build!: migrate clasweb/clas12maven dependencies to code.jlab.org

common-tools/clara-io/pom.xml

@@ -52,12 +52,11 @@
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
       <version>14.2.1-SNAPSHOT</version>
-    </dependency> 
+    </dependency>
 
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-text</artifactId>
-      <version>1.15.0</version>
     </dependency>
 
   </dependencies>

common-tools/clas-io/pom.xml

@@ -18,7 +18,6 @@
     <dependency>
       <groupId>org.jlab.coda</groupId>
       <artifactId>xmsg</artifactId>
-      <version>2.3</version>
     </dependency>
 
     <dependency>
@@ -45,7 +44,6 @@
     <dependency>
       <groupId>org.jlab.coda</groupId>
       <artifactId>et</artifactId>
-      <version>14.0</version>
     </dependency>
 
     <dependency>

common-tools/clas-jcsg/pom.xml

@@ -47,7 +47,6 @@
     <dependency>
       <groupId>java3d</groupId>
       <artifactId>vecmath</artifactId>
-      <version>1.3.1</version>
     </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>

common-tools/clas-reco/pom.xml

@@ -36,12 +36,6 @@
       <classifier>jar-with-dependencies</classifier>
     </dependency>
 
-    <dependency>
-      <groupId>org.jlab.coda</groupId>
-      <artifactId>jtools</artifactId>
-      <version>2.2</version>
-    </dependency>
-
     <dependency>
       <groupId>cnuphys</groupId>
       <artifactId>magfield</artifactId>

common-tools/clas-reco/src/main/java/org/jlab/clas/reco/Clas12Types.java

@@ -5,8 +5,6 @@
 import org.jlab.clara.base.error.ClaraException;
 import org.jlab.clara.engine.ClaraSerializer;
 import org.jlab.clara.engine.EngineDataType;
-import org.jlab.clas12.tools.MimeType;
-import org.jlab.clas12.tools.property.JPropertyList;
 import org.jlab.jnp.hipo4.data.Event;
 
 
@@ -30,22 +28,9 @@ public Object read(ByteBuffer buffer) throws ClaraException {
         }
     }
 
-	public static final EngineDataType EVIO = new EngineDataType(MimeType.EVIO.type(), EngineDataType.BYTES.serializer());
+	public static final EngineDataType EVIO = new EngineDataType("binary/data-evio", EngineDataType.BYTES.serializer());
 
         public static final EngineDataType HIPO =
                     new EngineDataType("binary/data-hipo", new HipoSerializer());
 
-	public static final EngineDataType PROPERTY_LIST = new EngineDataType(MimeType.PROPERTY_LIST.type(), new ClaraSerializer() {
-
-                @Override
-		public ByteBuffer write(Object data) throws ClaraException {
-			JPropertyList pl = (JPropertyList) data;
-			return ByteBuffer.wrap(pl.getStringRepresentation(true).getBytes());
-		}
-
-                @Override
-		public Object read(ByteBuffer buffer) throws ClaraException {
-			return new JPropertyList(new String(buffer.array()));
-		}
-	});
 }

common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/utilities/ProbChi2perNDF.java

@@ -0,0 +1,23 @@
+package org.jlab.clas.tracking.utilities;
+
+import org.apache.commons.math3.special.Gamma;
+
+/** Chi-square probability utilities */
+public class ProbChi2perNDF {
+
+  /**
+   * Returns the upper-tail probability (survival function, or p-value) of the
+   * chi-square distribution: P(X >= chi2) for X ~ χ²(ndf).
+   * @param chi2 the chi-square statistic
+   * @param ndf the number of degrees of freedom
+   * @return the probability of observing a chi-square value at least as large as {@code chi2}, in the range [0, 1]
+   */
+  public static double prob(double chi2, int ndf) {
+    if(ndf <= 0)
+      return 0.0;
+    if(chi2 <= 0.0) { // edge cases follow ROOT's `TMath::Prob` conventions
+      return chi2 < 0.0 ? 0.0 : 1.0;
+    }
+    return Gamma.regularizedGammaQ(0.5 * ndf, 0.5 * chi2);
+  }
+}

common-tools/clas-utils/pom.xml

@@ -17,7 +17,6 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-text</artifactId>
-      <version>1.15.0</version>
     </dependency>
     <dependency>
       <groupId>org.jlab.clas</groupId>

common-tools/coat-libs/pom.xml

@@ -24,7 +24,6 @@
     <dependency>
       <groupId>org.jlab.coda</groupId>
       <artifactId>et</artifactId>
-      <version>14.0</version>
     </dependency>
 
     <dependency>
@@ -37,24 +36,6 @@
       <artifactId>j4ml-clas12</artifactId>
     </dependency>
 
-    <dependency>
-      <groupId>org.jama</groupId>
-      <artifactId>jamapack</artifactId>
-      <version>1.0</version>
-    </dependency>
-
-    <dependency>
-      <groupId>org.jlab.plugins</groupId>
-      <artifactId>trackfitter</artifactId>
-      <version>1.0</version>
-    </dependency>
-
-    <dependency>
-      <groupId>org.jlab.plugins</groupId>
-      <artifactId>jMath</artifactId>
-      <version>1.0</version>
-    </dependency>
-
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
@@ -145,26 +126,10 @@
       <version>14.2.1-SNAPSHOT</version>
     </dependency>
 
-    <dependency>
-      <groupId>org.freehep</groupId>
-      <artifactId>jminuit</artifactId>
-    </dependency>
-
-    <dependency>
-      <groupId>de.erichseifert</groupId>
-      <artifactId>vectorgraphics2d</artifactId>
-      <version>1.0</version>
-    </dependency>
-
-    <dependency>
-      <groupId>net.objecthunter</groupId>
-      <artifactId>exp4j</artifactId>
-    </dependency>
-
   </dependencies>
 
   <build>
-  
+
     <resources>
         <resource>
             <directory>src/main/resources</directory>

pom.xml

@@ -20,13 +20,37 @@
 
   <repositories>
     <repository>
-      <id>code.jlab.org-hipo-java</id>  <!-- `jnp-hipo4` is now built and published from its own repository, https://code.jlab.org/hallb/clas12/hipo-java. Project 919's package registry is public -->
+      <id>code.jlab.org-hipo-java</id> <!-- `jnp-hipo4` -->
       <url>https://code.jlab.org/api/v4/projects/919/packages/maven</url>
     </repository>
     <repository>
-      <id>code.jlab.org-clara-java</id>
+      <id>code.jlab.org-clara-java</id> <!-- `jclara` -->
       <url>https://code.jlab.org/api/v4/projects/243/packages/maven</url>
     </repository>
+    <repository>
+      <id>code.jlab.org-xmsg-java</id>
+      <url>https://code.jlab.org/api/v4/projects/959/packages/maven</url>
+    </repository>
+    <repository>
+      <id>code.jlab.org-ccdbrcdb-java</id>
+      <url>https://code.jlab.org/api/v4/projects/245/packages/maven</url>
+    </repository>
+    <!-- <repository> -->
+    <!--   <id>code.jlab.org-evio</id> --> <!-- `jevio` -->
+    <!--   <url>https://code.jlab.org/api/v4/projects/1038/packages/maven</url> -->
+    <!-- </repository> -->
+    <!-- <repository> -->
+    <!--   <id>code.jlab.org-et</id> --> <!-- `et` -->
+    <!--   <url>https://code.jlab.org/api/v4/projects/1044/packages/maven</url> -->
+    <!-- </repository> -->
+    <repository>
+      <id>code.jlab.org-groot</id>
+      <url>https://code.jlab.org/api/v4/projects/388/packages/maven</url>
+    </repository>
+    <repository>
+      <id>freehep-SLAC</id>
+      <url>https://srs.slac.stanford.edu/nexus/content/groups/freehep-maven2-public</url>
+    </repository>
     <repository>
       <id>clasweb-clas12maven</id>
       <url>https://clasweb.jlab.org/.clas12maven</url>
@@ -106,6 +130,12 @@
         <classifier>linux</classifier>
       </dependency>
 
+      <dependency>
+        <groupId>java3d</groupId>
+        <artifactId>vecmath</artifactId>
+        <version>1.3.1</version>
+      </dependency>
+
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>slf4j-api</artifactId>
@@ -124,29 +154,41 @@
         <version>3.20.0</version>
       </dependency>
 
+      <dependency>
+        <groupId>org.apache.commons</groupId>
+        <artifactId>commons-text</artifactId>
+        <version>1.15.0</version>
+      </dependency>
+
       <dependency>
         <groupId>org.jlab</groupId>
         <artifactId>groot</artifactId>
-        <version>4.0.5</version>
+        <version>5.0.0</version> <!-- WARNING: if changed, check the `net.objecthunter:exp4j` version; see `docs/dependency_conflicts.md` -->
       </dependency>
 
       <dependency>
         <groupId>org.freehep</groupId>
-        <artifactId>jminuit</artifactId>
-        <version>1.0</version>
+        <artifactId>freehep-jminuit</artifactId>
+        <version>1.0.2</version>
       </dependency>
 
       <dependency>
         <groupId>org.jlab.coda</groupId>
         <artifactId>jclara</artifactId>
-        <version>4.3</version>
+        <version>6.2</version>
+      </dependency>
+
+      <dependency>
+        <groupId>org.jlab.coda</groupId>
+        <artifactId>xmsg</artifactId>
+        <version>2.5</version>
       </dependency>
 
       <dependency>
         <groupId>org.jlab.coda</groupId>
         <artifactId>jevio</artifactId>
         <classifier>jar-with-dependencies</classifier>
-        <version>6.2-SNAPSHOT</version>
+        <version>6.2-SNAPSHOT</version> <!-- FIXME: bump to code.jlab.org version 6.2.1 ? -->
         <exclusions>
           <exclusion>
             <groupId>net.jpountz.lz4</groupId>
@@ -167,6 +209,12 @@
         </exclusions>
       </dependency>
 
+      <dependency>
+        <groupId>org.jlab.coda</groupId>
+        <artifactId>et</artifactId>
+        <version>14.0</version> <!-- FIXME: bump to code.jlab.org version 16.6.1 ? -->
+      </dependency>
+
       <dependency>
         <groupId>org.jlab.jnp</groupId>
         <artifactId>jnp-hipo</artifactId>
@@ -176,7 +224,24 @@
       <dependency>
         <groupId>org.jlab.jnp</groupId>
         <artifactId>jnp-hipo4</artifactId>
-        <version>4.5</version> <!-- from code.jlab.org/hallb/clas12/hipo-java; WARNING: if changed, check the `net.objecthunter:exp4j` version; see `docs/dependency_conflicts.md` -->
+        <version>4.5</version> <!-- WARNING: if changed, check the `net.objecthunter:exp4j` version; see `docs/dependency_conflicts.md` -->
+      </dependency>
+
+      <dependency>
+        <groupId>org.jlab.ccdbrcdb</groupId>
+        <artifactId>ccdbrcdb</artifactId>
+        <version>2.1</version>
+        <exclusions>
+          <exclusion>
+            <!--
+              protobuf is transitive via `mysql-connector-j` and is only needed for
+              the X DevAPI (MySQL X Protocol); it also conflicts with the version
+              used by `xmsg`, so we exclude it here
+            -->
+            <groupId>com.google.protobuf</groupId>
+            <artifactId>protobuf-java</artifactId>
+          </exclusion>
+        </exclusions>
       </dependency>
 
       <dependency>
@@ -197,12 +262,6 @@
         <version>0.9-SNAPSHOT</version> <!-- WARNING: if changed, check the `org.ejml:ejml-simple` version; see `docs/dependency_conflicts.md` -->
       </dependency>
 
-      <dependency>
-        <groupId>org.jlab.ccdbrcdb</groupId>
-        <artifactId>ccdbrcdb</artifactId>
-        <version>2.0</version>
-      </dependency>
-
       <dependency>
         <groupId>gov.nist.math</groupId>
         <artifactId>jama</artifactId>
@@ -212,36 +271,29 @@
       <dependency> <!-- sets version number for all 'ai.djl' dependencies -->
         <groupId>ai.djl</groupId>
         <artifactId>bom</artifactId>
-        <version>0.38.0</version> <!-- WARNING: if changed, check the `com.google.code.gson:gson` version; see `docs/dependency_conflicts.md` -->
+        <version>0.38.0</version>
         <type>pom</type>
         <scope>import</scope>
       </dependency>
 
       <!-- BEGIN DEPENDENCY CONFLICT RESOLUTION -->
       <!--
-        the following dependency versions are specified to resolve dependency tree conflicts
+        the following dependency versions are pinned to resolve dependency tree conflicts
         - see also exclusions in `maven-enforcer-plugin`
         - see `docs/dependency_conflicts.md` for more info
       -->
 
-      <!-- resolve conflict between `org.jlab.jnp:jnp-hipo:jar:2.0-SNAPSHOT` and `org.jlab.jnp:jnp-hipo4:jar:4.5`
-           by choosing the later version of their `net.objecthunter:exp4j` dependency -->
+      <!-- resolve conflicting `net.objecthunter:exp4j` by choosing the latest used by
+          - `org.jlab.jnp:jnp-hipo`   uses version 0.4.4
+          - `org.jlab.jnp:jnp-hipo4`  uses version 0.4.8
+          - `org.jlab:groot`          uses version 0.4.8
+      -->
       <dependency>
         <groupId>net.objecthunter</groupId>
         <artifactId>exp4j</artifactId>
         <version>0.4.8</version> <!-- WARNING: if changed, see `docs/dependency_conflicts.md` -->
       </dependency>
 
-      <!-- resolve conflict between `org.jlab.coda:jclara` and `ai.djl:api`
-           by choosing the later version of their `com.google.code.gson:gson` dependency
-           - `djl`'s `gson` version is here: https://github.com/deepjavalibrary/djl/blob/master/gradle/libs.versions.toml
-      -->
-      <dependency>
-        <groupId>com.google.code.gson</groupId>
-        <artifactId>gson</artifactId>
-        <version>2.13.1</version> <!-- WARNING: if changed, see `docs/dependency_conflicts.md` -->
-      </dependency>
-
       <!-- resolve conflict between `j4ml:j4ml-clas12` and `clas-tracking`
            by using the version of `org.ejml:ejml-simple` used by `j4ml:j4ml-clas12:jar:0.9-SNAPSHOT` -->
       <dependency>
@@ -389,12 +441,7 @@
             </goals>
             <configuration>
               <rules>
-                <dependencyConvergence>
-                  <excludes>
-                    <!-- excluding conflicts that may be tricky to resolve -->
-                    <exclude>com.google.protobuf:protobuf-java</exclude> <!-- `org.jlab.ccdbrcdb:ccdbrcdb` use v3, but `org.jlab.coda.xmsg` uses v2 -->
-                  </excludes>
-                </dependencyConvergence>
+                <dependencyConvergence/>
               </rules>
             </configuration>
           </execution>

reconstruction/alert/pom.xml

@@ -137,7 +137,7 @@
             </goals>
             <configuration>
               <outputDirectory>${project.build.directory}/lib/services</outputDirectory>
-              <includeGroupIds>ai.djl</includeGroupIds>
+              <includeGroupIds>ai.djl,com.google.code.gson</includeGroupIds>
             </configuration>
           </execution>
         </executions>