use of org.molgenis.emx2.Operator.EQUALS in project molgenis-emx2 by molgenis.
the class ImportSchemaTask method rollback.
private void rollback(Task task) {
for (Step step : task.getSteps()) {
if (step.getStatus().equals(COMPLETED)) {
step.setStatus(SKIPPED);
step.setDescription("Rolled back: " + step.getDescription());
}
if (step instanceof Task) {
this.rollback((Task) step);
}
}
}
use of org.molgenis.emx2.Operator.EQUALS in project molgenis-emx2 by molgenis.
the class ImportDataTask method run.
@Override
public void run() {
this.start();
// create a task for each table
boolean skipped = true;
// create task for the import, including subtasks for each sheet
for (Table table : schema.getTablesSorted()) {
if (tableStore.containsTable(table.getName())) {
ImportTableTask importTableTask = new ImportTableTask(tableStore, table, isStrict());
this.addSubTask(importTableTask);
importTableTask.run();
skipped = false;
}
}
// check what files we skipped
Collection<String> tableNames = schema.getTableNames();
try {
for (String sheet : tableStore.tableNames()) {
if (!sheet.startsWith("_files/") && !"molgenis".equals(sheet) && !"molgenis_settings".equals(sheet) && !"molgenis_members".equals(sheet) && !tableNames.contains(sheet)) {
this.addSubTask("Sheet with name '" + sheet + "' was skipped: no table with that name found").setSkipped();
}
}
} catch (UnsupportedOperationException e) {
// ignore, not important
}
// execute the import tasks
if (skipped) {
this.addSubTask("Import data skipped: No data sheet included").setSkipped();
}
this.complete();
}
use of org.molgenis.emx2.Operator.EQUALS in project molgenis-emx2 by molgenis.
the class SqlTableMetadata method addTransaction.
// static to ensure we don't touch 'this' until complete
private static SqlTableMetadata addTransaction(Database db, String schemaName, String tableName, Column[] column) {
SqlTableMetadata tm = (SqlTableMetadata) db.getSchema(schemaName).getMetadata().getTableMetadata(tableName);
// first per-column actions, then multi-column action such as composite keys/refs
int position = MetadataUtils.getMaxPosition(tm.getJooq(), schemaName) + 1;
for (Column c : column) {
long start = System.currentTimeMillis();
if (tm.getLocalColumn(c.getName()) != null) {
tm.alterColumn(c);
} else {
Column newColumn = new Column(tm, c);
if (tm.getInherit() != null && tm.getInheritedTable().getColumn(c.getName()) != null && // this column is replicated in all subclass tables
!c.getName().equals(MG_TABLECLASS)) {
throw new MolgenisException("Cannot add column " + tm.getTableName() + "." + c.getName() + ": column exists in inherited class " + tm.getInherit());
}
if (!newColumn.isHeading()) {
validateColumn(newColumn);
if (newColumn.getPosition() == null) {
// positions are asumed to number up in a schema
newColumn.setPosition(position++);
}
executeCreateColumn(tm.getJooq(), newColumn);
tm.columns.put(c.getName(), newColumn);
if (newColumn.getKey() > 0) {
createOrReplaceKey(tm.getJooq(), newColumn.getTable(), newColumn.getKey(), newColumn.getTable().getKeyFields(newColumn.getKey()));
}
executeCreateRefConstraints(tm.getJooq(), newColumn);
} else {
saveColumnMetadata(tm.getJooq(), newColumn);
tm.columns.put(c.getName(), newColumn);
}
log(tm, start, "added column '" + newColumn.getName() + "' to table " + tm.getTableName());
}
}
return tm;
}
use of org.molgenis.emx2.Operator.EQUALS in project molgenis-emx2 by molgenis.
the class SqlTableMetadata method alterColumnTransaction.
// static to ensure we don't touch 'this' until transaction succesfull
private static SqlTableMetadata alterColumnTransaction(String schemaName, String tableName, String columnName, Column column, Database db) {
SqlTableMetadata tm = (SqlTableMetadata) db.getSchema(schemaName).getMetadata().getTableMetadata(tableName);
Column newColumn = new Column(tm, column);
Column oldColumn = tm.getColumn(columnName);
// primary keys by definition are required
if (newColumn.getKey() == 1) {
newColumn.setRequired(true);
}
validateColumn(newColumn);
// check if reference and of different size
if (newColumn.isRefArray() && !newColumn.getName().equals(oldColumn.getName()) && !newColumn.getColumnType().equals(oldColumn.getColumnType()) && newColumn.getRefTable().getPrimaryKeyFields().size() > 1) {
throw new MolgenisException("Alter column of '" + oldColumn.getName() + " failed: REF_ARRAY is not supported for composite keys of table " + newColumn.getRefTableName());
}
// if changing 'ref' then check if not refBack exists
if (!oldColumn.getColumnType().equals(newColumn.getColumnType())) {
tm.checkNotRefback(columnName, oldColumn);
}
// drop old key, if touched
if (oldColumn.getKey() > 0 && newColumn.getKey() != oldColumn.getKey()) {
executeDropKey(tm.getJooq(), oldColumn.getTable(), oldColumn.getKey());
}
// drop referential constraints around this column
executeRemoveRefConstraints(tm.getJooq(), oldColumn);
// remove refBacks if exist
executeRemoveRefback(oldColumn, newColumn);
// add ontology table if needed
if (newColumn.isOntology()) {
createOntologyTable(newColumn);
}
// rename and retype if needed
executeAlterType(tm.getJooq(), oldColumn, newColumn);
executeAlterName(tm.getJooq(), oldColumn, newColumn);
// only applies to key=1
if ((oldColumn.isPrimaryKey() || newColumn.isPrimaryKey()) && oldColumn.isRequired() && !oldColumn.isRequired() == newColumn.isRequired()) {
executeSetRequired(tm.getJooq(), newColumn);
}
// update the metadata so we can use it for new keys and references
if (column.getPosition() == null) {
column.setPosition(tm.columns.get(columnName).getPosition());
}
// remove the old
tm.columns.remove(columnName);
// add the new
tm.columns.put(column.getName(), column);
// reapply ref constrainst
executeCreateRefConstraints(tm.getJooq(), newColumn);
// check if refBack constraints need updating
reapplyRefbackContraints(oldColumn, newColumn);
// create/update key, if touched
if (newColumn.getKey() != oldColumn.getKey()) {
createOrReplaceKey(tm.getJooq(), tm, newColumn.getKey(), tm.getKeyFields(newColumn.getKey()));
}
// delete old column if name changed, then save any other metadata changes
if (!oldColumn.getName().equals(newColumn.getName()))
deleteColumn(tm.getJooq(), oldColumn);
saveColumnMetadata(tm.getJooq(), newColumn);
return tm;
}
use of org.molgenis.emx2.Operator.EQUALS in project molgenis-emx2 by molgenis.
the class FileApi method getFile.
public static String getFile(Request request, Response response) throws IOException {
String tableName = request.params("table");
String columnName = request.params("column");
String id = request.params("id");
Schema schema = getSchema(request);
Table t = schema.getTable(tableName);
if (t == null) {
throw new MolgenisException("Download failed: Table '" + tableName + "' not found in schema " + schema.getName());
}
Column c = t.getMetadata().getColumn(columnName);
if (c == null) {
throw new MolgenisException("Download failed: Column '" + columnName + "' not found in table " + schema.getName() + "." + tableName);
}
List<Row> result = t.query().select(t.getMetadata().getPrimaryKeyFields().stream().map(f -> s(f.getName())).toArray(SelectColumn[]::new)).select(s(columnName, s("contents"), s("mimetype"), s("extension"))).where(f(columnName, f("id", EQUALS, id))).retrieveRows();
if (result.size() != 1) {
throw new MolgenisException("Download failed: file id '" + id + "' not found in table " + tableName);
}
String ext = result.get(0).getString(columnName + "_extension");
String mimetype = result.get(0).getString(columnName + "_mimetype");
byte[] contents = result.get(0).getBinary(columnName + "_contents");
response.raw().setHeader("Content-Disposition", "attachment; filename=" + c.getName() + "." + ext);
response.raw().setContentType(mimetype);
try (OutputStream out = response.raw().getOutputStream()) {
// autoclosing
out.write(contents);
out.flush();
}
return "";
}
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