Changeset 16230

Show
Ignore:
Timestamp:
15/07/08 15:18:43 (1 month ago)
Author:
julie
Message:

updated path queries to use new methods. Refs #1733

Files:

Legend:

Unmodified
Added
Removed
Modified
Copied
Moved

  • trunk/flymine/webapp/src/org/flymine/web/widget/BDGPinsituGraphURLGenerator.java

    r15992 r16230  
    1111 */ 
    1212 
    13 import java.util.ArrayList; 
    14 import java.util.List; 
    15  
    16 import org.intermine.objectstore.query.ConstraintOp; 
    17  
    1813import org.intermine.metadata.Model; 
    1914import org.intermine.objectstore.ObjectStore; 
    20 import org.intermine.path.Path; 
    21 import org.intermine.pathquery.Constraint; 
    22 import org.intermine.pathquery.PathNode; 
    2315import org.intermine.pathquery.PathQuery; 
    2416import org.intermine.web.logic.bag.InterMineBag; 
     17import org.intermine.web.logic.query.Constraints; 
    2518import org.intermine.web.logic.widget.GraphCategoryURLGenerator; 
    26  
    2719import org.jfree.data.category.CategoryDataset; 
    2820 
    …… 
    3426public class BDGPinsituGraphURLGenerator implements GraphCategoryURLGenerator 
    3527{ 
    36     String bagName; 
     28    private String bagName; 
     29    private static final String DATASET = "BDGP in situ data set"; 
    3730 
    3831    /** 
    …… 
    9184        PathQuery q = new PathQuery(model); 
    9285 
    93         List<Path> view = new ArrayList<Path>(); 
    94         view.add(PathQuery.makePath(model, q, "Gene.primaryIdentifier")); 
    95         view.add(PathQuery.makePath(model, q, "Gene.secondaryIdentifier")); 
    96         view.add(PathQuery.makePath(model, q, "Gene.name")); 
    97         view.add(PathQuery.makePath(model, q, "Gene.organism.name")); 
    98         view.add(PathQuery.makePath(model, q, "Gene.mRNAExpressionResults.stageRange")); 
    99         view.add(PathQuery.makePath(model, q, "Gene.mRNAExpressionResults.expressed")); 
     86        q.setView("Gene.primaryIdentifier,Gene.secondaryIdentifier,Gene.name,Gene.organism.name," 
     87                  + "Gene.mRNAExpressionResults.stageRange,Gene.mRNAExpressionResults.expressed"); 
    10088 
    101         q.setViewPaths(view); 
     89        // bag constraint 
     90        q.addConstraint("Gene",  Constraints.in(bag.getName())); 
    10291 
    103         String bagType = bag.getType(); 
    104         ConstraintOp constraintOp = ConstraintOp.IN; 
    105         String constraintValue = bag.getName(); 
    106  
    107         String label = null, id = null, code = q.getUnusedConstraintCode(); 
    108         Constraint c = new Constraint(constraintOp, constraintValue, false, label, code, id, null); 
    109         q.addNode(bagType).getConstraints().add(c); 
    110  
    111         // filter out BDGP 
    112         constraintOp = ConstraintOp.EQUALS; 
    113         code = q.getUnusedConstraintCode(); 
    114         PathNode datasetNode = q.addNode("Gene.mRNAExpressionResults.dataSet.title"); 
    115         String dataset = "BDGP in situ data set"; 
    116         Constraint datasetConstraint 
    117                         = new Constraint(constraintOp, dataset, false, label, code, id, null); 
    118         datasetNode.getConstraints().add(datasetConstraint); 
     92        // filter out flyFish 
     93        q.addConstraint("Gene.mRNAExpressionResults.dataSet.title",  Constraints.eq(DATASET)); 
    11994 
    12095        // stage (series) 
    121         constraintOp = ConstraintOp.EQUALS; 
    122         code = q.getUnusedConstraintCode(); 
    123         PathNode stageNode = q.addNode("Gene.mRNAExpressionResults.stageRange"); 
    124         String stageRange = series + " (BDGP in situ)"; 
    125         Constraint stageConstraint 
    126                         = new Constraint(constraintOp, stageRange, false, label, code, id, null); 
    127         stageNode.getConstraints().add(stageConstraint); 
     96        q.addConstraint("Gene.mRNAExpressionResults.stageRange", 
     97                        Constraints.eq(series + " (BDGP in situ)")); 
    12898 
    12999        // expressed (category) 
    130         constraintOp = ConstraintOp.EQUALS; 
    131         Boolean expressed = Boolean.FALSE; 
    132         if (category.equals("true")) { 
    133             expressed = Boolean.TRUE; 
    134         } 
    135         code = q.getUnusedConstraintCode(); 
    136         PathNode expressedNode = q.addNode("Gene.mRNAExpressionResults.expressed"); 
    137         Constraint expressedConstraint 
    138                         = new Constraint(constraintOp, expressed, false, label, code, id, null); 
    139         expressedNode.getConstraints().add(expressedConstraint); 
     100        Boolean expressed = (category.equals("true") ? Boolean.TRUE : Boolean.FALSE); 
     101        q.addConstraint("Gene.mRNAExpressionResults.expressed",  Constraints.eq(expressed)); 
    140102 
    141103        q.setConstraintLogic("A and B and C and D"); 

  • trunk/flymine/webapp/src/org/flymine/web/widget/FlyAtlasGraphURLGenerator.java

    r15993 r16230  
    1111 */ 
    1212 
    13 import java.util.ArrayList; 
    14 import java.util.List; 
    15  
    16 import org.intermine.objectstore.query.ConstraintOp; 
    17  
    1813import org.intermine.metadata.Model; 
    1914import org.intermine.objectstore.ObjectStore; 
    20 import org.intermine.path.Path; 
    21 import org.intermine.pathquery.Constraint; 
    22 import org.intermine.pathquery.OrderBy; 
    23 import org.intermine.pathquery.PathNode; 
    2415import org.intermine.pathquery.PathQuery; 
    2516import org.intermine.web.logic.bag.InterMineBag; 
     17import org.intermine.web.logic.query.Constraints; 
    2618import org.intermine.web.logic.widget.GraphCategoryURLGenerator; 
    27  
    2819import org.jfree.data.category.CategoryDataset; 
    2920/** 
    …… 
    8172        PathQuery q = new PathQuery(model); 
    8273 
    83         Path secondaryIdentifier = PathQuery.makePath(model, q, 
    84                                                        "FlyAtlasResult.genes.secondaryIdentifier"); 
    85         Path primaryIdentifier = PathQuery.makePath(model, q, 
    86                                                      "FlyAtlasResult.genes.primaryIdentifier"); 
    87         Path name = PathQuery.makePath(model, q, "FlyAtlasResult.genes.name"); 
    88         Path org = PathQuery.makePath(model, q, "FlyAtlasResult.genes.organism.name"); 
    89         Path assays = PathQuery.makePath(model, q, "FlyAtlasResult.assays.name"); 
    90         Path enrichment = PathQuery.makePath(model, q, "FlyAtlasResult.enrichment"); 
    91         Path affyCall = PathQuery.makePath(model, q, "FlyAtlasResult.affyCall"); 
    92         Path signal = PathQuery.makePath(model, q, "FlyAtlasResult.mRNASignal"); 
    93         Path sem = PathQuery.makePath(model, q, "FlyAtlasResult.mRNASignalSEM"); 
    94         Path presentCall = PathQuery.makePath(model, q, "FlyAtlasResult.presentCall"); 
     74        q.setView("FlyAtlasResult.genes.secondaryIdentifier, FlyAtlasResult.genes.primaryIdentifier" 
     75                  + ",FlyAtlasResult.genes.name,FlyAtlasResult.genes.organism.name," 
     76                  + "FlyAtlasResult.assays.name,FlyAtlasResult.enrichment,FlyAtlasResult.affyCall," 
     77                  + "FlyAtlasResult.mRNASignal,FlyAtlasResult.mRNASignalSEM," 
     78                  + "FlyAtlasResult.presentCall"); 
    9579 
    96         List<Path> view = new ArrayList<Path>(); 
     80        q.addConstraint("Gene",  Constraints.in(bag.getName())); 
     81        q.addConstraint("FlyAtlasResult.affyCall",  Constraints.eq(category)); 
     82        q.addConstraint("FlyAtlasResult.assays.name",  Constraints.eq(series)); 
    9783 
    98         view.add(secondaryIdentifier); 
    99         view.add(primaryIdentifier); 
    100         view.add(name); 
    101         view.add(org); 
    102         view.add(assays); 
    103         view.add(affyCall); 
    104         view.add(enrichment); 
    105         view.add(signal); 
    106         view.add(sem); 
    107         view.add(presentCall); 
     84        Boolean sortAscending = (category.equalsIgnoreCase("up") ? Boolean.FALSE : Boolean.TRUE); 
    10885 
    109         q.setViewPaths(view); 
    110  
    111         ConstraintOp constraintOp = ConstraintOp.IN; 
    112         String constraintValue = bag.getName(); 
    113  
    114         String label = null, id = null, code = q.getUnusedConstraintCode(); 
    115         PathNode geneNode = q.addNode("FlyAtlasResult.genes"); 
    116         Constraint c = new Constraint(constraintOp, constraintValue, false, label, code, id, null); 
    117         geneNode.getConstraints().add(c); 
    118  
    119         constraintOp = ConstraintOp.EQUALS; 
    120         code = q.getUnusedConstraintCode(); 
    121         PathNode categoryNode = q.addNode("FlyAtlasResult.affyCall"); 
    122         Constraint categoryConstraint 
    123                         = new Constraint(constraintOp, category, false, label, code, id, null); 
    124         categoryNode.getConstraints().add(categoryConstraint); 
    125  
    126         constraintOp = ConstraintOp.EQUALS; 
    127         code = q.getUnusedConstraintCode(); 
    128         PathNode seriesNode = q.addNode("FlyAtlasResult.assays.name"); 
    129         Constraint seriesConstraint 
    130                         = new Constraint(constraintOp, series, false, label, code, id, null); 
    131         seriesNode.getConstraints().add(seriesConstraint); 
     86        q.setOrderBy("FlyAtlasResult.enrichment", sortAscending); 
     87        q.addOrderBy("FlyAtlasResult.genes.secondaryIdentifier"); 
    13288 
    13389        q.setConstraintLogic("A and B and C"); 
    134  
    135         String direction = "asc"; 
    136         if (category.toLowerCase().equals("up")) { 
    137             direction = "desc"; 
    138         } 
    139  
    140         List<OrderBy>  sortOrder = new ArrayList<OrderBy>(); 
    141  
    142         sortOrder.add(new OrderBy(enrichment, direction)); 
    143         sortOrder.add(new OrderBy(secondaryIdentifier)); 
    144         sortOrder.add(new OrderBy(primaryIdentifier)); 
    145         sortOrder.add(new OrderBy(name)); 
    146         sortOrder.add(new OrderBy(assays)); 
    147         sortOrder.add(new OrderBy(affyCall)); 
    148  
    149         q.setSortOrder(sortOrder); 
    150  
    15190        q.syncLogicExpression("and"); 
    15291 

  • trunk/flymine/webapp/src/org/flymine/web/widget/FlyFishGraphURLGenerator.java

    r16105 r16230  
    1313import org.intermine.metadata.Model; 
    1414import org.intermine.objectstore.ObjectStore; 
    15 import org.intermine.objectstore.query.ConstraintOp; 
    16 import org.intermine.pathquery.Constraint; 
    17 import org.intermine.pathquery.PathNode; 
    1815import org.intermine.pathquery.PathQuery; 
    1916import org.intermine.web.logic.bag.InterMineBag; 
     17import org.intermine.web.logic.query.Constraints; 
    2018import org.intermine.web.logic.widget.GraphCategoryURLGenerator; 
    2119import org.jfree.data.category.CategoryDataset; 
    …… 
    2927{ 
    3028    String bagName; 
     29    private static final  String DATASET = "fly-Fish data set"; 
    3130 
    3231    /** 
    …… 
    8584        PathQuery q = new PathQuery(model); 
    8685 
    87         q.setView("Gene.primaryIdentifier, Gene.secondaryIdentifier, Gene.name"); 
    88         q.addView("Gene.organism.name, Gene.mRNAExpressionResults.stageRange"); 
    89         q.addView("Gene.mRNAExpressionResults.expressed"); 
     86        q.setView("Gene.primaryIdentifier, Gene.secondaryIdentifier, Gene.name, Gene.organism.name," 
     87                  + "Gene.mRNAExpressionResults.stageRange, Gene.mRNAExpressionResults.expressed"); 
    9088 
    91         String bagType = bag.getType(); 
    92         ConstraintOp constraintOp = ConstraintOp.IN; 
    93         String constraintValue = bag.getName(); 
    94  
    95         String label = null, id = null, code = q.getUnusedConstraintCode(); 
    96         Constraint c = new Constraint(constraintOp, constraintValue, false, label, code, id, null); 
    97         q.addNode(bagType).getConstraints().add(c); 
     89        // bag constraint 
     90        q.addConstraint("Gene",  Constraints.in(bag.getName())); 
    9891 
    9992        // filter out BDGP 
    100         constraintOp = ConstraintOp.EQUALS; 
    101         code = q.getUnusedConstraintCode(); 
    102         PathNode datasetNode = q.addNode("Gene.mRNAExpressionResults.dataSet.title"); 
    103         String dataset = "fly-Fish data set"; 
    104         Constraint datasetConstraint 
    105                         = new Constraint(constraintOp, dataset, false, label, code, id, null); 
    106         datasetNode.getConstraints().add(datasetConstraint); 
     93        q.addConstraint("Gene.mRNAExpressionResults.dataSet.title",  Constraints.eq(DATASET)); 
    10794 
    10895        // stage (series) 
    109         constraintOp = ConstraintOp.EQUALS; 
    110         code = q.getUnusedConstraintCode(); 
    111         PathNode stageNode = q.addNode("Gene.mRNAExpressionResults.stageRange"); 
    112         String stageRange = series + " (fly-FISH)"; 
    113         Constraint stageConstraint 
    114                         = new Constraint(constraintOp, stageRange, false, label, code, id, null); 
    115         stageNode.getConstraints().add(stageConstraint); 
     96        q.addConstraint("Gene.mRNAExpressionResults.stageRange", 
     97                        Constraints.eq(series + " (fly-FISH)")); 
    11698 
    11799        // expressed (category) 
    118         constraintOp = ConstraintOp.EQUALS; 
    119         Boolean expressed = Boolean.FALSE; 
    120         if (category.equals("true")) { 
    121             expressed = Boolean.TRUE; 
    122         } 
    123         code = q.getUnusedConstraintCode(); 
    124         PathNode expressedNode = q.addNode("Gene.mRNAExpressionResults.expressed"); 
    125         Constraint expressedConstraint 
    126                         = new Constraint(constraintOp, expressed, false, label, code, id, null); 
    127         expressedNode.getConstraints().add(expressedConstraint); 
     100        Boolean expressed = (category.equals("true") ? Boolean.TRUE : Boolean.FALSE); 
     101        q.addConstraint("Gene.mRNAExpressionResults.expressed",  Constraints.eq(expressed)); 
    128102 
    129103        q.setConstraintLogic("A and B and C and D"); 

  • trunk/flymine/webapp/src/org/flymine/web/widget/TiffinURLQuery.java

    r15963 r16230  
    4343     * {@inheritDoc} 
    4444     */ 
    45     public PathQuery generatePathQuery(Collection<InterMineObject> keys) { 
     45    public PathQuery generatePathQuery(@SuppressWarnings("unused") Collection<InterMineObject> keys) 
     46    { 
    4647        // TODO this method 
    4748        return null;