- support cross references

fbergmann · Mar 29, 2019 · 23606cf · 23606cf
1 parent 0969e93
commit 23606cf
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Showing 4 changed files with 79 additions and 18 deletions.
diff --git a/CombineCLI/Program.cs b/CombineCLI/Program.cs
@@ -80,29 +80,34 @@ static void Main(string[] args)
                     Console.WriteLine("  org  : " + creator.Organization);
                     Console.WriteLine();
                 }
+                Console.WriteLine();
 
-
-            }
+                foreach (var xref in entry.CrossReferences)
+                    Console.WriteLine("  xref  : " + xref);
 
-            //var archive = 
-            //    CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\isola_oscillations_sed.sed.omex");
 
-            //Console.WriteLine("Num SEDML files: {0}", archive.GetNumFilesWithFormat("SEDML"));
-            //Console.WriteLine("Num SBML files: {0}", archive.GetNumFilesWithFormat("sbml"));
-            //Console.WriteLine("Num SBML files: {0}", archive.GetNumFilesWithFormat("sbml"));
 
-            //archive.SaveTo(@"C:\Users\fbergmann\Desktop\isola.omex");
+      }
 
+      //var archive = 
+      //    CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\isola_oscillations_sed.sed.omex");
 
+      //Console.WriteLine("Num SEDML files: {0}", archive.GetNumFilesWithFormat("SEDML"));
+      //Console.WriteLine("Num SBML files: {0}", archive.GetNumFilesWithFormat("sbml"));
+      //Console.WriteLine("Num SBML files: {0}", archive.GetNumFilesWithFormat("sbml"));
 
-            //var omex = CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\Boris.omex");
+      //archive.SaveTo(@"C:\Users\fbergmann\Desktop\isola.omex");
 
-            //if (omex.HasEntriesWithFormat("pdf"))
-            //    omex.GetEntriesWithFormat("PDF").First().OpenLocation();
 
 
-            //Console.ReadKey();
-        }
+      //var omex = CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\Boris.omex");
+
+      //if (omex.HasEntriesWithFormat("pdf"))
+      //    omex.GetEntriesWithFormat("PDF").First().OpenLocation();
+
+
+      //Console.ReadKey();
+    }
     }
 }
 
diff --git a/FormsCombineArchive/MainForm.cs b/FormsCombineArchive/MainForm.cs
@@ -91,6 +91,21 @@ private void AddEntry(Entry entry)
         ToolTipText = GetToolTip(entry)
       };
 
+      foreach (var xref in entry.CrossReferences)
+      {
+        var xentry = Archive[xref];
+        if (xentry == null)
+          continue;
+
+        var xitem = new ListViewItem.ListViewSubItem
+        {
+          Text = GetNameForLocation(xref),
+          Tag = xentry,
+
+        };
+        item.SubItems.Add(xitem);
+      }
+
       lstEntries.Items.Add(item);
     }
     private void UpdateUI()
@@ -125,7 +140,7 @@ public void OpenFile(string fileName)
       }
       catch (Exception ex)
       {
-        MessageBox.Show("An error occured while opening the file. The exception was: " + Environment.NewLine + Environment.NewLine + ex.Message, "Could not open archive", MessageBoxButtons.OK, MessageBoxIcon.Error);
+        MessageBox.Show("An error occurred while opening the file. The exception was: " + Environment.NewLine + Environment.NewLine + ex.Message, "Could not open archive", MessageBoxButtons.OK, MessageBoxIcon.Error);
       }
     }
 
@@ -160,7 +175,7 @@ public void SaveFile(string fileName)
       }
       catch (Exception ex)
       {
-        MessageBox.Show("An error occured while saving the file. Please ensure that all files in this archive are closed, so they can be read. The exception was: " + Environment.NewLine + Environment.NewLine + ex.Message, "Could not save archive", MessageBoxButtons.OK, MessageBoxIcon.Error);
+        MessageBox.Show("An error occurred while saving the file. Please ensure that all files in this archive are closed, so they can be read. The exception was: " + Environment.NewLine + Environment.NewLine + ex.Message, "Could not save archive", MessageBoxButtons.OK, MessageBoxIcon.Error);
       }
     }
 

diff --git a/LibCombine/CombineArchive.cs b/LibCombine/CombineArchive.cs
@@ -109,6 +109,17 @@ public Entry AddEntry(string fileName, string format, OmexDescription descriptio
 
     }
 
+    public Entry this[int index]
+    {
+      get { return Entries[index]; }
+    }
+
+    public Entry this[string location]
+    {
+      get { return Entries.Where(e => e.Location == location).FirstOrDefault(); }
+    }
+
+
     public List<Entry> GetEntriesWithFormat(string format)
     {
       UpdateRefs();
@@ -211,6 +222,14 @@ private void ParseManifest(string fileName)
               entry.IsMaster = true;
               MainEntry = entry;              
             }
+
+            var xrefs = element.GetElementsByTagName("crossRef", currentNs);
+            foreach (var node in xrefs)
+            {
+              var xref = ((XmlElement)node).GetAttribute("location");
+              entry.CrossReferences.Add(xref);
+            }
+
             Entries.Add(entry);
 
           }
@@ -364,8 +383,7 @@ public string ToManifest()
       var root = new XElement(ns + "omexManifest");
       foreach (var entry in Entries)
       {
-        root.Add(
-            new XElement(ns + "content",
+        var el = new XElement(ns + "content",
                 new XAttribute("location",
                     entry.Location
                     .Replace(BaseDir, "./")
@@ -375,7 +393,18 @@ public string ToManifest()
                     .Replace("./manifest.xml", ".")
                     ),
                 new XAttribute("format", entry.Format),
-                new XAttribute("master", entry == MainEntry || entry.IsMaster ? "true" : "false")));
+                new XAttribute("master", entry == MainEntry || entry.IsMaster ? "true" : "false"));
+        foreach (var xref in entry.CrossReferences)
+        {
+          el.Add(new XElement(ns + "crossRef"),
+            new XAttribute("location", xref
+                    .Replace(BaseDir, "./")
+                    .Replace("././", "./")
+                    .Replace("./\\", "./")
+                    .Replace(".//", "./")
+            ));
+        }
+        root.Add(el);
       }
       var srcTree = new XDocument(root);
       return

diff --git a/LibCombine/Entry.cs b/LibCombine/Entry.cs
@@ -293,6 +293,17 @@ public static Dictionary<string, string> KnownFormats
     /// </summary>
     public bool IsMaster { get; set; }
 
+
+    /// <summary>
+    /// A list of cross references to other entries this entry is related too. It is optional
+    /// </summary>
+    public List<string> CrossReferences { get; set;  }
+
+    public Entry()
+    {
+      CrossReferences = new List<string> ();
+    }
+
     /// <summary>
     /// Resolves the local file name of this entry
     /// </summary>
@@ -332,6 +343,7 @@ public static string GuessFormat(string fileName)
           if (snippet.Contains("<sbml")) return LookupFormat("sbml");
           if (snippet.Contains("<sedML")) return LookupFormat("sedml");
           if (snippet.Contains("<cell")) return LookupFormat("cellml");
+          if (snippet.Contains("<COPASI ")) return LookupFormat("copasi");
         }
       }
       string extension = ext.Replace(".", "");