/**
* @param dbre
* @param template
* @return
*/
private boolean checkAssembly(DatabaseRegistryEntry dbre, SqlTemplate template, int speciesId) {
boolean passes = true;
// 1. get assembly.default
String assDef = template.queryForDefaultObject(META_QUERY, String.class, ASS_DEF, speciesId);
if (StringUtils.isEmpty(assDef)) {
passes = false;
ReportManager.problem(
this,
dbre.getConnection(),
"Meta value for " + ASS_DEF + " is not set for species " + speciesId);
}
if (passes) {
// 2. check to see if it matches the default coord_system version
String version =
template.queryForDefaultObject(COORD_VERSION_QUERY, String.class, speciesId, speciesId);
if (!assDef.equals(version)) {
passes = false;
ReportManager.problem(
this,
dbre.getConnection(),
"Meta value for "
+ ASS_DEF
+ " ("
+ assDef
+ ") does not match min rank coord_system version "
+ version
+ " for species "
+ speciesId);
}
}
return passes;
}
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
List<Integer> numRepeatFeaturesList =
getTemplate(dbre)
.queryForDefaultObjectList("select count(*) from repeat_feature;", Integer.class);
Integer numRepeatFeatures = numRepeatFeaturesList.get(0);
if (numRepeatFeatures == 0) {
ReportManager.problem(this, dbre.getConnection(), "No repeat features found!");
return false;
}
if (numRepeatFeatures < 100) {
ReportManager.problem(
this,
dbre.getConnection(),
"Number of repeat features (" + numRepeatFeatures + ") is suspiciously low!");
return false;
}
return true;
}
/**
* Check that any _rna_edit attribute represents a substitution rather than an insertion or
* deletion
*/
private boolean checkRnaEditAttributes(final DatabaseRegistryEntry dbre) {
boolean ok = true;
RowMapper<Attrib> mapper =
new RowMapper<Attrib>() {
public Attrib mapRow(ResultSet rs, int row) throws SQLException {
return new Attrib(rs.getString(1), rs.getLong(2), rs.getString(3));
}
};
String sql =
"select sr.name, sr.seq_region_id, sra.value "
+ "from seq_region sr join seq_region_attrib sra using (seq_region_id) "
+ "join attrib_type at using (attrib_type_id) where at.code =?";
List<Attrib> attributes = getSqlTemplate(dbre).queryForList(sql, mapper, "_rna_edit");
for (Attrib a : attributes) {
if (!a.isOk()) {
ReportManager.warning(this, dbre.getConnection(), a.toString());
ok = false;
}
}
if (!ok) {
ReportManager.problem(
this,
dbre.getConnection(),
"Detected sequence regions with incorrectly formatted _rna_edit attributes. Check warnings");
}
return ok;
}
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean result = true;
for (Map.Entry<String, String[]> method_tags : getMandatoryTags().entrySet()) {
Vector<String> quoted_tags = new Vector<String>();
for (String t : method_tags.getValue()) {
quoted_tags.add(String.format("'%s'", t));
}
List<String> mlsss =
getTemplate(dbre)
.queryForDefaultObjectList(
String.format(
QUERY,
StringUtils.join(quoted_tags, ","),
method_tags.getKey(),
method_tags.getValue().length),
String.class);
if (mlsss.size() > 0) {
ReportManager.problem(
this,
dbre.getConnection(),
"MLSSs for "
+ method_tags.getKey()
+ " found with no statistics: "
+ StringUtils.join(mlsss, ","));
result = false;
} else {
ReportManager.correct(this, dbre.getConnection(), "PASSED ");
}
}
return result;
}
/**
* Test various things about marker features.
*
* @param dbre The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// only check for human, mouse, rat and zebrafish
Species s = dbre.getSpecies();
if ((dbre.getType() != DatabaseType.SANGER_VEGA
&& (s.equals(Species.HOMO_SAPIENS)
|| s.equals(Species.MUS_MUSCULUS)
|| s.equals(Species.RATTUS_NORVEGICUS)))
|| s.equals(Species.DANIO_RERIO)) { // for
// sangervega
// only
// run
// the
// test
// for
// zebrafish
result &= checkFeaturesAndMapWeights(con);
result &= checkMarkerPriorities(con);
result &= checkAllChromosomesHaveMarkers(con);
}
return result;
} // run
/**
* Check that the meta table exists and has data and the entries correspond to the database name.
*
* @param dbre The database to check.
* @return True if the test passed.
*/
public boolean run(final DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
Species species = dbre.getSpecies();
result &= checkTableExists(con);
result &= tableHasRows(con);
result &= checkSchemaVersionDBName(dbre);
if (species == Species.ANCESTRAL_SEQUENCES) {
// The rest of the tests are not relevant for the ancestral
// sequences DB
return result;
}
if (dbre.getType() == DatabaseType.CORE) {
result &= checkKeysPresent(con);
}
// -------------------------------------------
result &= checkDuplicates(dbre);
// -------------------------------------------
result &= checkArrays(dbre);
return result;
} // run
private boolean checkCodingCountAttributes(final DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
String code = (dbre.getType() == DatabaseType.SANGER_VEGA) ? "KnwnPCCount" : "coding_cnt";
SqlTemplate t = DBUtils.getSqlTemplate(dbre);
String sql =
"select distinct g.seq_region_id from gene g where g.biotype = ? and g.seq_region_id not in (select distinct g.seq_region_id from gene g, seq_region_attrib sa, attrib_type at where g.seq_region_id = sa.seq_region_id and sa.attrib_type_id = at.attrib_type_id and at.code in (?,?))";
List<String> toplevel =
t.queryForDefaultObjectList(sql, String.class, "protein_coding", "LRG", "non_ref");
sql =
"select distinct g.seq_region_id from gene g, seq_region_attrib sa, attrib_type at where g.seq_region_id = sa.seq_region_id and sa.attrib_type_id = at.attrib_type_id and code =? ";
List<String> known = t.queryForDefaultObjectList(sql, String.class, code);
Set<String> missing = new HashSet<String>(toplevel);
missing.removeAll(known);
if (missing.isEmpty()) {
ReportManager.correct(
this,
con,
"All seq_regions with protein_coding genes have a coding_cnt attribute associated with them");
} else {
String msg =
String.format(
"%s regions with protein_coding genes do not have the coding_cnt attribute associated",
missing.size());
ReportManager.problem(this, con, msg);
result = false;
}
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
if (tableHasRows(con, "method_link_species_set")) {
/* Check if have both BLASTZ_NET and LASTZ_NET entries for the same species set */
int numOfBLASTZ_LASTZSpeciesSets =
DBUtils.getRowCount(
con,
"SELECT species_set_id, count(*) FROM method_link_species_set JOIN method_link USING (method_link_id) WHERE TYPE in ('BLASTZ_NET', 'LASTZ_NET') GROUP BY species_set_id HAVING count(*) > 1");
if (numOfBLASTZ_LASTZSpeciesSets > 0) {
ReportManager.problem(
this,
con,
"FAILED method_link_species_set table contains "
+ numOfBLASTZ_LASTZSpeciesSets
+ " entries with a BLASTZ_NET and LASTZ_NET entry for the same species_set");
ReportManager.problem(
this,
con,
"USEFUL SQL: SELECT species_set_id, count(*) FROM method_link_species_set JOIN method_link USING (method_link_id) WHERE TYPE in ('BLASTZ_NET', 'LASTZ_NET') GROUP BY species_set_id HAVING count(*) > 1");
result = false;
}
// Everything below will be ignored on the master database
if (isMasterDB(dbre.getConnection())) {
return result;
}
/* Check method_link_species_set <-> synteny_region */
/* All method_link for syntenies must have an internal ID between 101 and 199 */
result &=
checkForOrphansWithConstraint(
con,
"method_link_species_set",
"method_link_species_set_id",
"synteny_region",
"method_link_species_set_id",
"method_link_id >= 101 and method_link_id < 200");
result &=
checkForOrphans(
con,
"synteny_region",
"method_link_species_set_id",
"method_link_species_set",
"method_link_species_set_id");
} else {
ReportManager.correct(
this, con, "NO ENTRIES in method_link_species_set table, so nothing to test IGNORED");
}
return result;
}
/** Check that the schema_version in the meta table is present and matches the database name. */
private boolean checkSchemaVersionDBName(DatabaseRegistryEntry dbre) {
boolean result = true;
// get version from database name
String dbNameVersion = dbre.getSchemaVersion();
logger.finest("Schema version from database name: " + dbNameVersion);
// get version from meta table
Connection con = dbre.getConnection();
if (dbNameVersion == null) {
ReportManager.warning(this, con, "Can't deduce schema version from database name.");
return false;
}
String schemaVersion =
DBUtils.getRowColumnValue(
con, "SELECT meta_value FROM meta WHERE meta_key='schema_version'");
logger.finest("schema_version from meta table: " + schemaVersion);
if (schemaVersion == null || schemaVersion.length() == 0) {
ReportManager.problem(this, con, "No schema_version entry in meta table");
return false;
} else if (!schemaVersion.matches("[0-9]+")) {
ReportManager.problem(this, con, "Meta schema_version " + schemaVersion + " is not numeric");
return false;
} else if (!dbNameVersion.equals(schemaVersion) && !isSangerVega) { // do
// not
// report
// for
// sangervega
ReportManager.problem(
this,
con,
"Meta schema_version "
+ schemaVersion
+ " does not match version inferred from database name ("
+ dbNameVersion
+ ")");
return false;
} else {
ReportManager.correct(
this,
con,
"schema_version " + schemaVersion + " matches database name version " + dbNameVersion);
}
return result;
}
/**
* Test various things about ditag features.
*
* @param dbre The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
int rows =
DBUtils.getRowCount(
con, "SELECT COUNT(*) FROM identity_xref WHERE cigar_line REGEXP '^[MDI]'");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows + " cigar lines in identity_xref appear to be in the wrong format (number first)");
result = false;
} else {
ReportManager.correct(
this, con, "All cigar lines in identity_xref are in the correct format");
}
return result;
}
public boolean checkTreeStatsArePresent(final DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
if (!tableHasRows(con, "species_tree_root")) {
return true;
}
int n_tags_root =
DBUtils.getRowCount(
con, "SELECT COUNT(*) FROM species_tree_node_tag WHERE tag LIKE 'root\\_%'");
int n_tags_genes =
DBUtils.getRowCount(
con, "SELECT COUNT(*) FROM species_tree_node_tag WHERE tag LIKE 'nb%\\_genes%'");
boolean result = true;
if (n_tags_root == 0) {
ReportManager.problem(
this,
con,
"There are no species_tree_node_tags to describe properties of the root nodes");
result = false;
} else if (n_tags_genes == 0) {
ReportManager.problem(
this, con, "There are no species_tree_node_tags to summarize the gene counts");
result = false;
}
return result;
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
boolean result = true;
result &=
checkForOrphans(con, "gene_align_member", "gene_align_id", "gene_align", "gene_align_id");
result &=
checkForOrphans(con, "gene_align_member", "gene_align_id", "gene_align", "gene_align_id");
result &=
checkForOrphans(con, "gene_align_member", "seq_member_id", "seq_member", "seq_member_id");
result &=
checkOptionalRelation(
con, "gene_tree_root", "gene_align_id", "gene_align", "gene_align_id");
result &=
checkForOrphansWithConstraint(
con,
"gene_tree_root_attr",
"mcoffee_scores_gene_align_id",
"gene_align",
"gene_align_id",
"mcoffee_scores_gene_align_id IS NOT NULL");
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// list of transcript analysis logic_names which are allowed to not have supporting features
String allowed = "'" + StringUtils.join(allowedNoSupporting, "','") + "'";
String sql =
String.format(
"SELECT COUNT(*),t.analysis_id FROM transcript t LEFT JOIN transcript_supporting_feature tsf ON t.transcript_id = tsf.transcript_id JOIN analysis a ON a.analysis_id=t.analysis_id WHERE a.analysis_id=t.analysis_id and tsf.transcript_id IS NULL AND a.logic_name NOT IN (%s) group by t.analysis_id",
allowed);
int rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " transcripts which should have transcript_supporting_features do not have them\nUseful SQL: "
+ sql);
result = false;
} else {
ReportManager.correct(
this, con, "All transcripts that require supporting features have them");
}
return result;
} // run
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
int rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db WHERE db_display_name IS NULL OR db_display_name LIKE ' %'");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " rows in external_db have null or blank db_display_name - this will mean their label is missing on the web page");
result = false;
} else {
ReportManager.correct(this, con, "No blank db_display_name fields in external_db");
}
return result;
} // run
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// --------------------------------
// MGI - dbprimary_acc should have MGI: prefix
int rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db e, xref x WHERE x.external_db_id=e.external_db_id AND e.db_name='MGI' AND x.dbprimary_acc NOT LIKE 'MGI:%'");
if (rows > 0) {
ReportManager.problem(
this, con, rows + " MGI xrefs do not have MGI: prefixes in the dbprimary_acc column");
result = false;
} else {
ReportManager.correct(this, con, "All MGI xrefs have the correct prefix");
}
// --------------------------------
// GO - dbprimary_acc and display_label should have GO: prefix
rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db e, xref x WHERE x.external_db_id=e.external_db_id AND e.db_name='GO' AND (x.dbprimary_acc NOT LIKE 'GO:%' OR x.display_label NOT LIKE 'GO:%')");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " GO xrefs do not have GO: prefixes in the dbprimary_acc and/or display_label columns");
result = false;
} else {
ReportManager.correct(this, con, "All GO xrefs have the correct prefix");
}
// --------------------------------
// ZFIN - dbprimary_acc should begin with ZDB
rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db e, xref x WHERE x.external_db_id=e.external_db_id AND e.db_name='ZFIN_ID' AND x.dbprimary_acc NOT LIKE 'ZDB%'");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " ZFIN xrefs do not have ZDB: prefixes in the dbprimary_acc and/or display_label columns");
result = false;
} else {
ReportManager.correct(this, con, "All ZFIN xrefs have the correct prefix");
}
return result;
} // run
protected void init(DatabaseRegistryEntry dbre) {
super.init();
testDbConn = dbre.getConnection();
sqlTemplateTestDb = getSqlTemplate(testDbConn);
setTeamResponsible(Team.ENSEMBL_GENOMES);
}
/**
* @param dbre
* @param template
* @return
*/
private boolean checkGeneBuild(DatabaseRegistryEntry dbre, SqlTemplate template, int speciesId) {
boolean passes = true;
String gbStart = template.queryForDefaultObject(META_QUERY, String.class, GB_START, speciesId);
if (StringUtils.isEmpty(gbStart)) {
passes = false;
ReportManager.problem(
this, dbre.getConnection(), "Meta value for " + GB_START + " is not set ");
}
return passes;
}
/**
* Override of the test method which makes sure we only test those tables which are required by
* the schema. If a table appears in the list specified by {@link #notRequiredTables()}.
*/
@Override
protected boolean compareTable(Connection master, DatabaseRegistryEntry targetDbre, String table)
throws SQLException {
Species species = targetDbre.getSpecies();
Set<String> notRequired = getSets(notRequiredTables(), species);
Set<String> required = getSets(requiredTables(), species);
if (notRequired.contains(table) || required.contains(table)) {
return true;
}
return super.compareTable(master, targetDbre, table);
}
protected boolean runTest(DatabaseRegistryEntry dbre) {
SqlTemplate template = getTemplate(dbre);
boolean passes = true;
for (int speciesId : dbre.getSpeciesIds()) {
// 2. check genebuild start date is set
passes &= checkGeneBuild(dbre, template, speciesId);
// 3. check that assembly.default matches version for rank 1
// coordsystem
passes &= checkAssembly(dbre, template, speciesId);
}
return passes;
}
/*
* (non-Javadoc)
*
* @see
* org.ensembl.healthcheck.testcase.eg_core.AbstractEgCoreTestCase#runTest
* (org.ensembl.healthcheck.DatabaseRegistryEntry)
*/
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
int n =
getTemplate(dbre)
.queryForDefaultObject(
"Select count(*) from xref where external_db_id=60014", Integer.class);
if (n > 0) {
ReportManager.problem(this, dbre.getConnection(), "IGI xrefs found");
}
return passes;
}
/**
* Check the data in the assembly_exception table. Note referential integrity checks are done in
* CoreForeignKeys.
*
* @param dbre The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
String qry =
"select count(*) from gene,transcript,translation "
+ "where gene.biotype like '%pseudogene%'"
+ " and transcript.gene_id=gene.gene_id "
+ " and translation.transcript_id=transcript.transcript_id and gene.biotype!= 'polymorphic_pseudogene' ";
if (dbre.getType()
== DatabaseType
.SANGER_VEGA) { // for sangervega ignore genes that do not have source havana or WU and
// allow
// polymorphic_pseudogene to have translations
qry += " and (gene.source='havana' or gene.source='WU')";
}
if (dbre.getType() == DatabaseType.SANGER_VEGA || dbre.getType() == DatabaseType.VEGA) {
// Vega allows translations on translated_processed_pseudogene-s
qry += " and gene.biotype != 'translated_processed_pseudogene'";
}
int rows = DBUtils.getRowCount(con, qry);
if (rows > 0) {
result = false;
ReportManager.problem(
this,
con,
"Translation table contains "
+ rows
+ " rows for pseudogene types - should contain none");
}
if (result) {
ReportManager.correct(this, con, "No pseudogenes have translations");
}
return result;
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
if (!DBUtils.checkTableExists(con, "species_tree_node_tag")) {
ReportManager.problem(this, con, "species_tree_node_tag table not present");
return false;
}
// These methods return false if there is any problem with the test
boolean result = true;
result &= checkTreeStatsArePresent(dbre);
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
Map tableToLetter = new HashMap();
tableToLetter.put("gene", "G");
tableToLetter.put("transcript", "T");
tableToLetter.put("translation", "P");
Iterator it = tableToLetter.keySet().iterator();
while (it.hasNext()) {
String table = (String) it.next();
String letter = (String) tableToLetter.get(table);
String regexp = "EST" + letter + "[0-9]+";
String sql =
"SELECT COUNT(*) FROM "
+ table
+ " x, analysis a WHERE a.analysis_id=x.analysis_id "
+ "AND a.logic_name LIKE '%est%' AND x.stable_id NOT REGEXP '"
+ regexp
+ "'";
if (table.equals("translation")) {
// need extra join to transcript table
sql =
"SELECT COUNT(*) FROM translation x, transcript t, analysis a WHERE a.analysis_id=t.analysis_id AND x.transcript_id=t.transcript_id AND a.logic_name LIKE '%est%' AND x.stable_id NOT REGEXP 'ESTP[0-9]+'";
}
int rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
ReportManager.problem(
this, con, rows + " " + table + " stable IDs do not contain EST" + letter);
result = false;
} else {
ReportManager.correct(this, con, "All stable IDs contain EST" + letter);
}
}
return result;
} // run
/*
* (non-Javadoc)
*
* @see
* org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase#runTest(org
* .ensembl.healthcheck.DatabaseRegistryEntry)
*/
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
for (String name :
getTemplate(dbre).queryForDefaultObjectList("select name from seq_region", String.class)) {
if (!name.matches(VALID_NAME)) {
ReportManager.problem(
this,
dbre.getConnection(),
"Seq_region name " + name + " does not match expected expression " + VALID_NAME);
passes = false;
}
}
return passes;
}
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
if (!DBUtils.checkTableExists(con, "method_link_species_set_tag")) {
result = false;
ReportManager.problem(this, con, "method_link_species_set_tag table not present");
return result;
}
result &= checkLowCoverageMLSSAreLinkedToHighCoverageMLSS(dbre);
return result;
}
public boolean checkLowCoverageMLSSAreLinkedToHighCoverageMLSS(final DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
String sql =
"SELECT mlss1.method_link_species_set_id, tag, value, mlss2.method_link_species_set_id, ml2.type"
+ " FROM method_link_species_set mlss1 JOIN method_link ml1 USING (method_link_id)"
+ " LEFT JOIN method_link_species_set_tag mlsst ON mlsst.method_link_species_set_id = mlss1.method_link_species_set_id AND tag = 'high_coverage_mlss_id'"
+ " LEFT JOIN (method_link_species_set mlss2 JOIN method_link ml2 USING (method_link_id)) ON value = mlss2.method_link_species_set_id"
+ " WHERE ml1.type = 'EPO_LOW_COVERAGE'";
List<String[]> all_rows = DBUtils.getRowValuesList(con, sql);
boolean result = true;
for (String[] row : all_rows) {
// Check all the potential errors
if (row[1] == null) {
ReportManager.problem(
this,
con,
String.format("The MLSS ID %s is missing its 'high_coverage_mlss_id' tag", row[0]));
} else if (row[2] == null) {
ReportManager.problem(
this,
con,
String.format(
"The 'high_coverage_mlss_id' tag for MLSS ID %s has a NULL value", row[0]));
} else if (row[3] == null) {
ReportManager.problem(
this,
con,
String.format(
"The value of the 'high_coverage_mlss_id' tag for MLSS ID %s does not link to a valid MLSS ID: '%s'",
row[0], row[2]));
} else if (!row[4].equals("EPO")) {
ReportManager.problem(
this,
con,
String.format(
"The value of the 'high_coverage_mlss_id' tag for MLSS ID %s does not link to a 'EPO' MLSS but '%s' (ID %s)",
row[0], row[4], row[3]));
} else {
// This row is correct: everything is non-NULL, and the EPO_LOW_COVERAGE mlss is linked to a
// EPO
continue;
}
result = false;
}
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if all foreign key relationships are valid.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
result &=
checkForOrphansWithConstraint(
con,
"seq_region",
"seq_region_id",
"dna",
"seq_region_id",
"coord_system_id = (SELECT coord_system_id FROM coord_system WHERE attrib LIKE '%sequence_level%')");
return result;
}
/**
* Check that the phenotype table does not have empty descriptions
*
* @param dbre The database to check.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
boolean result = true;
try {
if (!checkCountIsZero(con, "phenotype", "description is null ")) {
ReportManager.problem(this, con, "Phenotypes with empty descriptions");
result = false;
}
} catch (Exception e) {
ReportManager.problem(this, con, "HealthCheck caused an exception: " + e.getMessage());
result = false;
}
return result;
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
boolean result = true;
result &= checkForOrphansSameTable(con, "species_tree_node", "root_id", "node_id", false);
result &= checkForOrphansSameTable(con, "species_tree_node", "parent_id", "node_id", true);
result &=
checkForOrphans(con, "species_tree_node_tag", "node_id", "species_tree_node", "node_id");
result &= checkForOrphans(con, "species_tree_root", "root_id", "species_tree_node", "node_id");
result &=
checkOptionalRelation(
con, "species_tree_node", "genome_db_id", "genome_db", "genome_db_id");
result &=
checkOptionalRelation(con, "species_tree_node", "taxon_id", "ncbi_taxa_node", "taxon_id");
result &=
checkOptionalRelation(con, "species_tree_node", "taxon_id", "ncbi_taxa_name", "taxon_id");
return result;
}
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
boolean passed = true;
for (String currentTable : table) {
String currentSql = create_sql_for_table(currentTable);
try {
Statement stmt = con.createStatement();
ResultSet rs = stmt.executeQuery(currentSql);
if (rs != null) {
while (rs.next()) {
int numProblemRows = rs.getInt("c");
if (numProblemRows > 0) {
ReportManager.problem(
this,
con,
"The table "
+ currentTable
+ " has "
+ numProblemRows
+ " rows in which the start or "
+ "end coordinates are not positive integers.");
ReportManager.problem(this, con, "USEFUL SQL: " + currentSql);
passed = false;
}
}
}
rs.close();
stmt.close();
} catch (Exception e) {
e.printStackTrace();
}
}
return passed;
}