Move specimen module to customModules repository

specimen/build.gradle

@@ -0,0 +1,27 @@
+/*
+ * Copyright (c) 2021-2026 LabKey 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.
+ */
+import org.labkey.gradle.util.BuildUtils
+
+plugins {
+    id 'org.labkey.build.module'
+}
+
+dependencies {
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "study"), depProjectConfig: "apiJarFile")
+    BuildUtils.addLabKeyDependency(project: project, config: "jspImplementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "study"), depProjectConfig: "apiJarFile")
+
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "study"), depProjectConfig: "published", depExtension: "module")
+}

specimen/module.properties

@@ -0,0 +1,8 @@
+ModuleClass: org.labkey.specimen.SpecimenModule
+Label: Legacy specimen tracking system
+Description: A system for tracking specimens as part of a study. \
+    This system has been deprecated, replaced by LabKey Sample Manager.
+URL: https://www.labkey.com/products-services/sample-management-software/
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+ManageVersion: true

specimen/schemas/specimens.xsd

@@ -0,0 +1,201 @@
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+           xmlns:sec="http://labkey.org/security/xml"
+           xmlns="http://labkey.org/study/xml"
+           targetNamespace="http://labkey.org/study/xml"
+           attributeFormDefault="unqualified"
+           elementFormDefault="qualified">
+
+    <xs:import namespace="http://labkey.org/study/xml" schemaLocation="../../api/schemas/study.xsd"/>
+    <xs:import namespace="http://labkey.org/security/xml" schemaLocation="../../api/schemas/security.xsd"/>
+
+    <xs:element name="specimens" type="specimenSettingsType">
+        <xs:annotation>
+            <xs:documentation>
+                Provides information on the files that describe the specimens in the study.
+            </xs:documentation>
+        </xs:annotation>
+    </xs:element>
+
+    <xs:complexType name="specimenSettingsType">
+        <xs:sequence>
+            <xs:element name="webPartGroupings" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence minOccurs="0" maxOccurs="unbounded">
+                        <xs:element name="grouping">
+                            <xs:complexType>
+                                <xs:sequence minOccurs="0" maxOccurs="unbounded">
+                                    <xs:element name="groupBy" type="xs:string"/>
+                                </xs:sequence>
+                            </xs:complexType>
+                        </xs:element>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="locationTypes" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="repository" type="locationTypeType" minOccurs="0" maxOccurs="1"/>
+                        <xs:element name="clinic" type="locationTypeType" minOccurs="0" maxOccurs="1"/>
+                        <xs:element name="siteAffiliatedLab" type="locationTypeType" minOccurs="0" maxOccurs="1"/>
+                        <xs:element name="endpointLab" type="locationTypeType" minOccurs="0" maxOccurs="1"/>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="requestStatuses" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="status" minOccurs="0" maxOccurs="unbounded">
+                            <xs:complexType>
+                                <xs:attribute name="label" type="xs:string"/>
+                                <xs:attribute name="finalState" type="xs:boolean"/>
+                                <xs:attribute name="lockSpecimens" type="xs:boolean"/>
+                            </xs:complexType>
+                        </xs:element>
+                    </xs:sequence>
+                    <xs:attribute name="multipleSearch" type="xs:boolean" />
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="requestActors" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="actor" minOccurs="0" maxOccurs="unbounded">
+                            <xs:complexType>
+                                <xs:sequence>
+                                    <xs:element name="groups" type="sec:groupsType" minOccurs="0"/>
+                                </xs:sequence>
+                                <xs:attribute name="label" type="xs:string"/>
+                                <xs:attribute name="type">
+                                    <xs:simpleType>
+                                        <xs:restriction base="xs:string">
+                                            <xs:enumeration value="study"/>
+                                            <xs:enumeration value="location"/>
+                                        </xs:restriction>
+                                    </xs:simpleType>
+                                </xs:attribute>
+                            </xs:complexType>
+                        </xs:element>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="defaultRequirements" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="originatingLab" type="defaultRequirementsType" minOccurs="0" maxOccurs="unbounded" />
+                        <xs:element name="providingLab" type="defaultRequirementsType" minOccurs="0" maxOccurs="unbounded" />
+                        <xs:element name="receivingLab" type="defaultRequirementsType" minOccurs="0" maxOccurs="unbounded" />
+                        <xs:element name="general" type="defaultRequirementsType" minOccurs="0" maxOccurs="unbounded" />
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="displaySettings" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="commentsAndQC" minOccurs="0">
+                            <xs:complexType>
+                                <xs:attribute name="defaultToCommentsMode" type="xs:boolean"/>
+                                <xs:attribute name="enableManualQCFlagging" type="xs:boolean"/>
+                            </xs:complexType>
+                        </xs:element>
+                        <xs:element name="lowSpecimenWarnings" minOccurs="0">
+                            <xs:complexType>
+                                <xs:attribute name="lastVial" type="xs:string"/>
+                                <xs:attribute name="zeroVials" type="xs:string"/>
+                            </xs:complexType>
+                        </xs:element>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="requestForms" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="form" minOccurs="0" maxOccurs="unbounded">
+                            <xs:complexType>
+                                <xs:sequence>
+                                    <xs:element name="title" type="xs:string" minOccurs="0"/>
+                                    <xs:element name="helpText" type="xs:string" minOccurs="0"/>
+                                </xs:sequence>
+                                <xs:attribute name="multiLine" type="xs:boolean"/>
+                                <xs:attribute name="required" type="xs:boolean"/>
+                                <xs:attribute name="rememberSiteValue" type="xs:boolean"/>
+                                <xs:attribute name="displayOrder" type="xs:int"/>
+                            </xs:complexType>
+                        </xs:element>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="notifications" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="replyTo" type="xs:string" minOccurs="0"/>
+                        <xs:element name="cc" type="xs:string" minOccurs="0"/>
+                        <xs:element name="subjectSuffix" type="xs:string" minOccurs="0"/>
+                        <xs:element name="newRequestNotify" type="xs:string" minOccurs="0"/>
+                        <xs:element name="defaultEmailNotify" type="xs:string" minOccurs="0"/>
+                        <xs:element name="specimensAttachment" type="xs:string" minOccurs="0"/>
+                    </xs:sequence>
+                    <xs:attribute name="ccCheckbox" type="xs:boolean"/>
+                    <xs:attribute name="newRequestNotifyCheckbox" type="xs:boolean"/>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="requestabilityRules" minOccurs="0">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="rule" minOccurs="0" maxOccurs="unbounded">
+                            <xs:complexType>
+                                <xs:attribute name="type" type="xs:string"/>
+                                <xs:attribute name="ruleData" type="xs:string"/>
+                            </xs:complexType>
+                        </xs:element>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+        </xs:sequence>
+        <xs:attribute name="repositoryType" type="specimenRepositoryType">
+            <xs:annotation>
+                <xs:documentation xmlns="http://www.w3.org/1999/xhtml">
+                    Indicates the type of repository.
+                    See <a href="https://www.labkey.org/Documentation/wiki-page.view?name=manageSpecimens" target="_top">Manage Specimens</a>.
+                </xs:documentation>
+            </xs:annotation>
+        </xs:attribute>
+        <xs:attribute name="enableRequests" type="xs:boolean">
+            <xs:annotation>
+                <xs:documentation>True if specimens can be requested in this repository.</xs:documentation>
+            </xs:annotation>
+        </xs:attribute>
+        <xs:attribute name="editableRepository" type="xs:boolean">
+            <xs:annotation>
+                <xs:documentation>True if specimens can be edited directly.</xs:documentation>
+            </xs:annotation>
+        </xs:attribute>
+    </xs:complexType>
+
+    <xs:complexType name="locationTypeType">
+        <xs:attribute name="allowRequests" type="xs:boolean">
+            <xs:annotation>
+                <xs:documentation>True if specimen requests are allowed from this location type.</xs:documentation>
+            </xs:annotation>
+        </xs:attribute>
+    </xs:complexType>
+
+    <xs:complexType name="defaultRequirementsType">
+        <xs:sequence>
+            <xs:element name="requirement" type="defaultRequirementType" minOccurs="0" maxOccurs="unbounded"/>
+        </xs:sequence>
+    </xs:complexType>
+
+    <xs:complexType name="defaultRequirementType">
+        <xs:sequence>
+            <xs:element name="description" type="xs:string"/>
+        </xs:sequence>
+        <xs:attribute name="actor" type="xs:string"/>
+    </xs:complexType>
+
+    <xs:simpleType name="specimenRepositoryType">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="STANDARD"/>
+            <xs:enumeration value="ADVANCED"/>
+        </xs:restriction>
+    </xs:simpleType>
+
+</xs:schema>

specimen/src/org/labkey/specimen/AmbiguousLocationException.java

@@ -0,0 +1,54 @@
+/*
+ * Copyright (c) 2021-2026 LabKey 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 org.labkey.specimen;
+
+import org.labkey.api.data.Container;
+import org.labkey.api.specimen.location.LocationImpl;
+import org.labkey.api.specimen.location.LocationManager;
+
+import java.util.Collection;
+
+public class AmbiguousLocationException extends Exception
+{
+    private final Container _container;
+    private final Collection<Integer> _possibleLocationIds;
+
+    private LocationImpl[] _possibleLocations = null;
+
+    public AmbiguousLocationException(Container container, Collection<Integer> possibleLocationIds)
+    {
+        _container = container;
+        _possibleLocationIds = possibleLocationIds;
+    }
+
+    public Collection<Integer> getPossibleLocationIds()
+    {
+        return _possibleLocationIds;
+    }
+
+    public LocationImpl[] getPossibleLocations()
+    {
+        if (_possibleLocations == null)
+        {
+            _possibleLocations = new LocationImpl[_possibleLocationIds.size()];
+            int idx = 0;
+
+            for (Integer id : _possibleLocationIds)
+                _possibleLocations[idx++] = LocationManager.get().getLocation(_container, id.intValue());
+        }
+        return _possibleLocations;
+    }
+}

specimen/src/org/labkey/specimen/RequestEventType.java

@@ -0,0 +1,43 @@
+/*
+ * Copyright (c) 2021-2026 LabKey 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 org.labkey.specimen;
+
+public enum RequestEventType
+{
+    REQUEST_CREATED("Request Created"),
+    REQUEST_STATUS_CHANGED("Request Status Changed"),
+    REQUIREMENT_ADDED("Requirement Created"),
+    REQUIREMENT_REMOVED("Requirement Removed"),
+    REQUIREMENT_UPDATED("Requirement Updated"),
+    REQUEST_UPDATED("Request Updated"),
+    SPECIMEN_ADDED("Specimen Added"),
+    SPECIMEN_REMOVED("Specimen Removed"),
+    SPECIMEN_LIST_GENERATED("Specimen List Generated"),
+    COMMENT_ADDED("Comment/Attachment(s) Added"),
+    NOTIFICATION_SENT("Notification Sent");
+
+    private final String _displayText;
+
+    RequestEventType(String displayText)
+    {
+        _displayText = displayText;
+    }
+
+    public String getDisplayText()
+    {
+        return _displayText;
+    }
+}