Ioc page improvements

CLAUDE.md

@@ -0,0 +1,123 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Environment bootstrap
+
+Every shell that builds, deploys, or runs CDB **must first source `setup.sh`** from the repo root. It sets `CDB_ROOT_DIR`, `CDB_INSTALL_DIR`, `CDB_DATA_DIR`, `CDB_VAR_DIR`, `CDB_SUPPORT_DIR`, `CDB_GLASSFISH_DIR`, `CDB_PYTHON_DIR`, `PYTHONPATH`, and prepends `bin/`, Ant, Java, Payara, NetBeans-bundled Maven, the support Python, and MariaDB to `PATH`. Most `make` targets and `sbin/` scripts assume those variables exist; running them without sourcing first will fail in non-obvious ways.
+
+The layout is intentionally **out-of-tree**: `CDB_ROOT_DIR` is the source checkout, but the dependency tree lives at `$CDB_INSTALL_DIR/support-<hostname>/` (Payara, Java, Ant, NetBeans, MariaDB, Python) created by `make support`. The deployed app, data, logs, and config live under `$CDB_INSTALL_DIR/{etc,var,data,backup}`. Do not commit or read anything from `support-*/` — it is host-specific.
+
+## Common commands
+
+All `make` targets must be run from the repo root after `source setup.sh`.
+
+```sh
+# First-time / dev environment setup
+make support                       # downloads & builds Payara, Java, Python, etc. into support-<hostname>/
+make support-mysql                 # optional bundled MariaDB
+make support-netbeans              # optional NetBeans IDE bundle
+make dev-config                    # interactive: writes LDAP/email config & per-host build properties
+
+# Database (production "cdb" vs dev "cdb_dev" — every db/deploy target has a -dev twin)
+make clean-db                      # drop & recreate cdb with seed data from db/sql/clean
+make test-db                       # recreate cdb with fixtures from db/sql/test
+make db                            # recreate cdb without populating (schema only)
+make backup                        # dumps cdb to $CDB_INSTALL_DIR/backup/cdb/<YYYYMMDD>/
+make clean-db-dev                  # same, against cdb_dev
+
+# Build & deploy the Java web portal (WAR -> Payara)
+make configure-web-portal          # one-time: writes glassfish-resources.xml, etc.
+make deploy-web-portal             # builds dist/CdbWebPortal.war via Ant and deploys to Payara
+make undeploy-web-portal
+make deploy-web-portal-dev         # deploys to dev domain, uses cdb_dev
+
+# Plugins
+make deploy-cdb-plugin             # interactive picker; see tools/developer_tools/cdb_plugins/plugins/
+
+# Full test suite (interactive — prompts for DB root password)
+make test                          # runs ./sbin/cdb_test.sh: backs up cdb, swaps in test DB,
+                                   # runs Maven unit tests + pytest API tests + Selenium GUI tests,
+                                   # then restores the backup
+```
+
+### Test targets in isolation
+
+```sh
+# Java unit tests (Arquillian + embedded Glassfish)
+cd tools/developer_tools/code_testing/CdbWebPortalTest && mvn test
+mvn test -Dtest=ClassName#methodName    # single test
+
+# Python API tests — require the portal to be running on localhost:8080
+cd tools/developer_tools/python-client && ./generatePyClient.sh http://localhost:8080/cdb
+cd tools/developer_tools/python-client/test && pytest api_test.py
+pytest api_test.py::TestClass::test_method    # single test
+
+# Selenium GUI tests
+cd tools/developer_tools/portal_testing/PythonSeleniumTest && pytest gui_test.py
+```
+
+### Server / log management
+
+```sh
+./etc/init.d/cdb-glassfish restart
+./etc/init.d/cdb-mysqld start            # only if using bundled MariaDB
+tail -f $CDB_SUPPORT_DIR/payara/$CDB_HOST_ARCH/glassfish/domains/production/logs/server.log
+```
+
+## High-level architecture
+
+ComponentDB has **three deployable pieces** plus a generated client. They communicate through the database and through the portal's REST API.
+
+### 1. Java web portal — `src/java/CdbWebPortal/`
+
+A JSF (PrimeFaces) + JAX-RS application packaged as a WAR and deployed to **Payara 5**. Built with **Ant via the NetBeans project** (`build.xml` → `nbproject/build-impl.xml`); the `make` target invokes `cdb-ant` from the support dir. Maven `pom-wip-jdk11.xml` exists but is not the build of record.
+
+Source root: `src/java/CdbWebPortal/src/java/gov/anl/aps/cdb/` with these top-level packages:
+
+- `portal/` — the JSF webapp.
+  - `model/db/entities/` — JPA entities (EclipseLink). Item hierarchy is the core domain model: `Item` is the abstract parent; `ItemDomain*` subclasses (`ItemDomainCatalog`, `ItemDomainInventory`, `ItemDomainLocation`, `ItemDomainMachineDesign`, `ItemDomainCableCatalog`, `ItemDomainCableDesign`, `ItemDomainCableInventory`, `ItemDomainApp`, `ItemDomainMAARC`, `ItemDomainAppDeployment`) implement domain-specific behavior. Catalog/Inventory base classes are shared.
+  - `model/db/beans/` — `@Stateless` EJB facades wrapping JPA queries.
+  - `controllers/` — `@SessionScoped`/`@ViewScoped` JSF managed beans. Naming mirrors the entity: e.g. `ItemDomainCatalogController` ↔ `ItemDomainCatalog`. `CdbDomainEntityController` is the common base. `controllers/extensions/` adds cross-cutting helpers, `controllers/settings/` persists user UI prefs.
+  - `import_export/` — wizard-driven spreadsheet (XLSX) import/export framework; `import_/objects/specs/` defines per-domain column specs and `handlers/` define value coercion.
+  - `view/` — JSF beans and value objects backing views.
+  - `plugins/` — `CdbPluginManager` discovers plugin JARs deployed under `support/`; see `tools/developer_tools/cdb_plugins/` for the plugin install tooling.
+- `rest/` — JAX-RS endpoints exposed at `/cdb/api`. One `*Route` class per resource (`ItemRoute`, `MachineDesignItemRoute`, `CableDesignItemRoute`, `UsersRoute`, `AuthenticationRoute`, etc.) under `rest/routes/`. `rest/entities/` are the request/response DTOs; `rest/authentication/` issues JWTs; `rest/provider/` registers JAX-RS providers. The OpenAPI surface is declared in `src/java/openapi.yaml` and drives Python client generation — keep it in sync when adding/changing routes.
+- `common/` — shared exceptions, constants, value objects used by both `portal/` and `rest/`.
+- `api/`, `connectors/` — internal API surfaces and external system connectors.
+
+**JSF views, templates, and static assets** live in `web/` (`web/views/`, `web/templates/`, `web/resources/`, `web/WEB-INF/`). `web/WEB-INF/glassfish-web.xml` and `src/java/cdb.portal.properties` are generated from `.template` files by `make dev-config` / `make configure-web-portal` — never edit the generated files; edit the templates.
+
+### 2. Python CDB web service — `src/python/cdb/`
+
+A CherryPy service that runs on port 10232 (`./sbin/cdbWebService.sh`), handling email notifications, async tasks, and a legacy SOAP/REST surface. Marked **deprecated** but still part of the distribution for legacy integrations. Layout follows the `common/` + `cdb_web_service/` split with `api/`, `cli/`, `impl/`, `service/`, `tasks/`, `plugins/`, `java_api/` (Python wrappers around the Java REST API). New features should go in the Java REST layer instead.
+
+### 3. Python client + CLI — `tools/developer_tools/python-client/`
+
+- `cdbApi/` is **generated** from `openapi.yaml` by `./generatePyClient.sh <portal-url>` (uses openapi-generator). Do not hand-edit it — regenerate after changing the Java REST routes. `setup-api.py` packages it as `ComponentDB_API` for PyPI.
+- `CdbApiFactory.py` is the hand-written entry point that hides authentication & client wiring.
+- `cdbCli/` is the user-facing CLI (`cdbSearch`, `cdbInfo`, `cdb-cli`); see `docs/CLI.md` for usage and option reference. `cli-template/` holds skeletons for new commands.
+
+### Database — `db/sql/`
+
+MariaDB 10.5. Authoritative schema is the set of `create_cdb_tables.sql`, `create_stored_procedures.sql`, `create_triggers.sql`, `create_views.sql` in `db/sql/`, applied by `sbin/cdb_create_db.sh`. Initial reference data lives in `db/sql/clean/populate_*.sql` (used by `make clean-db`). Test fixtures in `db/sql/test/`.
+
+**Releases bump the version in `etc/version` and add `db/sql/updates/updateTo<NEW_VERSION>.sql`** containing the idempotent (INSERT IGNORE / ALTER ... IF NOT EXISTS) migrations needed to bring an existing prod DB to the new schema. Header comments in each update file document how to run it. The existing version chain (e.g. `updateTo3.15.5.sql` → `updateTo3.17.0.sql`) is the template; do not retroactively edit older update scripts.
+
+**Adding a setting:** `setting_type` ids are organized into per-type blocks with numeric gaps between blocks (e.g. `15xxx` Search, `16xxx` Source, `22xxx` MAARC) so each type has room for new entries. A new setting takes the next free id at the end of its type block — never reuse an id or insert one mid-block (the gap before the next block is the room reserved for this). Add the identical row to all seed copies (`db/sql/{clean,test,static}/populate_setting_type.sql`) and to the current release's `db/sql/updates/updateTo<VERSION>.sql`.
+
+## Repo-specific conventions
+
+- **Generated files that look like sources** are common: `cdb.portal.properties`, `web/WEB-INF/glassfish-web.xml`, `web/WEB-INF/web.xml`, `setup/glassfish-resources.xml`, `nbproject/private/private.properties`, and everything under `tools/developer_tools/python-client/cdbApi/`. They are produced from `*.template` files (or via openapi-generator) by `dev-config` / `configure-web-portal` / `dist` targets and are in `.gitignore`. Edit the template, regenerate, then commit only the template.
+- **`cdb` vs `cdb_dev`**: every db, deploy, undeploy, and backup target has a `-dev` variant that targets a separate database name and Payara domain, so a developer can run both side-by-side. When adding new admin scripts, follow the same pattern (first arg is DB name, defaulting to `cdb`).
+- **Single canonical version string**: update `etc/version`, `src/java/CdbWebPortal/src/java/openapi.yaml` (`info.version`), `tools/developer_tools/python-client/setup-api.py`, and `tools/developer_tools/python-client/setup-cli.py` together. Past release commits (`git log --grep "Prepare relase"`) show the full set of files that need bumping.
+- **Plugins** under `tools/developer_tools/cdb_plugins/plugins/<name>/` extend both the Java portal (deployed via `make deploy-cdb-plugin` → `update_plugin_generated_files.py`) and the Python web service. `pluginTemplates/` is the scaffold.
+- **REST changes touch three places**: the Java route, `openapi.yaml`, and (after `generatePyClient.sh`) the regenerated `cdbApi/` package. The Python API tests in `tools/developer_tools/python-client/test/api_test.py` are the integration check.
+
+## Reference docs
+
+- `README.md` — full deployment and upgrade walk-through (commands here are abbreviated).
+- `docs/CLI.md` — `cdbSearch` / `cdbInfo` / `cdb-cli` reference.
+- `docs/release-notes/<version>.md` — per-release notes; mirror this format for new releases.
+- `docs/db/CdbSchema-v3.0-3.pdf` — ER diagram (somewhat dated but useful for the Item hierarchy).
+- External developer guide: <https://confluence.aps.anl.gov/display/APSUCMS/Developer+Guide> (referenced from README).

db/sql/clean/populate_setting_type.sql

@@ -285,6 +285,9 @@ INSERT INTO `setting_type` VALUES
 (15011,'Search.Display.Users','Display search result for users.','false'),
 (15012,'Search.Display.UserGroups','Display search result for user groups.','false'),
 (15013,'Search.DisplayItemDomainMachineDesign','Display search result for machine design items','true'),
+(15018,'Search.Display.ItemDomainMachineDesignIOC','Display search result for IOC items.','true'),
+(15019,'Search.Display.ItemDomainApp','Display search result for application items.','true'),
+(15020,'Search.Display.PropertyValue','Display search result for property values.','true'),
 (16000,'Source.List.Display.ContactInfo','Display source contact info.','true'),
 (16001,'Source.List.Display.Description','Display source description.','true'),
 (16002,'Source.List.Display.Url','Display source URL.','true'),

db/sql/create_stored_procedures.sql

@@ -95,6 +95,34 @@ BEGIN
 	LIMIT limit_row;
 END //
 
+DROP PROCEDURE IF EXISTS search_ioc_items;//
+CREATE PROCEDURE `search_ioc_items` (IN limit_row int, IN search_string VARCHAR(255))
+BEGIN
+	DECLARE ioc_entity_type_id INT;
+	SET ioc_entity_type_id = 11;   -- EntityTypeName.IOC_ID
+
+	SET search_string = CONCAT('%', search_string, '%');
+	SELECT DISTINCT item.* from item
+	INNER JOIN v_item_self_element ise ON item.id = ise.item_id
+	INNER JOIN item_element ie ON ise.self_element_id = ie.id
+	INNER JOIN entity_info ei ON ise.entity_info_id = ei.id
+	INNER JOIN user_info owneru ON ei.owner_user_id = owneru.id
+	INNER JOIN user_info creatoru ON ei.created_by_user_id = creatoru.id
+	INNER JOIN user_info updateu ON ei.last_modified_by_user_id = updateu.id
+	INNER JOIN item_entity_type iet ON iet.item_id = item.id AND iet.entity_type_id = ioc_entity_type_id
+	WHERE (
+		item.name LIKE search_string
+		OR item.qr_id LIKE search_string
+		OR item.item_identifier1 LIKE search_string
+		OR item.item_identifier2 LIKE search_string
+		OR ie.description LIKE search_string
+		OR owneru.username LIKE search_string
+		OR creatoru.username LIKE search_string
+		OR updateu.username LIKE search_string
+	)
+	LIMIT limit_row;
+END //
+
 DROP PROCEDURE IF EXISTS search_item_elements;//
 CREATE PROCEDURE `search_item_elements` (IN limit_row int, IN search_string VARCHAR(255)) 
 BEGIN

db/sql/static/populate_setting_type.sql

@@ -284,7 +284,10 @@ description.','true'),
 (15014,'Search.Display.ItemDomainCableCatalog','Display search result for cable catalog items.','true'),
 (15015,'Search.Display.ItemDomainCableInventory','Display search result for cable inventory items.','true'),
 (15016,'Search.Display.ItemDomainCableDesign','Display search result for cable design items.','true'),
-(15017,'Search.Display.ItemDomainMAARC', 'Display search result for MAARC items', 'false'), 
+(15017,'Search.Display.ItemDomainMAARC', 'Display search result for MAARC items', 'false'),
+(15018,'Search.Display.ItemDomainMachineDesignIOC','Display search result for IOC items.','true'),
+(15019,'Search.Display.ItemDomainApp','Display search result for application items.','true'),
+(15020,'Search.Display.PropertyValue','Display search result for property values.','true'),
 (16000,'Source.List.Display.ContactInfo','Display source contact info.','true'),
 (16001,'Source.List.Display.Description','Display source description.','true'),
 (16002,'Source.List.Display.Url','Display source URL.','true'),

db/sql/test/populate_setting_type.sql

@@ -284,6 +284,9 @@ INSERT INTO `setting_type` VALUES
 (15015,'Search.Display.ItemDomainCableInventory','Display search result for cable inventory items.','true'),
 (15016,'Search.Display.ItemDomainCableDesign','Display search result for cable design items.','true'),
 (15017,'Search.Display.ItemDomainMAARC','Display search result for MAARC items','false'),
+(15018,'Search.Display.ItemDomainMachineDesignIOC','Display search result for IOC items.','true'),
+(15019,'Search.Display.ItemDomainApp','Display search result for application items.','true'),
+(15020,'Search.Display.PropertyValue','Display search result for property values.','true'),
 (16000,'Source.List.Display.ContactInfo','Display source contact info.','true'),
 (16001,'Source.List.Display.Description','Display source description.','true'),
 (16002,'Source.List.Display.Url','Display source URL.','true'),

db/sql/updates/updateTo3.18.0.sql

@@ -0,0 +1,46 @@
+--
+-- Copyright (c) UChicago Argonne, LLC. All rights reserved.
+-- See LICENSE file.
+--
+
+-- Execute by running `mysql CDB_DB_NAME -h 127.0.0.1 -u cdb -p < updateTo3.16.2.sql`
+
+INSERT IGNORE INTO `setting_type` VALUES
+(15018,'Search.Display.ItemDomainMachineDesignIOC','Display search result for IOC items.','true'),
+(15019,'Search.Display.ItemDomainApp','Display search result for application items.','true'),
+(15020,'Search.Display.PropertyValue','Display search result for property values.','true');
+
+-- Add text property value (value/text/tag) matching to the item search procedures
+-- and a dedicated IOC item search procedure (used to search markdown IOC instructions).
+
+delimiter //
+
+DROP PROCEDURE IF EXISTS search_ioc_items;//
+CREATE PROCEDURE `search_ioc_items` (IN limit_row int, IN search_string VARCHAR(255))
+BEGIN
+	DECLARE ioc_entity_type_id INT;
+	SET ioc_entity_type_id = 11;   -- EntityTypeName.IOC_ID
+
+	SET search_string = CONCAT('%', search_string, '%');
+	SELECT DISTINCT item.* from item
+	INNER JOIN v_item_self_element ise ON item.id = ise.item_id
+	INNER JOIN item_element ie ON ise.self_element_id = ie.id
+	INNER JOIN entity_info ei ON ise.entity_info_id = ei.id
+	INNER JOIN user_info owneru ON ei.owner_user_id = owneru.id
+	INNER JOIN user_info creatoru ON ei.created_by_user_id = creatoru.id
+	INNER JOIN user_info updateu ON ei.last_modified_by_user_id = updateu.id
+	INNER JOIN item_entity_type iet ON iet.item_id = item.id AND iet.entity_type_id = ioc_entity_type_id
+	WHERE (
+		item.name LIKE search_string
+		OR item.qr_id LIKE search_string
+		OR item.item_identifier1 LIKE search_string
+		OR item.item_identifier2 LIKE search_string
+		OR ie.description LIKE search_string
+		OR owneru.username LIKE search_string
+		OR creatoru.username LIKE search_string
+		OR updateu.username LIKE search_string
+	)
+	LIMIT limit_row;
+END //
+
+delimiter ;

src/java/CdbWebPortal/nbproject/build-impl.xml

@@ -1026,8 +1026,8 @@ exists or setup the property manually. For example like this:
         <copyfiles files="${file.reference.xmpcore-6.1.10.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <copyfiles files="${file.reference.metadata-extractor-2.17.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <copyfiles files="${file.reference.javax.xml.soap-api-1.4.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
-        <copyfiles files="${file.reference.log4j-api-2.17.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
-        <copyfiles files="${file.reference.log4j-core-2.17.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.log4j-api-2.26.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
+        <copyfiles files="${file.reference.log4j-core-2.26.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <copyfiles files="${file.reference.dm-api-3.3.1.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <copyfiles files="${file.reference.dm-base-3.3.1.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
         <copyfiles files="${file.reference.flexmark-0.64.8.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
@@ -1089,8 +1089,8 @@ exists or setup the property manually. For example like this:
         <copyfiles files="${file.reference.xmpcore-6.1.10.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
         <copyfiles files="${file.reference.metadata-extractor-2.17.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
         <copyfiles files="${file.reference.javax.xml.soap-api-1.4.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
-        <copyfiles files="${file.reference.log4j-api-2.17.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
-        <copyfiles files="${file.reference.log4j-core-2.17.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.log4j-api-2.26.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
+        <copyfiles files="${file.reference.log4j-core-2.26.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
         <copyfiles files="${file.reference.dm-api-3.3.1.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
         <copyfiles files="${file.reference.dm-base-3.3.1.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
         <copyfiles files="${file.reference.flexmark-0.64.8.jar}" todir="${build.web.dir}/WEB-INF/lib"/>