Examples with Table org.molgenis.emx2.Table used on opensource projects

Example 26 with Table

use of org.molgenis.emx2.Table in project molgenis-emx2 by molgenis.

the class LinkedDataFragmentsApi method ttlTable.

private static String ttlTable(Request request, Response response) {
    Table table = getTable(request);
    StringWriter sw = new StringWriter();
    LinkedDataService.getTtlForTable(table, new PrintWriter(sw));
    return sw.getBuffer().toString();
}

Example 27 with Table

use of org.molgenis.emx2.Table in project molgenis-emx2 by molgenis.

the class SqlColumnRefBackExecutor method createRefBackColumnConstraints.

// will create a dummy array column matching the toColumn we will link to
// will create a before insert trigger to update all REF instances in the other table that needs
// updating
static void createRefBackColumnConstraints(DSLContext jooq, Column ref) {
    try {
        // get ref table
        validateColumn(ref);
        String columNames = ref.getReferences().stream().map(Reference::getName).collect(Collectors.joining(","));
        // get the via column which is also in the 'toTable'
        String refBackColumnName = ref.getRefBack();
        if (refBackColumnName == null) {
            throw new MolgenisException("Create column failed: Create of REFBACK column '" + ref.getQualifiedName() + "' failed because refBack was not set.");
        }
        // create the trigger so that insert/update/delete on REFBACK column updates the
        // relationship
        Column refBack = ref.getRefBackColumn();
        if (refBack == null) {
            throw new MolgenisException("Set refBack on column '" + ref.getTableName() + "." + ref.getName() + "'failed: refBack column '" + ref.getRefBack() + "'not found");
        }
        if (refBack.isRef()) {
            createTriggerForRef(jooq, ref, true);
            createTriggerForRef(jooq, ref, false);
        } else if (refBack.isRefArray()) {
            createTriggerForRefArray(jooq, ref);
        } else {
            throw new MolgenisException("Create column failed: Create of REFBACK column(s) '" + ref.getTableName() + "." + getNames(ref) + "' failed because refBack '" + ref.getRefBack() + "' was not of type REF, REF_ARRAY");
        }
    } catch (DataAccessException dae) {
        throw new SqlMolgenisException("REFBACK column(s) '" + getNames(ref) + "' could not be created in table '" + ref.getTableName() + "'", dae);
    }
}

Example 28 with Table

use of org.molgenis.emx2.Table in project molgenis-emx2 by molgenis.

the class SqlColumnRefBackExecutor method createTriggerForRef.

private static void createTriggerForRef(DSLContext jooq, Column column, boolean isUpdateTrigger) {
    // check if any refBack array has non-existing pkey
    // remove refs from other table if not any more in refBack array
    // update refs from other table to new identifier ( automatic via cascade , nothing to
    // do here)
    // add refs from other table if new in refBack array
    String schemaName = column.getTable().getSchema().getName();
    String triggerName = refBackUpdateTriggerName(column) + (isUpdateTrigger ? "_UPDATE" : "_INSERT");
    List<Reference> columns = column.getReferences();
    // begin
    String sql = "CREATE FUNCTION {0}() RETURNS trigger AS $BODY$ " + "\nDECLARE my_row RECORD;" + "\nBEGIN";
    // add check if the refs actually exist
    sql += "\n\t-- raise error for first refColumn value that does not in refTable key values " + "\n\tFOR my_row IN SELECT {1} FROM newtab EXCEPT (SELECT {2} FROM {3}) LOOP" + "\n\t\tRAISE EXCEPTION USING ERRCODE='23503', " + "\n\t\tMESSAGE = 'insert on table '||{4}||' violates foreign key constraint for refback column(s)'," + "\n\t\tDETAIL = 'Key ('||{5}||')=('|| {6} ||') is not present in table '||{7}||', column '||{8};" + "\n\tEND LOOP;";
    // in case of update, we should also remove the references not in the 'old'
    if (isUpdateTrigger) {
        sql += "\n\t-- remove ref to 'oldtable'.key if not anymore in refarray" + "\n\tFOR my_row IN SELECT {13},{1} FROM oldtab EXCEPT (SELECT {13},{1} FROM newtab) LOOP" + "\n\t\tUPDATE {3} set {9} WHERE {12};" + "\n\tEND LOOP;";
        sql += "\n\t-- set to ref to 'newtable'.key if in refBack values list" + "\n\tFOR my_row IN SELECT {13},{1} FROM newtab EXCEPT (SELECT {13},{1} FROM oldtab) LOOP" + "\n\t\tUPDATE {3} set {11} WHERE {12};" + "\n\tEND LOOP;";
    } else {
        // in case of insert
        sql += "\n\t-- set to ref to 'newtable'.key if in refBack values list" + "\n\tFOR my_row IN SELECT {13},{1} FROM newtab LOOP" + "\n\t\tUPDATE {3} set {11} WHERE {12};" + "\n\tEND LOOP;";
    }
    // end
    sql += "\n\tRETURN NEW;" + "\nEND; $BODY$ LANGUAGE plpgsql;";
    RowCountQuery q = jooq.query(sql, // 0 function name
    name(schemaName, triggerName), // 1 selection of unnested inputs
    keyword(columns.stream().map(r -> "unnest(" + name(r.getName()) + ") as " + name(r.getName())).collect(Collectors.joining(","))), // 2 foreign key column names refBack refers to
    keyword(columns.stream().map(r -> name(r.getRefTo()).toString()).collect(Collectors.joining(","))), // 3 refTable
    table(name(schemaName, column.getRefTableName())), // 4 inline string of table for debug message
    inline(column.getTable().getTableName()), // 5 inline columns
    keyword(columns.stream().map(r -> inline(r.getName()).toString()).collect(Collectors.joining("||','||"))), // 6 concat of the error column values
    keyword(columns.stream().map(r -> "COALESCE(my_row." + name(r.getRefTo()).toString() + ",'NULL')").collect(Collectors.joining("||','||"))), // 7 inline refTable
    inline(column.getRefTable().getTableName()), // 8 inline toColumns
    keyword(columns.stream().map(r -> inline(r.getRefTo()).toString()).collect(Collectors.joining("||','||"))), // 9 set refBack to null
    keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getName()) + "=NULL").collect(Collectors.joining(","))), // 10 where references old key and not new key
    keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getName()) + "=OLD." + name(r.getRefTo())).collect(Collectors.joining(" AND "))), // 11 set to point to this.key(s)
    keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getName()) + "=my_row." + name(r.getRefTo())).collect(Collectors.joining(","))), // 12 where reftable.key=refback
    keyword(columns.stream().map(r -> name(r.getRefTo()) + "=my_row." + name(r.getName())).collect(Collectors.joining(" AND "))), // 13 keys of this table
    keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getRefTo()).toString()).collect(Collectors.joining(","))), // 14 where this keys
    keyword(column.getRefBackColumn().getReferences().stream().map(Reference::getRefTo).map(s -> name(s) + "=NEW." + name(s)).collect(Collectors.joining(" AND "))));
    // System.out.println("sql: " + q.getSQL());
    q.execute();
    String trigger = isUpdateTrigger ? "CREATE TRIGGER {0} " + "\n\tAFTER UPDATE ON {2}" + "\n\tREFERENCING NEW TABLE AS newtab OLD TABLE AS oldtab" + "\n\tEXECUTE PROCEDURE {3}()" : "CREATE TRIGGER {0} " + "\n\tAFTER INSERT ON {2}" + "\n\tREFERENCING NEW TABLE AS newtab" + "\n\tEXECUTE PROCEDURE {3}()";
    jooq.execute(trigger, // 0 name of the trigger
    name(triggerName), // 1 the columns of the refBack that should be set to trigger the trigger
    keyword(columns.stream().map(r -> name(r.getName()).toString()).collect(Collectors.joining(","))), // name of the table
    name(schemaName, column.getTable().getTableName()), // reference to the trigger function
    name(schemaName, triggerName));
}

Example 29 with Table

use of org.molgenis.emx2.Table in project molgenis-emx2 by molgenis.

the class CatalogueSiteMapTest method buildSiteMap.

@Test
public void buildSiteMap() {
    Schema schema = mock(Schema.class);
    Table table = mock(Table.class);
    Query query = mock(Query.class);
    List<Row> row = Collections.singletonList(new Row("pid", "my-cohort-pid"));
    when(schema.getTable("Cohorts")).thenReturn(table);
    when(table.select(any())).thenReturn(query);
    when(query.retrieveRows()).thenReturn(row);
    CatalogueSiteMap catalogueSiteMap = new CatalogueSiteMap(schema, "https://my/base/url");
    String expected = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<urlset xmlns=\"http://www.sitemaps.org/schemas/sitemap/0.9\" >\n" + "  <url>\n" + "    <loc>https://my/base/url/ssr-catalogue/Cohorts/my-cohort-pid</loc>\n" + "  </url>\n" + "</urlset>";
    assertEquals(expected, catalogueSiteMap.buildSiteMap());
}

Example 30 with Table

use of org.molgenis.emx2.Table in project molgenis-emx2 by molgenis.

the class Column method getReferences.

/**
 * will return self in case of single, and multiple in case of composite key wrapper
 */
public List<Reference> getReferences() {
    // no ref
    if (getRefTable() == null) {
        return new ArrayList<>();
    }
    List<Column> pkeys = getRefTable().getPrimaryKeyColumns();
    List<Reference> refColumns = new ArrayList<>();
    // check if primary key exists
    if (pkeys.size() == 0) {
        throw new MolgenisException("Error in column '" + getName() + "': Reference to " + getRefTableName() + " fails because that table has no primary key");
    }
    // create the refs
    Column refLink = getRefLinkColumn();
    for (Column keyPart : pkeys) {
        if (keyPart.isReference()) {
            for (Reference ref : keyPart.getReferences()) {
                ColumnType type = ref.getPrimitiveType();
                if (!isRef()) {
                    type = getArrayType(type);
                }
                List<String> path = ref.getPath();
                path.add(0, keyPart.getName());
                String name = null;
                if (refLink != null) {
                    for (Reference overlap : refLink.getReferences()) {
                        if (overlap.getTargetTable().equals(ref.getTargetTable()) && overlap.getTargetColumn().equals(ref.getTargetColumn())) {
                            name = overlap.getName();
                        }
                    }
                }
                if (name == null) {
                    name = getName();
                    if (pkeys.size() > 1) {
                        name += COMPOSITE_REF_SEPARATOR + ref.getName();
                    }
                }
                refColumns.add(new Reference(this, name, ref.getName(), getColumnType(), type, keyPart.getColumnType().isArray(), ref.getTargetTable(), ref.getTargetColumn(), ref.isRequired() || this.isRequired(), path));
            }
        } else {
            ColumnType type = keyPart.getColumnType();
            // all but ref is array
            if (!isRef()) {
                type = getArrayType(type);
            }
            // create the ref
            String name = getName();
            if (pkeys.size() > 1) {
                name += COMPOSITE_REF_SEPARATOR + keyPart.getName();
            }
            refColumns.add(new Reference(this, name, keyPart.getName(), getColumnType(), type, getColumnType().isArray(), getRefTableName(), keyPart.getName(), keyPart.isRequired() || this.isRequired(), new ArrayList<>(List.of(keyPart.getName()))));
        }
    }
    // clean up in case only one
    if (refColumns.stream().filter(r -> r.getName().startsWith(getName())).count() == 1) {
        refColumns = refColumns.stream().map(r -> {
            if (r.getName().startsWith(getName()))
                r.setName(getName());
            return r;
        }).collect(Collectors.toList());
    }
    // remove duplicates
    HashSet<Object> seen = new HashSet<>();
    refColumns.removeIf(e -> !seen.add(e.getName()));
    return refColumns;
}