[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc AbstractChadoInstance.java,1.16,1.17 ChadoInstance.java,1.26,1.27 JdbcChadoAdapter.java,1.118,1.119

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12043/src/java/apollo/dataadapter/chado/jdbc

Modified Files:
	AbstractChadoInstance.java ChadoInstance.java 
	JdbcChadoAdapter.java 
Log Message:
moved seqType chado jdbc configuration from chado db to chado instance
where it really belongs - i think seqType predates the chado instance
and thats why it wasnt there to begin with. also "chromosomes" config
is now "values" inside the seqtype itself - i think this only works
for location seq types - which may be the only type that needs it -
but can easily ammend it to work for other types (dont think one would
want to config a gene list).



Index: AbstractChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/AbstractChadoInstance.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** AbstractChadoInstance.java	23 Sep 2005 17:28:13 -0000	1.16
--- AbstractChadoInstance.java	28 Sep 2005 22:19:54 -0000	1.17
***************
*** 11,16 ****
--- 11,18 ----
  import apollo.datamodel.SequenceI;
  import apollo.datamodel.StrandedFeatureSet;
+ import apollo.dataadapter.DataInput;
  import apollo.dataadapter.chado.ChadoAdapter;
  import apollo.dataadapter.chado.ChadoTransaction;
+ import apollo.dataadapter.chado.SeqType;
  
  abstract class AbstractChadoInstance implements ChadoInstance {
***************
*** 33,38 ****
--- 35,44 ----
    private String transProtRelationCvTerm = "derives_from"; // default
    private boolean retrieveAnnotations = true;
+   private String topLevelFeatType;
+   private String id;
    private final static Double Z = new Double(0.0);
    private final static Double D100 = new Double(100.0);
+   /** A list of seq types allowing the user to choose from */
+   private List seqTypes;
  
    protected AbstractChadoInstance() {}
***************
*** 51,54 ****
--- 57,62 ----
    }
  
+   public void setId(String id) { this.id = id; }
+ 
    public void setChadoAdapter(JdbcChadoAdapter jdbcAdapter) {
      this.jdbcChadoAdapter = jdbcAdapter;
***************
*** 305,308 ****
--- 313,451 ----
    }
  
+   public void setSeqTypeList(List seqTypes) {
+     this.seqTypes = seqTypes;
+   }
+ 
+   public int getSeqTypesSize() { 
+     if (seqTypes == null)
+       return 0;
+     return seqTypes.size();
+   }
+   public SeqType getSeqType(int i) { return (SeqType)seqTypes.get(i); }
+ 
+   /** Assumes theres only 1 location seq type - returns first it finds */
+   public SeqType getLocationSeqType() {
+     for (int i=0; i<getSeqTypesSize(); i++) {
+       SeqType seqType = getSeqType(i);
+        if (seqType.hasStartAndEnd())
+          return seqType;
+     }
+     return null; // shouldnt happen
+   }
+ 
+   /** Top level feature type is needed for saving back to chado. Also for querying
+       locations from the command line (where type isnt given). This is configured
+       in chado-adapter cfg file under <seqTypes> <type> with <isTopLevel>true. 
+       If top level is not configged tries to gleen from seq types - if theres any
+       seqTypes with start&end, uses that, if no locs then just looks for 'chromosome'
+       in type name, and if all that fails just sets to "chromosome". */
+   public String getTopLevelFeatType() {
+     if (topLevelFeatType != null)
+       return topLevelFeatType;
+ 
+     // check first if explicitly set with <isTopLevel> in chado config
+     for (int i=0; i<getSeqTypesSize(); i++) {
+       SeqType seqType = getSeqType(i);
+       if (seqType.isTopLevelFeatType()) {
+         topLevelFeatType = seqType.getName();
+         return topLevelFeatType;
+       }
+     }
+ 
+     // not explicitly set, usually the seqType with start&end is top level, and
+     // usually there is only one of these (if theres more than one print msg)
+     for (int i=0; i<getSeqTypesSize(); i++) {
+       SeqType seqType = getSeqType(i);
+ 
+        if (seqType.hasStartAndEnd()) {
+ 
+          // not set - 1st location - hopefully there is only 1 location
+          if (topLevelFeatType == null) { 
+            topLevelFeatType = seqType.getName();
+          }
+ 
+          // there are 2 locations! yikes
+          else {
+ 
+            String m = "2 locations specified in seq types for instance "+id;
+ 
+            if (hasChromosomeInString(seqType.getName()))
+              topLevelFeatType = seqType.getName();
+ 
+            if (hasChromosomeInString(topLevelFeatType)) {
+              m += "using "+topLevelFeatType+" for top level feat because it has "
+                +"'chromosome' in it";
+            }
+ 
+            else {// chromosome not in either type
+              m += "Arbitrarily setting top level feat to "+topLevelFeatType+
+                ". Set top level feat type explicitly with <isTopLevel>";
+            }
+ 
+            System.out.println(m);
+          }
+ 
+       }
+ 
+     }
+     if (topLevelFeatType != null) // got it with location
+       return topLevelFeatType;
+ 
+     // isTopLevel not explicitly set nor is there a location - look for chrom
+     for (int i=0; i<getSeqTypesSize(); i++) {
+       SeqType seqType = getSeqType(i);
+       if (hasChromosomeInString(seqType.getName())) {
+         topLevelFeatType = seqType.getName();
+         
+         System.out.println("Setting top level feat type to "+topLevelFeatType+
+                            " because it had 'chromosome' in it. Set explicitly "+
+                            "with <isTopLevel>true in <sequenceTypes> <type>");
+         return topLevelFeatType;
+       }
+     }
+ 
+     // everything failed - just set to chromosome and hope it works 
+     // lets hope it doesnt get to this point - it shouldnt
+     topLevelFeatType = "chromosome";
+     System.out.println("Couldnt discern top level feat type from config. Just setting "
+                        +"it to 'choromosome' and hoping to get lucky. Top level "
+                        +"seq type needs to be configured.");
+     return topLevelFeatType;
+   }
+ 
+   private boolean hasChromosomeInString(String type) {
+     return type.indexOf("chromosome") != -1;
+   }
+ 
+   /** If dataInputs type is configured as a location, then change dataInput to be
+       a location - is there a better way to do this? */
+   public void checkForLocation(DataInput dataInput) {
+     if (dataInput.getSoType() == null && dataInput.isRegion())
+       dataInput.setSoType(getLocationSeqType().getName());
+     if (isLocation(dataInput.getSoType()) && !dataInput.isRegion()) {
+       // it is a location - make it so, this causes loc in string to be parsed
+       // which is the desired effect
+       dataInput.makeDataTypeRegion(); // a little silly
+     }
+   }
+   private boolean isLocation(String type) {
+     SeqType st = getSeqType(type);
+     if (st == null)
+       return false;
+     return st.hasStartAndEnd();
+   }
+   public SeqType getSeqType(String name) {
+     for (int i=0; i<getSeqTypesSize(); i++) {
+       if (getSeqType(i).getName().equals(name))
+         return getSeqType(i);
+     }
+     return null;
+   }
+   public boolean typeHasStartAndEnd(String typeName) {
+     SeqType st = getSeqType(typeName);
+     if (st == null) return false;
+     return st.hasStartAndEnd();
+   }
+ 
    protected void debugPrintTime() { JdbcChadoAdapter.debugPrintTime(); }
  

Index: ChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/ChadoInstance.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** ChadoInstance.java	22 Sep 2005 12:48:47 -0000	1.26
--- ChadoInstance.java	28 Sep 2005 22:19:54 -0000	1.27
***************
*** 8,11 ****
--- 8,13 ----
  import apollo.dataadapter.Region;
  import apollo.dataadapter.chado.ChadoAdapter;
+ import apollo.dataadapter.DataInput;
+ import apollo.dataadapter.chado.SeqType;
  import apollo.datamodel.CurationSet;
  import apollo.datamodel.Transcript;
***************
*** 40,43 ****
--- 42,47 ----
  
  
+   public void setId(String id);
+ 
    /** Field from query result to use for gene name (fb uses gene_name, 
        tigr uses gene_uniquename)
***************
*** 190,193 ****
--- 194,217 ----
    public List getChadoTransMacros();
  
+   public void setSeqTypeList(List seqTypes);
+ 
+   /** Top level feature type is needed for saving back to chado. Also for querying
+       locations from the command line (where type isnt given). This is configured
+       in chado-adapter cfg file */
+   public String getTopLevelFeatType();
+   /** Return number of seq types for instance */
+   public int getSeqTypesSize();
+   /** Return ith SeqType */
+   public SeqType getSeqType(int i);
+   /** SeqType for name */
+   public SeqType getSeqType(String name);
+   /** Returns seq type that has location */
+   public SeqType getLocationSeqType();
+   /** Does type require start & end data */
+   public boolean typeHasStartAndEnd(String typeName);
+   /** If dataInputs type is configured as a location, then change dataInput to be
+       a location */
+   public void checkForLocation(DataInput dataInput);
+ 
    public ChadoInstance cloneInstance();
  }

Index: JdbcChadoAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v
retrieving revision 1.118
retrieving revision 1.119
diff -C2 -d -r1.118 -r1.119
*** JdbcChadoAdapter.java	22 Sep 2005 15:54:16 -0000	1.118
--- JdbcChadoAdapter.java	28 Sep 2005 22:19:54 -0000	1.119
***************
*** 2816,2820 ****
    }
  
!   protected static void debugPrintTime() {
      if (!debug) return;
      Calendar now = Calendar.getInstance();
--- 2816,2820 ----
    }
  
!   public static void debugPrintTime() {
      if (!debug) return;
      Calendar now = Calendar.getInstance();