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Add and fill software configuration bank
- Modify all poms to include version numbers in jar manifests - Add JSON utility class for reading/writing/appending a JSON bank - Add YAML filterer for recon-util to emulate the EngineData services receive from CLARA - Create/append COAT::config bank by all ReconstructionEngines -- including service/coatjava versions and YAML contents - Copy COAT::config to new tag-1 event in postprocessing
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-330
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24 files changed

+1056
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‎build-coatjava.sh‎

Lines changed: 1 addition & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -98,19 +98,6 @@ if [ $? != 0 ] ; then echo "mvn package failure" ; exit 1 ; fi
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cd -
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100100
cp common-tools/coat-lib/target/coat-libs-*-SNAPSHOT.jar coatjava/lib/clas/
101-
cp reconstruction/dc/target/clas12detector-dc-*-SNAPSHOT.jar coatjava/lib/services/
102-
cp reconstruction/tof/target/clas12detector-tof-*-SNAPSHOT.jar coatjava/lib/services/
103-
cp reconstruction/cvt/target/clas12detector-cvt-*-SNAPSHOT.jar coatjava/lib/services/
104-
cp reconstruction/ft/target/clas12detector-ft-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/ec/target/clas12detector-ec-*-SNAPSHOT.jar coatjava/lib/services/
106-
cp reconstruction/ltcc/target/clas12detector-ltcc-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/htcc/target/clas12detector-htcc-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/cnd/target/clas12detector-cnd-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/rich/target/clas12detector-rich-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/fvt/target/clas12detector-fmt-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/eb/target/clas12detector-eb-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/band/target/clas12detector-band-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/rtpc/target/clas12detector-rtpc-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/swaps/target/clas12detector-swaps-*-SNAPSHOT.jar coatjava/lib/services/
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cp reconstruction/*/target/clas12detector-*-SNAPSHOT.jar coatjava/lib/services/
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echo "COATJAVA SUCCESSFULLY BUILT !"

‎common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Tag1ToEvent.java‎

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Original file line numberDiff line numberDiff line change
@@ -24,6 +24,8 @@
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* and beam charge from tag-1 events, and outputs a file with modified
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* REC::Event.helicity/beamCharge/liveTime.
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*
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* Also, adds tag-1 events for configuration banks (e.g. SOFT::config)
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*
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* Usage: Tag1ToEvent outputFile inputFile1 [inputFile2 [inputFile3 [...]]]
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*
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* FIXME: DaqScalersSequence doesn't manage run numbers. Until then, we
@@ -35,6 +37,10 @@
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public class Tag1ToEvent {
3739

40+
public static final String[] CREATE_TAG1_EVENTS = {
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"SOFT::config"
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};
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public static void main(String[] args) {
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4046
OptionParser parser = new OptionParser("postprocess");
@@ -75,12 +81,20 @@ public static void main(String[] args) {
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Event event = new Event();
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Event configEvent = new Event();
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7886
// we're going to modify this bank:
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Bank recEventBank = new Bank(writer.getSchemaFactory().getSchema("REC::Event"));
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// we're going to modify this bank if doHelicityFlip is set:
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Bank helFlipBank = new Bank(writer.getSchemaFactory().getSchema("HEL::flip"));
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92+
// we're going to copy these banks to new tag-1 events:
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List<Bank> configBanks = new ArrayList<>();
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for (String bankName : CREATE_TAG1_EVENTS) {
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configBanks.add(new Bank(writer.getSchemaFactory().getSchema(bankName)));
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}
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long badCharge = 0;
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long goodCharge = 0;
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long badHelicity = 0;
@@ -129,6 +143,16 @@ public static void main(String[] args) {
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}
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}
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// copy config banks to new tag-1 events:
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configEvent.reset();
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for (Bank bank : configBanks) {
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event.read(bank);
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if (bank.getRows()>0) {
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configEvent.write(bank);
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}
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writer.addEvent(configEvent,1);
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}
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// update the output file:
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event.write(recEventBank);
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writer.addEvent(event, event.getEventTag());

‎common-tools/clas-io/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -28,6 +28,12 @@
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<dependencies>
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<dependency>
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<groupId>org.jlab.coda</groupId>
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<artifactId>jclara</artifactId>
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<version>4.3-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>javax.xml.bind</groupId>
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<artifactId>jaxb-api</artifactId>

‎common-tools/clas-io/src/main/java/org/jlab/utils/JsonUtils.java‎

Lines changed: 269 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,269 @@
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package org.jlab.utils;
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import java.util.Map;
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import java.io.IOException;
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import java.io.BufferedWriter;
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import java.io.OutputStreamWriter;
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import org.jlab.io.base.DataBank;
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import org.jlab.io.base.DataEvent;
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import org.jlab.jnp.utils.json.JsonArray;
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import org.jlab.jnp.utils.json.JsonObject;
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import org.jlab.jnp.utils.json.JsonValue;
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import org.jlab.jnp.utils.json.PrettyPrint;
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import org.json.JSONObject;
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/**
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* Stuff to read and manipulate HIPO banks with JSON objects.
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* @author baltzell
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*/
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public class JsonUtils {
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/**
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* Just print it to the screen, nicely.
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* @param json
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*/
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public static void show(JsonObject json) {
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BufferedWriter buffWriter = new BufferedWriter(new OutputStreamWriter(System.out));
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try {
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json.writeTo(buffWriter,PrettyPrint.indentWithSpaces(4));
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buffWriter.newLine();
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buffWriter.flush();
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}
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catch (IOException e) {}
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}
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/**
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* Just print it to the screen, nicely.
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* @param bank
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* @param varName
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*/
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public static void show(DataBank bank, String varName) {
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show(read(bank,varName));
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}
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/**
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* Convenience method to get a JsonObject from a bank.
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* @param bank bank to read
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* @param varName name of byte variable to read
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* @return JSON generated from array of bytes
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*/
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public static JsonObject read(DataBank bank, String varName) {
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return JsonObject.readFrom(new String(bank.getByte(varName)));
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}
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/**
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* This won't be useful once DataBank.setByte(String,byte[]) is implemented
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* @param bank bank to modify
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* @param varName name of bank byte variable to modify
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* @param contents contents of the variable, one byte per row
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* @return the input bank after modification
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*/
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public static DataBank fill(DataBank bank, String varName, String contents) {
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byte[] bytes = contents.getBytes();
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for (int row=0; row<bank.rows(); row++) {
64+
if (row >= bytes.length) {
65+
break;
66+
}
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bank.setByte(varName, row, bytes[row]);
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}
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return bank;
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}
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/**
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* Convert a map to JNP's JsonObject
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* WARNING: presumably not generic to extended JSONs, but sufficient for
75+
* configuration sections of CLARA YAMLs.
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* @param map
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* @return
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*/
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public static JsonObject Map2Json(Map<String,Object> map) {
80+
JsonObject ret = new JsonObject();
81+
for (Map.Entry<String,Object> entry : map.entrySet()) {
82+
String topKey = entry.getKey();
83+
if (entry.getValue() instanceof String) {
84+
ret.add(topKey, (String)entry.getValue());
85+
}
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else if (entry.getValue() instanceof Map) {
87+
ret.add(topKey,Map2Json((Map)entry.getValue()));
88+
}
89+
else {
90+
throw new RuntimeException("non-String non-Supported.");
91+
}
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}
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return ret;
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}
95+
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/**
97+
* Convert from Map to JNP's JsonObject
98+
* @param json an org.json.JSONObject
99+
* @return the corresponding org.jlab.jnp.utils.json.JsonObject
100+
*/
101+
public static JsonObject JSON2Json(JSONObject json) {
102+
return Map2Json(json.toMap());
103+
}
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/**
106+
* Convenience method to create a bank containing a JsonObject.
107+
* @param event event used to generate the bank
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* @param bankName name of bank to create
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* @param varName name of variable to put the JSON object in
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* @param json contents for the variable
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* @return new bank
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*/
113+
public static DataBank create(DataEvent event, String bankName, String varName, JsonObject json) {
114+
DataBank bank = event.createBank(bankName, json.toString().length());
115+
fill(bank, varName, json.toString());
116+
return bank;
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}
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/**
120+
* Convenience method to create a bank containing a JsonObject.
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* @param event event used to generate the bank
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* @param bankName name of bank to create
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* @param varName name of variable to put the JSON object in
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* @param json contents for the variable
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* @return new bank
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*/
127+
public static DataBank create(DataEvent event, String bankName, String varName, JSONObject json) {
128+
return create(event, bankName, varName, JSON2Json(json));
129+
}
130+
131+
/**
132+
* Convenience method to create a bank containing a JsonObject.
133+
* @param event event used to generate the bank
134+
* @param bankName name of bank to create
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* @param varName name of variable to put the JSON object in
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* @param json contents for the variable
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* @return new bank
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*/
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public static DataBank create(DataEvent event, String bankName, String varName, Map json) {
140+
return create(event, bankName, varName, Map2Json(json));
141+
}
142+
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/**
144+
* JsonObject's merge method overwrites keys of the same name, this extends.
145+
* WARNING: presumably not generic to extended JSONs, but sufficient for
146+
* configuration sections of CLARA YAMLs.
147+
* @param a
148+
* @param b
149+
* @return a+b
150+
*/
151+
public static JsonObject add(JsonObject a, JsonObject b) {
152+
JsonObject ret = new JsonObject();
153+
for (String key : a.names()) {
154+
if (b.names().contains(key)) {
155+
JsonValue aval = a.get(key);
156+
JsonValue bval = b.get(key);
157+
if (aval instanceof JsonObject) {
158+
JsonObject obj = new JsonObject();
159+
JsonObject aobj = new JsonObject((JsonObject)aval);
160+
JsonObject bobj = new JsonObject((JsonObject)bval);
161+
for (String anam : aobj.names()) {
162+
obj.set(anam, aobj.get(anam));
163+
}
164+
for (String bnam : bobj.names()) {
165+
obj.set(bnam, bobj.get(bnam));
166+
}
167+
ret.set(key, obj);
168+
}
169+
else {
170+
JsonArray arr = new JsonArray();
171+
arr.add(a.get(key));
172+
arr.add(b.get(key));
173+
ret.set(key,arr);
174+
}
175+
}
176+
else {
177+
ret.set(key, a.get(key));
178+
}
179+
}
180+
for (String key : b.names()) {
181+
if (!a.names().contains(key)) {
182+
ret.set(key, b.get(key));
183+
}
184+
}
185+
return ret;
186+
}
187+
188+
/**
189+
* Modify event by extending bank by merging new JSON data to existing.
190+
* If bank doesn't exist, create it.
191+
* @param event event to get the bank from and put it back into
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* @param bankName name of bank
193+
* @param varName name of variable within bank
194+
* @param extension JSON object to extend with
195+
* @return
196+
*/
197+
public static DataBank extend(DataEvent event, String bankName, String varName, JsonObject extension) {
198+
JsonObject contents;
199+
if (event.hasBank(bankName)) {
200+
contents = add(read(event.getBank(bankName), varName),extension);
201+
event.removeBank(bankName);
202+
}
203+
else {
204+
contents = new JsonObject(extension);
205+
}
206+
DataBank bank = create(event, bankName, varName, contents);
207+
event.appendBank(bank);
208+
return bank;
209+
}
210+
211+
/**
212+
* Modify event by extending bank by merging new JSON data to existing.
213+
* If bank doesn't exist, create it.
214+
* @param event event to get the bank from and put it back into
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* @param bankName name of bank
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* @param varName name of variable within bank
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* @param extension JSON object to extend with
218+
* @return
219+
*/
220+
public static DataBank extend(DataEvent event, String bankName, String varName, JSONObject extension) {
221+
return extend(event, bankName, varName, JSON2Json(extension));
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}
223+
224+
/**
225+
* Modify event by extending bank by merging new JSON data to existing.
226+
* If bank doesn't exist, create it.
227+
* @param event event to get the bank from and put it back into
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* @param bankName name of bank
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* @param varName name of variable within bank
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* @param extension JSON object to extend with
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* @return
232+
*/
233+
public static DataBank extend(DataEvent event, String bankName, String varName, Map<String,Object> extension) {
234+
return extend(event, bankName, varName, Map2Json(extension));
235+
}
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237+
/**
238+
* Emulate the way CLARA parses the full YAML and presents it in EngineData.
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* The "global" and "service" subsections in the "configuration" section get
240+
* squashed into one namespace, and service-specific keys override any
241+
* globals of the same name.
242+
*
243+
* @param claraJson the full CLARA YAML contents
244+
* @param serviceName the name of the service in CLARA YAML (not class name)
245+
* @return data in the format the given CLARA service would see
246+
*/
247+
public static JSONObject filterClaraYaml(JSONObject claraJson, String serviceName) {
248+
JSONObject ret = new JSONObject();
249+
if (claraJson.has("configuration")) {
250+
JSONObject config = claraJson.getJSONObject("configuration");
251+
if (config.has("global")) {
252+
JSONObject globals = config.getJSONObject("global");
253+
for (String key : globals.keySet()) {
254+
ret.accumulate(key, globals.getString(key));
255+
}
256+
}
257+
if (config.has("services")) {
258+
if (config.getJSONObject("services").has(serviceName)) {
259+
JSONObject service = config.getJSONObject("services").getJSONObject(serviceName);
260+
for (String key : service.keySet()) {
261+
ret.put(key, service.getString(key));
262+
}
263+
}
264+
}
265+
}
266+
return ret;
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}
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}

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