preclinical-imaging · willhorton-xw · Jan 14, 2026 · Jun 3, 2025 · Jun 4, 2025 · Jun 4, 2025
diff --git a/CHANGELOG.MD b/CHANGELOG.MD
@@ -5,6 +5,33 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.5.0] - 2025-12-4
+
+This release includes ability to:
+
+  - import BioDistribution datatype
+
+  - ability to generate Statistics Summary for the BioDistribution data [Statistics Dashboard Plugin](https://bitbucket.org/xnatx/statisticsdashboard_plugin)
+
+  - integration of Contrast Data implementation within PIXI which was added to core XNAT in version 1.9.3
+
+  - bug fixes relating to PDX and cell line datatypes
+
+
+### Added
+- [PIXI-159](https://radiologics.atlassian.net/browse/PIXI-159): Add a Biodistribution subject assessor
+- [PIXI-163](https://radiologics.atlassian.net/browse/PIXI-163): Create importer for Biodistribution data from CSV input
+- [PIXI-164](https://radiologics.atlassian.net/browse/PIXI-164): Create Biodistribution Report with Summary Statistics
+
+### Fixed
+- [PIXI-197](https://radiologics.atlassian.net/browse/PIXI-197): BLI Session and Scans do not contain the modality field
+- [PIXI-215](https://radiologics.atlassian.net/browse/PIXI-215): Editing of PDX and removing passage number does not work via the Action -> Edit 
+- [PIXI-228](https://radiologics.atlassian.net/browse/PIXI-228): XFT cast error when saving cell line
+
+### Changed
+- [PIXI-204](https://radiologics.atlassian.net/browse/PIXI-204): Remove Statistics Dashboard files from Pixi Plugin. This is now located in the dedicated [Statistics Dashboard Plugin](https://bitbucket.org/xnatx/statisticsdashboard_plugin)
+- [PIXI-217](https://radiologics.atlassian.net/browse/PIXI-217): Tumor data model should be handled by Data Manager Role rather than the site admin
+
 ## [1.4.0] - 2024-12-19
 
 This release mainly addresses compatibility issues with XNAT 1.9. Prior releases may not work with XNAT 1.9.

diff --git a/README.md b/README.md
@@ -4,6 +4,8 @@ This is the repository for the PIXI XNAT plugin. PIXI is designed to help manage
 
 For detailed information, installation instructions, and usage guidelines, please visit [pixi.org](https://pixi.org).
 
+This plugin depends on the statisticsdashboard_plugin from XNAT
+
 ## Build
 
 To build the PIXI XNAT plugin, run the following command:

diff --git a/build.gradle b/build.gradle
@@ -8,7 +8,7 @@ plugins {
 }
 
 group "org.nrg.xnatx.plugins"
-version "1.4.0"
+version "1.5.0"
 description "PIXI Plugin for XNAT."
 
 repositories {
@@ -105,6 +105,7 @@ java {
 }
 
 jar {
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
     manifest = project.manifest {
         from gitManifest
     }

diff --git a/docs/source/images/biod_open_upload_page.png b/docs/source/images/biod_open_upload_page.png
diff --git a/docs/source/images/biod_same_sample_type_different_subject.png b/docs/source/images/biod_same_sample_type_different_subject.png
diff --git a/docs/source/images/biod_same_subject_different_sample_type.png b/docs/source/images/biod_same_subject_different_sample_type.png
diff --git a/docs/source/images/biod_same_subject_same_sample_type.png b/docs/source/images/biod_same_subject_same_sample_type.png
diff --git a/docs/source/images/biod_subjects_to_be_created.png b/docs/source/images/biod_subjects_to_be_created.png
diff --git a/docs/source/images/biod_upload_file_complete.png b/docs/source/images/biod_upload_file_complete.png
diff --git a/docs/source/images/biod_upload_successful.png b/docs/source/images/biod_upload_successful.png
diff --git a/docs/source/images/biodistribution_sample_type_sitewide_setting.png b/docs/source/images/biodistribution_sample_type_sitewide_setting.png
diff --git a/docs/source/images/invalid_sample_type.png b/docs/source/images/invalid_sample_type.png
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -53,12 +53,16 @@ These are available on the `XNAT Downloads Page <https://www.xnat.org/download>`
 +-----------------------------+------------------------------------+
 | `Container Service`_        | Highly Recommended                 |
 +-----------------------------+------------------------------------+
+| `Summary Statistics`_       | Highly Recommended                 |
++-----------------------------+------------------------------------+
 | `Batch Launch`_             | Extends Container Service          |
 +-----------------------------+------------------------------------+
 | `JupyterHub Integration`_   | XNAT/Python Integrated Environment |
 +-----------------------------+------------------------------------+
 
-Note that `Container Service`_ is required for using PIXI's hotel image splitting feature.
+Notes:
+- `Container Service`_ is required for using PIXI's hotel image splitting feature.
+- `Summary Statistics`_ is required for using PIXI's biodistribution group comparison feature.
 
 ------------------------
 Installation Environment
@@ -137,6 +141,7 @@ when you install Docker.
 .. _XNAT Setup - First Time Configuration: https://wiki.xnat.org/documentation/xnat-setup-first-time-configuration
 .. _XNAT OHIF Viewer: https://wiki.xnat.org/xnat-ohif-viewer
 .. _Container Service: https://wiki.xnat.org/container-service/
+.. _Summary Statistics: https://bitbucket.org/xnatx/statisticsdashboard_plugin/
 .. _Batch Launch: https://wiki.xnat.org/xnat-tools/batch-launch-plugin
 .. _JupyterHub Integration: https://wiki.xnat.org/jupyter-integration
 .. _XNAT Installation Guide page: https://wiki.xnat.org/documentation/xnat-installation-guide

diff --git a/docs/source/usage.rst b/docs/source/usage.rst
diff --git a/src/main/java/org/nrg/xdat/om/base/BasePixiBiodistributiondata.java b/src/main/java/org/nrg/xdat/om/base/BasePixiBiodistributiondata.java
@@ -0,0 +1,48 @@
+package org.nrg.xdat.om.base;
+
+import org.nrg.xdat.XDAT;
+import org.nrg.xdat.om.base.auto.AutoPixiBiodistributiondata;
+import org.nrg.xft.ItemI;
+import org.nrg.xft.security.UserI;
+import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
+import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
+
+import java.util.Hashtable;
+
+
+@SuppressWarnings({"unchecked", "rawtypes"})
+public abstract class BasePixiBiodistributiondata extends AutoPixiBiodistributiondata {
+
+    public BasePixiBiodistributiondata(ItemI item) {
+        super(item);
+    }
+
+    public BasePixiBiodistributiondata(UserI user) {
+        super(user);
+    }
+
+    /*
+     * @deprecated Use BasePixiBiodistributiondata(UserI user)
+     **/
+    public BasePixiBiodistributiondata() {
+    }
+
+    public BasePixiBiodistributiondata(Hashtable properties, UserI user) {
+        super(properties, user);
+    }
+
+    public static Integer getCountForSubject(final String subject_id) {
+        final NamedParameterJdbcTemplate template = XDAT.getContextService().getBean(NamedParameterJdbcTemplate.class);
+        return template.queryForObject(QUERY_COUNT_EXPERIMENTS_BY_SUBJECT_ID, new MapSqlParameterSource(SUBJECT_ID_PARAMETER, subject_id), Integer.class);
+    }
+
+    private static final String SUBJECT_ID_PARAMETER = "subject_id";
+    private static final String QUERY_COUNT_EXPERIMENTS_BY_SUBJECT_ID = "SELECT COUNT(*) " +
+            "FROM pixi_biodistributiondata as biod INNER JOIN (" +
+            "SELECT id, subject_id " +
+            "FROM xnat_subjectassessordata " +
+            "WHERE subject_id = :subject_id" +
+            ") as s " +
+            "ON biod.id = s.id";
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/Pixi_CMO_PDX_TemplateGenerator.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/Pixi_CMO_PDX_TemplateGenerator.java
@@ -0,0 +1,11 @@
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+
+public class Pixi_CMO_PDX_TemplateGenerator  extends SecureScreen {
+
+    @Override protected void doBuildTemplate(RunData data, Context context) throws Exception {}
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadBiodistribution.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadBiodistribution.java
@@ -0,0 +1,14 @@
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+
+@SuppressWarnings("unused")
+public class UploadBiodistribution extends SecureScreen {
+
+    @Override
+    protected void doBuildTemplate(RunData data, Context context) throws Exception {
+    }
+
+}
diff --git a/...n/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_edit_pixi_biodistributionData.java b/...n/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_edit_pixi_biodistributionData.java
@@ -0,0 +1,51 @@
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.om.PixiBiodistributiondata;
+import org.nrg.xdat.om.XnatSubjectdata;
+import org.nrg.xdat.turbine.utils.TurbineUtils;
+import org.nrg.xft.ItemI;
+import org.nrg.xft.XFTItem;
+import org.nrg.xft.security.UserI;
+
+import java.time.LocalDate;
+import java.util.Optional;
+
+@SuppressWarnings("unused")
+public class XDATScreen_edit_pixi_biodistributionData extends EditSubjectAssessorScreen {
+    static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_pixi_biodistributionData.class);
+
+    /* (non-Javadoc)
+     * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
+     */
+    public String getElementName() {
+        return "pixi:biodistributionData";
+    }
+
+    public ItemI getEmptyItem(RunData data) throws Exception {
+        final PixiBiodistributiondata pixiBiodistributiondata =
+                new PixiBiodistributiondata(XFTItem.NewItem(getElementName(), getUser()));
+
+        pixiBiodistributiondata.setDate(LocalDate.now());
+
+        final UserI user = getUser();
+        final Optional<Object> subject_id = Optional.ofNullable(TurbineUtils.GetPassedParameter("part_id", data));
+
+        if (subject_id.isPresent()) {
+            final int count = PixiBiodistributiondata.getCountForSubject((String) subject_id.get()) + 1;
+            final XnatSubjectdata subjectData = XnatSubjectdata.getXnatSubjectdatasById(subject_id.get(), getUser(), false);
+            final String label = subjectData.getLabel() + "_BIOD_" + count;
+            pixiBiodistributiondata.setLabel(label);
+        }
+
+        return pixiBiodistributiondata.getItem();
+    }
+
+    /* (non-Javadoc)
+     * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
+     */
+    public void finalProcessing(RunData data, Context context) {
+        super.finalProcessing(data, context);
+    }
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/PIXIPlugin.java b/src/main/java/org/nrg/xnatx/plugins/pixi/PIXIPlugin.java
@@ -10,6 +10,7 @@
 import org.nrg.xnat.services.XnatAppInfo;
 import org.nrg.xnat.services.system.HostInfoService;
 import org.nrg.xnat.turbine.utils.IDGenerator;
+import org.nrg.xnatx.plugins.pixi.biod.config.BiodConfig;
 import org.nrg.xnatx.plugins.pixi.bli.config.BliConfig;
 import org.nrg.xnatx.plugins.pixi.inveon.config.InveonConfig;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -78,11 +79,16 @@
                                          singular = "BLI Scan",
                                          plural = "BLI Scans",
                                          code = "BLIScan"),
+                          @XnatDataModel(value = PixiBiodistributiondata.SCHEMA_ELEMENT_NAME,
+                                         singular = "Biodistribution",
+                                         plural = "Biodistributions",
+                                         code = "BIOD"),
                           })
 @ComponentScan({"org.nrg.xnatx.plugins.pixi.xenografts.entities",
                 "org.nrg.xnatx.plugins.pixi.xenografts.repositories",
                 "org.nrg.xnatx.plugins.pixi.xenografts.services.impl",
                 "org.nrg.xnatx.plugins.pixi.xenografts.rest",
+                "org.nrg.xnatx.plugins.pixi.xenografts.services",
                 "org.nrg.xnatx.plugins.pixi.hotelsplitter.services.impl",
                 "org.nrg.xnatx.plugins.pixi.hotelsplitter.rest",
                 "org.nrg.xnatx.plugins.pixi.hotelsplitter.initialize",
@@ -91,8 +97,10 @@
                 "org.nrg.xnatx.plugins.pixi.imageAcqCtx.rest",
                 "org.nrg.xnatx.plugins.pixi.imageAcqCtx.services.impl",
                 "org.nrg.xnatx.plugins.pixi.rest",
+                "org.nrg.xnatx.plugins.pixi.security",
+                "org.nrg.xnatx.plugins.pixi.cmo.rest"
 })
-@Import({BliConfig.class, InveonConfig.class})
+@Import({BliConfig.class, InveonConfig.class, BiodConfig.class})
 @Slf4j
 public class PIXIPlugin {
 

diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/PixiUtils.java b/src/main/java/org/nrg/xnatx/plugins/pixi/PixiUtils.java
@@ -0,0 +1,8 @@
+package org.nrg.xnatx.plugins.pixi;
+
+public class PixiUtils {
+
+    public static final String BLI_SESSION_MODALITY = "BLI";
+    public static final String BLI_SCAN_MODALITY = "BLI";
+    public static final String PIXI_DATA_MANAGER_ROLE = "PIXIDataManager";
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/biod/config/BiodConfig.java b/src/main/java/org/nrg/xnatx/plugins/pixi/biod/config/BiodConfig.java
@@ -0,0 +1,15 @@
+package org.nrg.xnatx.plugins.pixi.biod.config;
+
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@ComponentScan({
+        "org.nrg.xnatx.plugins.pixi.biod.rest",
+        "org.nrg.xnatx.plugins.pixi.biod.services",
+        "org.nrg.xnatx.plugins.pixi.biod.services.impl",
+        "org.nrg.xnatx.plugins.pixi.biod.helpers",
+        "org.nrg.xnatx.plugins.pixi.biod.helpers.impl",
+})
+public class BiodConfig {
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/DefaultXnatExperimentDataHelper.java b/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/DefaultXnatExperimentDataHelper.java
@@ -0,0 +1,23 @@
+package org.nrg.xnatx.plugins.pixi.biod.helpers;
+
+import lombok.extern.slf4j.Slf4j;
+import org.nrg.xdat.model.XnatExperimentdataI;
+import org.nrg.xdat.om.XnatExperimentdata;
+import org.nrg.xft.security.UserI;
+import org.springframework.stereotype.Service;
+
+@Service
+@Slf4j
+public class DefaultXnatExperimentDataHelper implements XnatExperimentDataHelper {
+
+    @Override
+    public String createNewId() throws Exception {
+        return XnatExperimentdata.CreateNewID();
+    }
+
+    @Override
+    public XnatExperimentdataI getExptByProjectIdentifier(String project, String identifier, UserI user, boolean preLoad) {
+        return XnatExperimentdata.GetExptByProjectIdentifier(project, identifier, user, preLoad);
+    }
+
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/SaveItemHelper.java b/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/SaveItemHelper.java
@@ -0,0 +1,11 @@
+package org.nrg.xnatx.plugins.pixi.biod.helpers;
+
+import org.nrg.xft.ItemI;
+import org.nrg.xft.event.EventMetaI;
+import org.nrg.xft.security.UserI;
+
+public interface SaveItemHelper {
+
+    void authorizedSave(ItemI i, UserI user, boolean overrideSecurity, boolean quarantine, boolean overrideQuarantine, boolean allowItemRemoval, EventMetaI c) throws Exception;
+
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/XnatExperimentDataHelper.java b/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/XnatExperimentDataHelper.java
@@ -0,0 +1,11 @@
+package org.nrg.xnatx.plugins.pixi.biod.helpers;
+
+import org.nrg.xdat.model.XnatExperimentdataI;
+import org.nrg.xft.security.UserI;
+
+public interface XnatExperimentDataHelper {
+
+    String createNewId() throws Exception;
+    XnatExperimentdataI getExptByProjectIdentifier(String project, String identifier, UserI user, boolean preLoad);
+
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/XnatSubjectDataHelper.java b/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/XnatSubjectDataHelper.java
@@ -0,0 +1,11 @@
+package org.nrg.xnatx.plugins.pixi.biod.helpers;
+
+import org.nrg.xdat.om.XnatSubjectdata;
+import org.nrg.xft.security.UserI;
+
+public interface XnatSubjectDataHelper {
+
+    String createNewId() throws Exception;
+    XnatSubjectdata getSubjectByIdOrProjectlabelCaseInsensitive(String project, String identifier, UserI user, boolean preLoad);
+
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/impl/DefaultSaveItemHelper.java b/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/impl/DefaultSaveItemHelper.java
@@ -0,0 +1,19 @@
+package org.nrg.xnatx.plugins.pixi.biod.helpers.impl;
+
+import lombok.extern.slf4j.Slf4j;
+import org.nrg.xft.ItemI;
+import org.nrg.xft.event.EventMetaI;
+import org.nrg.xft.security.UserI;
+import org.nrg.xnatx.plugins.pixi.biod.helpers.SaveItemHelper;
+import org.springframework.stereotype.Service;
+
+@Service
+@Slf4j
+public class DefaultSaveItemHelper implements SaveItemHelper {
+
+    @Override
+    public void authorizedSave(ItemI i, UserI user, boolean overrideSecurity, boolean quarantine, boolean overrideQuarantine, boolean allowItemRemoval, EventMetaI c) throws Exception {
+        org.nrg.xft.utils.SaveItemHelper.authorizedSave(i, user, overrideSecurity, quarantine, overrideQuarantine, allowItemRemoval, c);
+    }
+
+}
diff --git a/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/impl/DefaultXnatSubjectDataHelper.java b/src/main/java/org/nrg/xnatx/plugins/pixi/biod/helpers/impl/DefaultXnatSubjectDataHelper.java
@@ -0,0 +1,23 @@
+package org.nrg.xnatx.plugins.pixi.biod.helpers.impl;
+
+import lombok.extern.slf4j.Slf4j;
+import org.nrg.xdat.om.XnatSubjectdata;
+import org.nrg.xft.security.UserI;
+import org.nrg.xnatx.plugins.pixi.biod.helpers.XnatSubjectDataHelper;
+import org.springframework.stereotype.Service;
+
+@Service
+@Slf4j
+public class DefaultXnatSubjectDataHelper implements XnatSubjectDataHelper {
+
+    @Override
+    public String createNewId() throws Exception {
+        return XnatSubjectdata.CreateNewID();
+    }
+
+    @Override
+    public XnatSubjectdata getSubjectByIdOrProjectlabelCaseInsensitive(String project, String identifier, UserI user, boolean preLoad) {
+        return XnatSubjectdata.GetSubjectByIdOrProjectlabelCaseInsensitive(project, identifier, user, preLoad);
+    }
+
+}