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com.marklogic.contentpump.DatabaseContentReader Maven / Gradle / Ivy
/*
* Copyright (c) 2019 MarkLogic Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package com.marklogic.contentpump;
import java.io.IOException;
import java.math.BigInteger;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import com.fasterxml.jackson.databind.JsonNode;
import com.marklogic.mapreduce.ContentType;
import com.marklogic.mapreduce.DocumentURI;
import com.marklogic.mapreduce.MarkLogicConstants;
import com.marklogic.mapreduce.MarkLogicCounter;
import com.marklogic.mapreduce.MarkLogicDocument;
import com.marklogic.mapreduce.MarkLogicInputSplit;
import com.marklogic.mapreduce.MarkLogicRecordReader;
import com.marklogic.mapreduce.utilities.InternalUtilities;
import com.marklogic.mapreduce.utilities.URIUtil;
import com.marklogic.xcc.AdhocQuery;
import com.marklogic.xcc.ContentSource;
import com.marklogic.xcc.RequestOptions;
import com.marklogic.xcc.ResultItem;
import com.marklogic.xcc.exceptions.QueryException;
import com.marklogic.xcc.exceptions.RequestException;
import com.marklogic.xcc.exceptions.XccConfigException;
import com.marklogic.xcc.types.JsonItem;
import com.marklogic.xcc.types.ValueType;
import com.marklogic.xcc.types.XSInteger;
import com.marklogic.xcc.types.XdmElement;
import com.marklogic.xcc.types.XdmItem;
/**
* A MarkLogicRecordReader that fetches data from MarkLogic server and generates
* key value pairs.
*
* @author ali
*
*/
//can't reuse MarkLogicRecordReader, because the prolog of the query need to be
//changed, can't simply change query body
public class DatabaseContentReader extends
MarkLogicRecordReader implements
ConfigConstants {
static final float DOCUMENT_TO_FRAGMENT_RATIO = 1;
public static final Log LOG = LogFactory
.getLog(DatabaseContentReader.class);
protected boolean copyCollection;
protected boolean copyPermission;
protected boolean copyProperties;
protected boolean copyQuality;
protected boolean copyMetadata;
protected HashMap metadataMap;
protected String ctsQuery = null;
protected boolean nakedDone = false;
protected boolean docDone = false;
/**
* Current key.
*/
protected DocumentURI currentKey;
/**
* Current value.
*/
protected DatabaseDocumentWithMeta currentValue;
protected int nakedCount;
public DatabaseContentReader(Configuration conf) {
super(conf);
copyCollection = conf.getBoolean(MarkLogicConstants.COPY_COLLECTIONS,
true);
copyPermission = conf.getBoolean(CONF_COPY_PERMISSIONS, true);
copyProperties = conf.getBoolean(CONF_COPY_PROPERTIES,true);
copyQuality = conf.getBoolean(MarkLogicConstants.COPY_QUALITY, true);
copyMetadata = conf.getBoolean(MarkLogicConstants.COPY_METADATA, true);
currentKey = new DocumentURI();
metadataMap = new HashMap();
}
@Override
public void initialize(InputSplit inSplit, TaskAttemptContext context)
throws IOException, InterruptedException {
mlSplit = (MarkLogicInputSplit) inSplit;
count = 0;
nakedCount = 0;
context.getCounter(MarkLogicCounter.ESTIMATED_INPUT_RECORDS)
.increment(mlSplit.getLength());
// construct the server URI
hostNames = mlSplit.getLocations();
if (hostNames == null || hostNames.length < 1) {
throw new IllegalStateException("Empty split locations.");
}
if (LOG.isDebugEnabled()) {
LOG.debug("split location: " + hostNames[0]);
}
replicas = mlSplit.getReplicas();
curForest = -1;
if (replicas != null) {
for (int i = 0; i < replicas.size(); i++) {
if (replicas.get(i).getHostName().equals(hostNames[0])) {
curForest = i;
break;
}
}
}
retry = 0;
sleepTime = 500;
init();
}
/* in case of failover, use init() instead of initialize() for retry */
private void init()
throws IOException, InterruptedException {
nakedDone = false;
// initialize the total length
float recToFragRatio = conf.getFloat(RECORD_TO_FRAGMENT_RATIO,
getDefaultRatio());
length = mlSplit.getLength() * recToFragRatio;
// generate the query
String queryText;
long start = mlSplit.getStart() + 1 + count;
long end = mlSplit.isLastSplit() ? Long.MAX_VALUE : start
+ mlSplit.getLength() - count - 1;
String src = conf.get(MarkLogicConstants.DOCUMENT_SELECTOR);
redactionRuleCol = conf.getStrings(REDACTION_RULE_COLLECTION);
Collection nsCol = null;
if (src != null) {
nsCol = conf.getStringCollection(
MarkLogicConstants.PATH_NAMESPACE);
} else {
src = "fn:collection()";
}
ctsQuery = conf.get(MarkLogicConstants.QUERY_FILTER);
StringBuilder buf = new StringBuilder();
if (ctsQuery != null) {
buildSearchQuery(src, ctsQuery, nsCol, buf);
} else {
buildDocExprQuery(src, nsCol, null, buf);
}
src = buf.toString();
buf = new StringBuilder();
buf.append("xquery version \"1.0-ml\"; \n");
buf.append("import module namespace hadoop = ");
buf.append("\"http://marklogic.com/xdmp/hadoop\" at ");
buf.append("\"/MarkLogic/hadoop.xqy\";\n");
if (redactionRuleCol != null) {
buf.append(
"import module namespace rdt = \"http://marklogic.com/xdmp/redaction\" at \"/MarkLogic/redaction.xqy\";\n");
}
buf.append(
"declare namespace mlmr=\"http://marklogic.com/hadoop\";\n");
buf.append("declare option xdmp:output \"indent=no\";\n");
buf.append("declare option xdmp:output \"indent-untyped=no\";\n");
buf.append(
"declare variable $mlmr:splitstart as xs:integer external;\n");
buf.append(
"declare variable $mlmr:splitend as xs:integer external;\n");
buf.append("let $cols := ");
buf.append(src);
buf.append("\nlet $all-meta :=");
buf.append("\nfor $doc in $cols");
buf.append("\nlet $uri := fn:base-uri($doc)\n return (");
buf.append("'META',");
buf.append("$uri,");
buf.append("if(fn:empty($doc/node())) then 0 ");
buf.append("else if (fn:count($doc/node())>1) then \"element\" ");
buf.append("else xdmp:node-kind($doc/node())");
if (copyCollection || copyPermission || copyProperties || copyQuality) {
buf.append(",");
if (copyCollection) {
buf.append("xdmp:document-get-collections($uri),\n");
}
if (copyPermission) {
buf.append("let $list := xdmp:document-get-permissions($uri)\n");
buf.append("return hadoop:get-permissions($list),");
}
// if copy-quality, else + 0
if (copyQuality) {
buf.append("xdmp:document-get-quality($uri),\n");
} else {
buf.append("0,");
}
// if copy-metadata
if (copyMetadata) {
buf.append(
"(let $f := fn:function-lookup(xs:QName('xdmp:document-get-metadata'),1)\n"
+ "return if (exists($f)) then $f($uri) else ()),\n");
}
// if copy-properties, else + (),\n
if (copyProperties) {
buf.append("xdmp:document-properties($uri)/prop:properties,\n");
}
} else {
buf.append(",0,"); // quality
buf.append("(),\n");//properties
}
// end-of-record marker
buf.append("0");
buf.append(" )\n");
buf.append("return ($all-meta");
buf.append(",'EOM',$cols)");
queryText = buf.toString();
if (LOG.isDebugEnabled()) {
LOG.debug(queryText);
}
// set up a connection to the server
while (retry < maxRetries) {
try {
if (retry == 1) {
LOG.info("Retrying connect");
}
String curForestName = "";
String curHostName = "";
if (curForest == -1) {
curForestName = mlSplit.getForestId().toString();
curHostName = hostNames[0];
} else {
curForestName = replicas.get(curForest).getForest();
curHostName = replicas.get(curForest).getHostName();
}
ContentSource cs = InternalUtilities.getInputContentSource(conf,
curHostName);
session = cs.newSession("#"+curForestName);
if (LOG.isDebugEnabled()) {
LOG.debug("Connect to forest "
+ curForestName + " on "
+ session.getConnectionUri().getHost());
}
AdhocQuery aquery = session.newAdhocQuery(queryText);
aquery.setNewIntegerVariable(MR_NAMESPACE, SPLIT_START_VARNAME,
start);
aquery.setNewIntegerVariable(MR_NAMESPACE, SPLIT_END_VARNAME, end);
RequestOptions options = new RequestOptions();
options.setCacheResult(false);
String ts = conf.get(INPUT_QUERY_TIMESTAMP);
if (ts != null) {
options.setEffectivePointInTime(new BigInteger(ts));
if (LOG.isDebugEnabled()) {
LOG.debug("Query timestamp: " + ts);
}
}
aquery.setOptions(options);
result = session.submitRequest(aquery);
initMetadataMap();
} catch (XccConfigException e) {
LOG.error("XccConfigException:" + e);
throw new IOException(e);
} catch (QueryException e) {
LOG.error("QueryException:" + e);
LOG.debug("Query: " + queryText);
throw new IOException(e);
} catch (Exception e) {
LOG.error("Exception:" + e.getMessage());
if (curForest != -1) {
if (++retry < maxRetries) {
// failover
try {
Thread.sleep(sleepTime);
} catch (Exception e2) {
}
sleepTime = Math.min(sleepTime * 2,maxSleepTime);
curForest = (curForest+1)%replicas.size();
continue;
}
LOG.info("Retry limit exceeded");
}
throw new IOException(e);
}
break;
}
}
protected void queryNakedProperties() throws RequestException {
StringBuilder buf = new StringBuilder();
buf.append("xquery version \"1.0-ml\"; \n");
buf.append("import module namespace hadoop = ");
buf.append("\"http://marklogic.com/xdmp/hadoop\" at ");
buf.append("\"/MarkLogic/hadoop.xqy\";\n");
buf.append("let $props := cts:search(");
String cFilter = null, dFilter = null;
cFilter = conf.get(MarkLogicConstants.COLLECTION_FILTER);
if (cFilter != null) {
buf.append("xdmp:collection-properties(");
buf.append(cFilter);
buf.append(")");
} else {
dFilter = conf.get(MarkLogicConstants.DIRECTORY_FILTER);
if (dFilter != null) {
buf.append("xdmp:directory-properties(");
buf.append(dFilter);
buf.append(", \"infinity\")");
} else {
buf.append("xdmp:collection-properties()");
}
}
buf.append(",");
if (ctsQuery == null) {
buf.append(
"cts:not-query(cts:document-fragment-query(");
buf.append("cts:and-query(()))),");
buf.append("(\"unfiltered\",\"score-zero\"))\n");
} else {
buf.append("cts:and-query((cts:query(xdmp:unquote('");
ctsQuery = ctsQuery.replaceAll("&", "&");
ctsQuery = ctsQuery.replaceAll("'", "'");
buf.append(ctsQuery);
buf.append("')/*),cts:not-query(cts:document-fragment-query(");
buf.append("cts:and-query(()))))),");
buf.append("(\"unfiltered\",\"score-zero\"))\n");
}
buf.append("for $doc in $props\n");
buf.append("let $uri := fn:base-uri($doc)\n return (");
buf.append("'META',");
buf.append("$uri,");
buf.append("if(fn:empty($doc/node())) then 0 else xdmp:node-kind($doc/node()),");
if (copyCollection) {
buf.append("xdmp:document-get-collections($uri),\n");
}
if (copyPermission) {
buf.append("let $list := xdmp:document-get-permissions($uri)\n");
buf.append("return hadoop:get-permissions($list),");
}
// if copy-quality, else + 0
if (copyQuality) {
buf.append("xdmp:document-get-quality($uri),\n");
} else {
buf.append("0,");
}
// copy-metadata
if (copyMetadata) {
buf.append("(let $f := fn:function-lookup(xs:QName('xdmp:document-get-metadata'),1)\n"
+ "return if (exists($f)) then $f($uri) else ()),\n");
}
buf.append("document {$doc/prop:properties}/*, \n");
// end-of-record marker
buf.append("0");
buf.append(")");
String queryText = buf.toString();
if (LOG.isDebugEnabled()) {
LOG.debug(queryText);
}
// set up a connection to the server
AdhocQuery aquery = session.newAdhocQuery(queryText);
RequestOptions options = new RequestOptions();
options.setCacheResult(false);
String ts = conf.get(INPUT_QUERY_TIMESTAMP);
if (ts != null) {
options.setEffectivePointInTime(new BigInteger(ts));
if (LOG.isDebugEnabled()) {
LOG.debug("Query timestamp: " + ts);
}
}
aquery.setOptions(options);
result = session.submitRequest(aquery);
nakedDone = true;
}
private void initMetadataMap() throws IOException {
while (result.hasNext()) {
ResultItem item = result.next();
String type = null;
if (item != null && item.getItemType() == ValueType.XS_STRING) {
type = item.asString();
} else {
throw new IOException("incorrect format:" + item.getItem()
+ "\n" + result.asString());
}
if ("META".equals(type)) {
DocumentMetadata metadata = new DocumentMetadata();
String uri = parseMetadata(metadata);
metadataMap.put(uri, metadata);
} else if ("EOM".equals(type)) {
//end of metadata
return;
} else {
throw new IOException("incorrect type");
}
}
}
/**
* Parse metadata from the sequence, store it into the DocumentMetadata
* object passed in
*
* @param metadata
* @return uri of the document with this metadata
* @throws IOException
*/
private String parseMetadata(DocumentMetadata metadata) throws IOException {
ResultItem item = result.next();
String uri = item.asString();
if (uri == null) {
throw new IOException("Missing document URI for metadata.");
}
item = result.next();
//node-kind, must exist
String nKind = item.asString();
metadata.setFormat(nKind);
item = result.next();
// handle collections, may not be present
while (item != null && item.getItemType() == ValueType.XS_STRING) {
if (!copyCollection) {
item = result.next();
continue;
}
metadata.addCollection(item.asString());
item = result.next();
}
// handle permissions, may not be present
StringBuilder buf = new StringBuilder();
buf.append("");
while (item != null && ValueType.ELEMENT == item.getItemType()) {
if (!copyPermission) {
item = result.next();
continue;
}
try {
readPermission((XdmElement) item.getItem(), metadata, buf);
} catch (Exception e) {
throw new IOException(e);
}
item = result.next();
}
buf.append(" ");
metadata.setPermString(buf.toString());
// handle quality, always present even if not requested (barrier)
metadata.setQuality((XSInteger) item.getItem());
// handle metadata
item = result.next();
if (copyMetadata) {
XdmItem metaItem = item.getItem();
if (metaItem instanceof JsonItem) {
JsonNode node = ((JsonItem)metaItem).asJsonNode();
metadata.meta = new HashMap(node.size());
for (Iterator names = node.fieldNames();
names.hasNext();) {
String key = names.next();
JsonNode nodeVal = node.get(key);
metadata.meta.put(key, nodeVal.asText());
}
item = result.next();
}
}
// handle prop:properties node, optional
// if not present, there will be a 0 as a marker
if (copyProperties && ValueType.ELEMENT == item.getItemType()) {
String pString = item.asString();
if (pString != null) {
metadata.setProperties(pString);
}
item = result.next();
}
if (ValueType.XS_INTEGER != item.getItemType()) {
throw new IOException(uri + " unexpected " + item.getItemType() + " "
+ item.asString() + ", expected " + ValueType.XS_INTEGER
+ " 0");
}
return uri;
}
@Override
public boolean nextKeyValue() throws IOException, InterruptedException {
if (!docDone) {
retry = 0;
sleepTime = 500;
while (retry < maxRetries) {
try {
if (result != null && (result.hasNext())) {
ResultItem currItem = null;
currItem = result.next();
// docs
String uri = null;
uri = currItem.getDocumentURI();
if (uri == null) {
count++;
throw new IOException("Missing document URI for result "
+ currItem.toString());
}
currentValue = new DatabaseDocumentWithMeta();
DocumentMetadata metadata = metadataMap.get(uri);
uri = URIUtil.applyUriReplace(uri, conf);
uri = URIUtil.applyPrefixSuffix(uri, conf);
currentKey.setUri(uri);
if (metadata != null) {
currentValue.setMeta(metadata);
currentValue.set(currItem);
} else {
LOG.error("no meta for " + uri);
}
count++;
return true;
}
} catch (RuntimeException e) {
LOG.error("RuntimeException reading " + currentKey + " :"
+ e);
StringBuilder buf = new StringBuilder();
if (hostNames.length > 1) {
buf.append("host names: ");
} else {
buf.append("host name: ");
}
for (int i = 0; i < hostNames.length; i++) {
if (i > 0) {
buf.append(", ");
}
buf.append(hostNames[i]);
}
LOG.info(buf.toString());
if (curForest != -1) {
if (++retry < maxRetries) {
try {
Thread.sleep(sleepTime);
} catch (Exception e2) {
}
sleepTime = Math.min(sleepTime * 2,maxSleepTime);
curForest = (curForest+1)%replicas.size();
init();
continue;
}
LOG.info("Retry limit exceeded");
}
throw e;
}
break;
} // while
docDone = true;
}
if (copyProperties && mlSplit.getStart() == 0) {
retry = 0;
sleepTime = 500;
while (retry < maxRetries) {
try {
if (!nakedDone) {
queryNakedProperties();
int curCount = 0;
while (curCount < nakedCount) {
if (result.hasNext()) {
result.next();
curCount++;
} else {
return false;
}
}
}
if (result.hasNext()) {
ResultItem currItem = null;
currItem = result.next();
currentValue = new DatabaseDocumentWithMeta();
ResultItem item = currItem;
String type = null;
if (item != null && item.getItemType() == ValueType.XS_STRING) {
type = item.asString();
} else {
throw new IOException("incorrect format:" + item.getItem()
+ "\n" + result.asString());
}
if ("META".equals(type)) {
DocumentMetadata metadata = new DocumentMetadata();
String uri = parseMetadata(metadata);
metadata.setNakedProps(true);
uri = URIUtil.applyUriReplace(uri, conf);
uri = URIUtil.applyPrefixSuffix(uri, conf);
currentKey.setUri(uri);
currentValue.setMeta(metadata);
currentValue.setContentType(ContentType.XML);
} else {
throw new IOException("incorrect type");
}
nakedCount++;
return true;
}
} catch (RequestException e) {
LOG.error("RequestException:" + e);
if (curForest != -1) {
if (++retry < maxRetries) {
try {
Thread.sleep(sleepTime);
} catch (Exception e2) {
}
sleepTime = Math.min(sleepTime * 2,maxSleepTime);
curForest = (curForest+1)%replicas.size();
init();
continue;
}
LOG.info("Exceeded max retry");
}
throw new IOException(e);
} catch (RuntimeException e) {
LOG.error("RuntimeException:" + e);
if (curForest != -1) {
if (++retry < maxRetries) {
try {
Thread.sleep(sleepTime);
} catch (Exception e2) {
}
sleepTime = Math.min(sleepTime * 2,maxSleepTime);
curForest = (curForest+1)%replicas.size();
init();
continue;
}
LOG.info("Exceeded max retry");
}
throw e;
}
break;
} // while
}
return false;
}
@Override
protected boolean nextResult(ResultItem result) {
return false;
}
private void readPermission(XdmElement _permissionElement,
DocumentMetadata metadata, StringBuilder buf) throws Exception {
// permission: turn into a ContentPermission object
// each permission is a sec:permission element.
// children:
// sec:capability ("read", "insert", "update")
// and sec:role xs:unsignedLong (but we need string)
String permString = _permissionElement.asString();
int i = permString.indexOf("");
int j = permString.indexOf(" ");
if (i == -1 || j == -1)
throw new Exception("Error retrieving document permission");
buf.append(permString.substring(0, i));
buf.append(permString.substring(j+16));
Element permissionW3cElement = _permissionElement.asW3cElement();
NodeList capabilities = permissionW3cElement
.getElementsByTagName("sec:capability");
NodeList roles = permissionW3cElement
.getElementsByTagName("sec:role-name");
NodeList ids = permissionW3cElement
.getElementsByTagName("sec:role-id");
Node role;
Node capability;
Node id;
if (0 < roles.getLength() && 0 < capabilities.getLength()) {
role = roles.item(0);
capability = capabilities.item(0);
id = ids.item(0);
metadata.addPermission(capability.getTextContent(),
role.getTextContent(), id.getTextContent());
if (roles.getLength() > 1) {
LOG.warn("input permission: " + permissionW3cElement + ": "
+ roles.getLength() + " roles, using only 1");
}
if (capabilities.getLength() > 1) {
LOG.warn("input permission: " + permissionW3cElement + ": "
+ capabilities.getLength() + " capabilities, using only 1");
}
if (capabilities.getLength() > 1) {
LOG.warn("input permission: " + permissionW3cElement + ": "
+ ids.getLength() + " ids, using only 1");
}
} else {
// warn and skip
if (roles.getLength() < 1) {
LOG.warn("skipping input permission: " + permissionW3cElement
+ ": no roles");
}
if (capabilities.getLength() < 1) {
LOG.warn("skipping input permission: " + permissionW3cElement
+ ": no capabilities");
}
}
}
@Override
protected void endOfResult() {
currentKey = null;
currentValue = null;
}
@Override
protected float getDefaultRatio() {
return DOCUMENT_TO_FRAGMENT_RATIO;
}
@Override
public DocumentURI getCurrentKey() throws IOException,
InterruptedException {
return currentKey;
}
@Override
public MarkLogicDocument getCurrentValue() throws IOException,
InterruptedException {
return currentValue;
}
}
