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[Obo-svn-commit] SF.net SVN: obo:[3437] OBD-WS/trunk/src/org/phenoscape
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From: <ba...@us...> - 2010-07-13 15:35:47
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Revision: 3437
http://obo.svn.sourceforge.net/obo/?rev=3437&view=rev
Author: balhoff
Date: 2010-07-13 15:35:40 +0000 (Tue, 13 Jul 2010)
Log Message:
-----------
Bug fixes to gene annotations query.
Modified Paths:
--------------
OBD-WS/trunk/src/org/phenoscape/obd/query/GeneAnnotationsQueryBuilder.java
OBD-WS/trunk/src/org/phenoscape/obd/query/PhenoscapeDataStore.java
OBD-WS/trunk/src/org/phenoscape/ws/resource/GeneAnnotationsResource.java
Modified: OBD-WS/trunk/src/org/phenoscape/obd/query/GeneAnnotationsQueryBuilder.java
===================================================================
--- OBD-WS/trunk/src/org/phenoscape/obd/query/GeneAnnotationsQueryBuilder.java 2010-07-13 02:17:56 UTC (rev 3436)
+++ OBD-WS/trunk/src/org/phenoscape/obd/query/GeneAnnotationsQueryBuilder.java 2010-07-13 15:35:40 UTC (rev 3437)
@@ -10,6 +10,7 @@
public class GeneAnnotationsQueryBuilder extends QueryBuilder {
private final GeneAnnotationsQueryConfig config;
+ private final boolean totalOnly;
private static final Map<SORT_COLUMN, String> COLUMNS = new HashMap<SORT_COLUMN, String>();
static {
COLUMNS.put(SORT_COLUMN.GENE, "distinct_gene_annotation.gene_label");
@@ -18,25 +19,27 @@
COLUMNS.put(SORT_COLUMN.RELATED_ENTITY, "distinct_gene_annotation.related_entity_label");
}
- public GeneAnnotationsQueryBuilder(GeneAnnotationsQueryConfig config) {
+ public GeneAnnotationsQueryBuilder(GeneAnnotationsQueryConfig config, boolean totalOnly) {
this.config = config;
+ this.totalOnly = totalOnly;
}
@Override
protected void fillStatement(PreparedStatement statement) throws SQLException {
//TODO
- // maybe first shouldn't be a string parameter?
- statement.setString(1, COLUMNS.get(this.config.getSortColumn()));
- statement.setInt(2, this.config.getLimit());
- statement.setInt(3, this.config.getIndex());
+ if (!this.totalOnly) {
+ statement.setInt(1, this.config.getLimit());
+ statement.setInt(2, this.config.getIndex());
+ }
}
@Override
protected String getQuery() {
//TODO
- return "SELECT distinct_gene_annotation.* FROM distinct_gene_annotation " +
- "ORDER BY ? " +
- "LIMIT ? OFFSET ?";
+ final String select = this.totalOnly ? "SELECT count(distinct_gene_annotation.*) " : "SELECT distinct_gene_annotation.* ";
+ final String ending = this.totalOnly ? "" : "ORDER BY " + COLUMNS.get(this.config.getSortColumn()) + " " + "LIMIT ? OFFSET ?";
+ return select + "FROM distinct_gene_annotation " + ending;
+
}
}
Modified: OBD-WS/trunk/src/org/phenoscape/obd/query/PhenoscapeDataStore.java
===================================================================
--- OBD-WS/trunk/src/org/phenoscape/obd/query/PhenoscapeDataStore.java 2010-07-13 02:17:56 UTC (rev 3436)
+++ OBD-WS/trunk/src/org/phenoscape/obd/query/PhenoscapeDataStore.java 2010-07-13 15:35:40 UTC (rev 3437)
@@ -266,7 +266,7 @@
}
public List<GeneAnnotation> getGeneAnnotations(GeneAnnotationsQueryConfig config) throws SQLException {
- final QueryBuilder query = new GeneAnnotationsQueryBuilder(config);
+ final QueryBuilder query = new GeneAnnotationsQueryBuilder(config, false);
return (new QueryExecutor<List<GeneAnnotation>>(this.dataSource, query) {
@Override
public List<GeneAnnotation> processResult(ResultSet result) throws SQLException {
@@ -291,10 +291,10 @@
return annotation;
}
- public int getCountOfGeneAnnotations() throws SQLException {
+ public int getCountOfGeneAnnotations(GeneAnnotationsQueryConfig config) throws SQLException {
// returning distinct count for now because we aren't preserving useful information about different
// annotation statements in the data loader
- final QueryBuilder query = new SimpleQuery("SELECT count(*) FROM distinct_gene_annotation");
+ final QueryBuilder query = new GeneAnnotationsQueryBuilder(config, true);
final QueryExecutor<Integer> queryExecutor = new QueryExecutor<Integer>(this.dataSource, query) {
@Override
public Integer processResult(ResultSet result) throws SQLException {
Modified: OBD-WS/trunk/src/org/phenoscape/ws/resource/GeneAnnotationsResource.java
===================================================================
--- OBD-WS/trunk/src/org/phenoscape/ws/resource/GeneAnnotationsResource.java 2010-07-13 02:17:56 UTC (rev 3436)
+++ OBD-WS/trunk/src/org/phenoscape/ws/resource/GeneAnnotationsResource.java 2010-07-13 15:35:40 UTC (rev 3437)
@@ -35,7 +35,7 @@
* The maximum number of annotations to pull out of the database in one query.
* TODO: need to investigate ideal value for this to maximize performance with acceptable memory usage
*/
- private static final int QUERY_LIMIT = 500;
+ private static final int QUERY_LIMIT = 1000;
private JSONObject query = new JSONObject();
private String sortColumn = "gene";
private int limit;
@@ -70,15 +70,21 @@
public Representation getJSONRepresentation() {
try {
final Iterator<JSONObject> annotations = this.translateToJSON(this.queryForAnnotations());
- return new StreamableJSONRepresentation(annotations, "annotations");
+ final int total = this.queryForAnnotationsCount(this.createInitialQueryConfig());
+ final JSONObject otherValues = new JSONObject();
+ otherValues.put("total", total);
+ return new StreamableJSONRepresentation(annotations, "annotations", otherValues);
} catch (JSONException e) {
- this.setStatus(Status.SERVER_ERROR_INTERNAL, "Error creating JSON object");
+ this.log().error("Error creating JSON object", e);
+ this.setStatus(Status.SERVER_ERROR_INTERNAL, e);
return null;
} catch (SQLException e) {
- this.setStatus(Status.SERVER_ERROR_INTERNAL, "Error querying database");
+ this.log().error("Error querying database", e);
+ this.setStatus(Status.SERVER_ERROR_INTERNAL, e);
return null;
} catch (QueryException e) {
- this.setStatus(Status.SERVER_ERROR_INTERNAL, "Error querying database");
+ this.log().error("Error querying database", e);
+ this.setStatus(Status.SERVER_ERROR_INTERNAL, e);
return null;
}
}
@@ -89,13 +95,16 @@
final Iterator<String> annotations = this.translateToText(this.queryForAnnotations());
return new StreamableTextRepresentation(annotations, MediaType.TEXT_TSV);
} catch (JSONException e) {
- this.setStatus(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid annotation query");
+ this.log().error("Invalid annotation query", e);
+ this.setStatus(Status.CLIENT_ERROR_BAD_REQUEST, e);
return null;
} catch (SQLException e) {
- this.setStatus(Status.SERVER_ERROR_INTERNAL, "Error querying database");
+ this.log().error("Error querying database", e);
+ this.setStatus(Status.SERVER_ERROR_INTERNAL, e);
return null;
} catch (QueryException e) {
- this.setStatus(Status.SERVER_ERROR_INTERNAL, "Error querying database");
+ this.log().error("Error querying database", e);
+ this.setStatus(Status.SERVER_ERROR_INTERNAL, e);
return null;
}
}
@@ -217,17 +226,29 @@
@Override
public void remove() {}
private boolean needMore() {
- return this.gotten < limit;
+ if (limit > 0) {
+ return this.gotten < limit;
+ } else {
+ return true;
+ }
}
};
}
+ private int queryForAnnotationsCount(GeneAnnotationsQueryConfig config) throws SQLException {
+ return this.getDataStore().getCountOfGeneAnnotations(config);
+ }
+
private GeneAnnotationsQueryConfig createInitialQueryConfig() throws JSONException, QueryException {
final GeneAnnotationsQueryConfig config = new GeneAnnotationsQueryConfig();
config.setIndex(this.index);
config.setSortColumn(COLUMNS.get(this.sortColumn));
config.setSortDescending(this.sortDescending);
- config.setLimit(Math.min(this.limit, QUERY_LIMIT));
+ if (this.limit > 0) {
+ config.setLimit(Math.min(this.limit, QUERY_LIMIT));
+ } else {
+ config.setLimit(QUERY_LIMIT);
+ }
if (this.query.has("gene")) {
for (JSONObject gene : this.toIterable(this.query.getJSONArray("gene"))) {
config.addGeneID(gene.getString("id"));
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