From 7bc984884609959b721ca811a3d6a8e322859c3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alfonso=20Mu=C3=B1oz-Pomer?= Date: Thu, 7 Sep 2017 11:51:44 +0100 Subject: [PATCH] Prefix SC tables with SCA_ --- .../single-cell/20170607-create-markergenes-table.sql | 4 ++-- .../20170607-create-singlecellexpression-table.sql | 4 ++-- .../experimentimport/analytics/SingleCellBaselineDao.java | 4 ++-- .../java/uk/ac/ebi/atlas/markergenes/MarkerGeneDao.java | 8 ++++---- .../ebi/atlas/markergenes/MarkerGenesSearchServiceIT.java | 6 +++--- 5 files changed, 13 insertions(+), 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 index e5dba70fd..ab2d76603 100644 --- 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 index 002431a7b..cccdded21 100644 --- 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 index 7caef4349..45c15487d 100644 --- 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 index 93e4eecd6..488919ec8 100644 --- 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 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 index 771710b96..5a1faf030 100644 --- 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 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 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());