null && data.getFirst() == type ? data.getSecond() : null;
+    } catch (Exception e) {
+      throw new KlabIOException(e);
     }
-
-    return null;
   }
 
   /**
@@ -261,7 +261,7 @@ public URL getDocumentUrl(String path, String separator) {
                 + (path.startsWith(separator) ? path.substring(separator.length()) : path)
                     .replace(separator, File.separator));
     try {
-      return file.exists() ? file.toURI().toURL() : null;
+      return file.toURI().toURL();
     } catch (MalformedURLException e) {
     }
     return null;