Prefix SC tables with SCA_

elisabetb · Sep 8, 2017 · 7bc9848 · 7bc9848
1 parent 1fa64c2
commit 7bc9848
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Showing 5 changed files with 13 additions and 13 deletions.
diff --git a/atlas-misc/scripts/db_updates/single-cell/20170607-create-markergenes-table.sql b/atlas-misc/scripts/db_updates/single-cell/20170607-create-markergenes-table.sql
@@ -1,6 +1,6 @@
 -- Table for storing marker gene probabilities
-DROP TABLE MARKER_GENES CASCADE;
-CREATE TABLE MARKER_GENES (
+DROP TABLE SCA_MARKER_GENES CASCADE;
+CREATE TABLE SCA_MARKER_GENES (
     GENE_ID CHARACTER VARYING (255) NOT NULL,
     EXPERIMENT_ACCESSION CHARACTER VARYING (255) NOT NULL,
     K INTEGER NOT NULL,

diff --git a/atlas-misc/scripts/db_updates/single-cell/20170607-create-singlecellexpression-table.sql b/atlas-misc/scripts/db_updates/single-cell/20170607-create-singlecellexpression-table.sql
@@ -1,6 +1,6 @@
 -- Table for storing single cell expression levels
-DROP TABLE SINGLE_CELL_EXPRESSION CASCADE;
-CREATE TABLE SINGLE_CELL_EXPRESSION (
+DROP TABLE SCA_SINGLE_CELL_EXPRESSION CASCADE;
+CREATE TABLE SCA_SINGLE_CELL_EXPRESSION (
     EXPERIMENT_ACCESSION VARCHAR(255) NOT NULL,
     GENE_ID VARCHAR(255) NOT NULL,
     CELL_ID  VARCHAR(255) NOT NULL,

diff --git a/sc/src/main/java/uk/ac/ebi/atlas/experimentimport/analytics/SingleCellBaselineDao.java b/sc/src/main/java/uk/ac/ebi/atlas/experimentimport/analytics/SingleCellBaselineDao.java
@@ -16,7 +16,7 @@ public class SingleCellBaselineDao {
 
     // Based on experimentation, see https://www.ebi.ac.uk/seqdb/confluence/display/GXA/Single+Cell+Expression+data
     private static final int BATCH_SIZE = 2000;
-    private static final String SC_EXPRESSION_INSERT = "INSERT INTO SINGLE_CELL_EXPRESSION " +
+    private static final String SC_EXPRESSION_INSERT = "INSERT INTO sca_single_cell_expression " +
             "(EXPERIMENT_ACCESSION, GENE_ID, CELL_ID, EXPRESSION_LEVEL) VALUES (?, ?, ?, ?)";
 
     private final JdbcTemplate jdbcTemplate;
@@ -49,7 +49,7 @@ public void loadAnalytics(final String experimentAccession, SingleCellBaselineIn
 
     public void deleteAnalytics(String experimentAccession) {
         LOGGER.info("delete SingleCellExpression for experiment {}", experimentAccession);
-        jdbcTemplate.update("DELETE FROM SINGLE_CELL_EXPRESSION WHERE EXPERIMENT_ACCESSION = ?", experimentAccession);
+        jdbcTemplate.update("DELETE FROM sca_single_cell_expression WHERE EXPERIMENT_ACCESSION = ?", experimentAccession);
     }
 
 }
diff --git a/sc/src/main/java/uk/ac/ebi/atlas/markergenes/MarkerGeneDao.java b/sc/src/main/java/uk/ac/ebi/atlas/markergenes/MarkerGeneDao.java
@@ -24,10 +24,10 @@ public class MarkerGeneDao {
     // Based on experimentation, see https://www.ebi.ac.uk/seqdb/confluence/display/GXA/Single+Cell+Expression+data
     private static final int BATCH_SIZE = 2000;
     private static final String MARKER_GENE_INSERT_STATEMENT =
-            "INSERT INTO marker_genes " +
+            "INSERT INTO sca_marker_genes " +
             "(gene_id, experiment_accession, k, cluster_id, marker_probability) VALUES (?, ?, ?, ?, ?)";
     private static final String MARKER_GENE_SELECT_STATEMENT =
-            "SELECT * FROM marker_genes WHERE gene_id=? AND marker_probability>?";
+            "SELECT * FROM sca_marker_genes WHERE gene_id=? AND marker_probability>?";
 
 
     private final JdbcTemplate jdbcTemplate;
@@ -85,12 +85,12 @@ public ImmutableList<MarkerGeneProfile> fetchMarkerGenes(String geneId, double c
     }
 
     public void deleteAll() {
-        int rowCount = jdbcTemplate.update("DELETE FROM marker_genes");
+        int rowCount = jdbcTemplate.update("DELETE FROM sca_marker_genes");
         LOGGER.info("{} rows deleted", rowCount);
     }
 
     public void delete(String experimentAccession) {
-        int rowCount = jdbcTemplate.update("DELETE FROM marker_genes WHERE experiment_accession=?", experimentAccession);
+        int rowCount = jdbcTemplate.update("DELETE FROM sca_marker_genes WHERE experiment_accession=?", experimentAccession);
         LOGGER.info("{} rows deleted", rowCount);
     }
 

diff --git a/sc/src/test/java/uk/ac/ebi/atlas/markergenes/MarkerGenesSearchServiceIT.java b/sc/src/test/java/uk/ac/ebi/atlas/markergenes/MarkerGenesSearchServiceIT.java
@@ -37,7 +37,7 @@ public class MarkerGenesSearchServiceIT {
     public void searchIdsOfGenesWithHighProbability() throws Exception {
         List<String> fiveMarkerGeneIds =
                 jdbcTemplate.queryForList(
-                        "SELECT DISTINCT(gene_id) FROM marker_genes WHERE marker_probability>? LIMIT 5",
+                        "SELECT DISTINCT(gene_id) FROM sca_marker_genes WHERE marker_probability>? LIMIT 5",
                         DEFAULT_P_THRESHOLD).stream()
             .map(rowMap -> (String) rowMap.get("gene_id"))
             .collect(Collectors.toList());
@@ -57,8 +57,8 @@ public void searchIdsOfGenesWithHighProbability() throws Exception {
     @Test
     public void searchIdsOfGenesWithLowProbability() throws Exception {
         List<String> fiveNonMarkerGeneIds = jdbcTemplate.queryForList(
-                "SELECT all_p.gene_id FROM marker_genes all_p LEFT JOIN " +
-                "  (SELECT gene_id, marker_probability FROM marker_genes WHERE marker_probability>?) high_p ON all_p.gene_id=high_p.gene_id " +
+                "SELECT all_p.gene_id FROM sca_marker_genes all_p LEFT JOIN " +
+                "  (SELECT gene_id, marker_probability FROM sca_marker_genes WHERE marker_probability>?) high_p ON all_p.gene_id=high_p.gene_id " +
                 "WHERE high_p.gene_id IS NULL LIMIT 5", DEFAULT_P_THRESHOLD).stream()
                 .map(rowMap -> (String) rowMap.get("gene_id"))
                 .collect(Collectors.toList());