From bbe52860a54695977c80f4231c8ff740222a9805 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Thu, 10 Jul 2025 13:55:22 +0200
Subject: [PATCH 01/11] Added a feature to enable an open-source APM: glowroot
 to the tomcat service. It downloads the latest version (--glowroot) or you
 can specify an specific zip file that you already have downloaded
 (--glowroot-zip), by default it will listen on port 4000, but you can change
 it with --glowroot-port (only if glowroot is enabled by any of the other two
 ways). Latest version is prioritized over an specific file

---
 README.md                                     |  9 +++-
 setup.py                                      |  2 +-
 src/d2_docker/commands/start.py               |  6 +++
 src/d2_docker/config/dhis2-core-entrypoint.sh | 15 +++++++
 src/d2_docker/docker-compose.yml              |  2 +
 src/d2_docker/utils.py                        | 45 +++++++++++++++++--
 6 files changed, 73 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 0b1c2b8..33f4e04 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,8 @@
 
 - Operating System: GNU/Linux or Windows 10.
 - Python >= 3.5 (with setuptools)
-- Docker >= 18
-- Docker compose >= 1.17
+- Docker >= 20.10.13
+- Docker compose >= 2.0
 - RAM memory: At least 4Gb for instance, preferrably 8Gb.
 
 On Ubuntu 22.04:
@@ -69,6 +69,8 @@ Create a dhis2-data image from a .sql.gz SQL file and the apps and documents (or
 $ d2-docker create data docker.eyeseetea.com/eyeseetea/dhis2-data:2.37.9-sierra --sql=sierra-db.sql.gz [--apps-dir=path/to/apps] [--documents-dir=path/to/document] [--datavalues-dir=path/to/dataValue]
 ```
 
+There are demo database files at [databases.dhis2.org](https://databases.dhis2.org/) that may be used for testing purposses. The database downloaded should correspond to the core version created; if there is no database file for the created core version, a prior version of the database should work.
+
 ### Start a DHIS2 instance
 
 Start a new container from a _dhis2-data_ base image:
@@ -92,6 +94,9 @@ Some notes:
 - Use option `--java-opts="JAVA_OPTS"` to override the default JAVA_OPTS for the Tomcat process. That's tipically used to set the maximum/initial Heap Memory size (for example: `--java-opts="-Xmx3500m -Xms2500m"`)
 - Use option `--postgis-version=13-3.1-alpine` to specify the PostGIS version to use. By default, 10-2.5-alpine is used.
 - Use option `--debug-port=PORT` to specify the debug port of the Tomcat process.
+- Use option `--glowroot-port=PORT` to specify the APM glowroot port of the Tomcat process.
+- Use option `--glowroot` to use the latest version of glowroot in the Tomcat process.
+- Use option `--glowroot-zip=FILE` to specify the zip file with a version of glowroot to run in the Tomcat process.
 
 #### Custom DHIS2 dhis.conf
 
diff --git a/setup.py b/setup.py
index 86d1293..423e8ad 100644
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@
 
 setuptools.setup(
     name="d2_docker",
-    version="1.15.0.b2",
+    version="1.16.0",
     description="Dockers for DHIS2 instances",
     long_description=open("README.md", encoding="utf-8").read(),
     keywords=["python"],
diff --git a/src/d2_docker/commands/start.py b/src/d2_docker/commands/start.py
index 2ff59f4..bd6384c 100644
--- a/src/d2_docker/commands/start.py
+++ b/src/d2_docker/commands/start.py
@@ -41,6 +41,9 @@ def setup(parser):
     parser.add_argument("--postgis-version", type=str, help="Set PostGIS database version")
     parser.add_argument("--enable-postgres-queries-logging", action="store_true",
                         help="Enable Postgres queries logging")
+    parser.add_argument("--glowroot", action="store_true", help="Enables glowroot in tomcat in latest version")
+    parser.add_argument("--glowroot-zip", metavar="FILE", help="ZIP file with glowroot binaries")
+    parser.add_argument("--glowroot-port", metavar="PORT", help="Set glowroot port")
 
 
 def run(args):
@@ -113,6 +116,9 @@ def start(args):
             java_opts=args.java_opts,
             postgis_version=args.postgis_version,
             enable_postgres_queries_logging=args.enable_postgres_queries_logging,
+            glowroot=args.glowroot,
+            glowroot_zip=args.glowroot_zip,
+            glowroot_port=args.glowroot_port,
         )
 
     if args.detach:
diff --git a/src/d2_docker/config/dhis2-core-entrypoint.sh b/src/d2_docker/config/dhis2-core-entrypoint.sh
index 65610e4..d1756a7 100755
--- a/src/d2_docker/config/dhis2-core-entrypoint.sh
+++ b/src/d2_docker/config/dhis2-core-entrypoint.sh
@@ -12,6 +12,9 @@ WARFILE=/usr/local/tomcat/webapps/ROOT.war
 TOMCATDIR=/usr/local/tomcat
 DHIS2HOME=/DHIS2_home
 DATA_DIR=/data
+GLOWROOT_ZIP="/opt/glowroot.zip"
+GLOWROOT_DIR="/opt/glowroot"
+
 
 debug() {
     echo "[dhis2-core-entrypoint] $*" >&2
@@ -49,6 +52,18 @@ if [ "$(id -u)" = "0" ]; then
         rm -v $WARFILE # just to save space
     fi
 
+    if [ -f $GLOWROOT_ZIP ] && [ ! -d $GLOWROOT_DIR ] ; then
+        unzip -q $GLOWROOT_ZIP -d /opt/ || [ $? -le 1 ]
+        if [ -d $GLOWROOT_DIR ] ; then
+            echo '{ "web": { "bindAddress": "0.0.0.0", "port": "4000" }}' > $GLOWROOT_DIR/admin.json
+            chown -R tomcat:tomcat $GLOWROOT_DIR
+            chmod -R u=rwX,g=rX,o-rwx $GLOWROOT_DIR
+            echo 'export CATALINA_OPTS="$CATALINA_OPTS -javaagent:/opt/glowroot/glowroot.jar"' > /usr/local/tomcat/bin/setenv.sh
+            chmod ugo+x /usr/local/tomcat/bin/setenv.sh
+            chown tomcat:tomcat /usr/local/tomcat/bin/setenv.sh
+        fi
+    fi
+
     wait_for_data_container_to_finish_copy
 
     mkdir -p $DATA_DIR/apps
diff --git a/src/d2_docker/docker-compose.yml b/src/d2_docker/docker-compose.yml
index bf6d447..36a1ed7 100644
--- a/src/d2_docker/docker-compose.yml
+++ b/src/d2_docker/docker-compose.yml
@@ -5,6 +5,7 @@ services:
             - "com.eyeseetea.image-name=${DHIS2_DATA_IMAGE}"
         volumes:
             - home:/DHIS2_home
+            - ${GLOWROOT_ZIP}:/opt/glowroot.zip
             - ${DHIS_CONF}:/config/override/dhis2/dhis.conf
             - ${ROOT_PATH}/config:/config
             - data:/data
@@ -27,6 +28,7 @@ services:
             - "data"
         ports:
             - "${DHIS2_CORE_DEBUG_PORT}"
+            - "${GLOWROOT_PORT}"
     db:
         image: "postgis/postgis:${POSTGIS_VERSION:-14-3.2-alpine}"
         shm_size: 1gb
diff --git a/src/d2_docker/utils.py b/src/d2_docker/utils.py
index c92cec4..f95a3b2 100644
--- a/src/d2_docker/utils.py
+++ b/src/d2_docker/utils.py
@@ -10,6 +10,8 @@
 import time
 import yaml
 import urllib.request
+import json
+import zipfile
 from setuptools._distutils import dir_util
 from pathlib import Path
 from typing import Optional
@@ -39,6 +41,16 @@ def get_dhis2_war_url(version):
     )
     return releases_base_url + "/" + path
 
+def get_latest_glowroot_url():
+    glowroot_releases_url = "https://api.github.com/repos/glowroot/glowroot/releases/latest"
+    glowroot_download_url = "https://github.com/glowroot/glowroot/releases/download"
+    with urllib.request.urlopen(glowroot_releases_url) as response:
+        data = response.read().decode()
+        release_info = json.loads(data)
+
+    tag_name = release_info["tag_name"]
+    return "{}/{}/glowroot-{}-dist.zip".format(glowroot_download_url, tag_name, tag_name.lstrip("v"))
+
 
 def docker_build(directory, tag):
     return run(["docker", "build", "--platform", "linux/amd64", "--tag", tag, directory])
@@ -261,6 +273,9 @@ def run_docker_compose(
     tomcat_server=None,
     postgis_version=None,
     enable_postgres_queries_logging=False,
+    glowroot=None,
+    glowroot_zip=None,
+    glowroot_port=None,
     **kwargs,
 ):
     """
@@ -270,11 +285,30 @@ def run_docker_compose(
 
     The DHIS2_CORE_IMAGE is inferred from the data repo, if not specified.
     """
+
     final_image_name = data_image or get_running_image_name()
     project_name = get_project_name(final_image_name)
     core_image_name = core_image or get_core_image_name(data_image)
     post_sql_dir_abs = get_absdir_for_docker_volume(post_sql_dir)
     scripts_dir_abs = get_absdir_for_docker_volume(scripts_dir)
+    glowroot_path=None
+
+    if args[0] == "up":
+        glowroot_file = tempfile.NamedTemporaryFile(delete=False, prefix="glowroot_", suffix=".zip", dir="/tmp")
+        glowroot_path = glowroot_file.name
+
+        atexit.register(lambda: os.remove(glowroot_path) if os.path.exists(glowroot_path) else None)
+        if glowroot_zip:
+            logger.debug("Copy zip file: {} -> {}".format(glowroot_zip, glowroot_path))
+            shutil.copy(glowroot_zip, glowroot_path)
+        elif glowroot:
+            glowroot_url = get_latest_glowroot_url()
+            logger.info("Download file: {}".format(glowroot_url))
+            urllib.request.urlretrieve(glowroot_url, glowroot_path)
+        else:
+            # empty zipfile
+            with zipfile.ZipFile(glowroot_path, mode="w") as zf:
+                pass
 
     env_pairs = [
         ("DHIS2_DATA_IMAGE", final_image_name),
@@ -296,13 +330,18 @@ def run_docker_compose(
         # Add ROOT_PATH from environment (required when run inside a docker)
         ("ROOT_PATH", ROOT_PATH),
         ("PSQL_ENABLE_QUERY_LOGS", "") if not enable_postgres_queries_logging else None,
+        ("GLOWROOT_PORT", "{}:4000".format(glowroot_port) if glowroot_port else "4000:4000") if (glowroot or glowroot_zip) else ("GLOWROOT_PORT", None),
+        ("GLOWROOT_ZIP", get_absfile_for_docker_volume(glowroot_path)),
     ]
     env = dict((k, v) for (k, v) in [pair for pair in env_pairs if pair] if v is not None)
 
     def process_yaml(data):
-        if "DHIS2_CORE_DEBUG_PORT" not in env:
-            core = data["services"]["core"]
-            core["ports"] = [port for port in core["ports"] if "DHIS2_CORE_DEBUG_PORT" not in port]
+        # Removes ports for "core" service in docker-compose if the environmental variables are not established
+        core = data["services"]["core"]
+        env_ports = ["DHIS2_CORE_DEBUG_PORT", "GLOWROOT_PORT"]
+        for env_port in env_ports:
+            if env_port not in env:
+                core["ports"] = [port for port in core["ports"] if env_port not in port]
 
         return data
 

From 7011a1f44173afff7eabd256430ba262f333d6a2 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Tue, 29 Jul 2025 15:32:27 +0200
Subject: [PATCH 02/11] Code cleanup

---
 README.md                                     | 17 +++++--
 src/d2_docker/commands/start.py               |  1 +
 src/d2_docker/config/dhis2-core-entrypoint.sh | 22 ++++++---
 src/d2_docker/glowroot.py                     | 46 +++++++++++++++++++
 src/d2_docker/utils.py                        | 35 ++------------
 5 files changed, 79 insertions(+), 42 deletions(-)
 create mode 100644 src/d2_docker/glowroot.py

diff --git a/README.md b/README.md
index 33f4e04..08db6a6 100644
--- a/README.md
+++ b/README.md
@@ -94,9 +94,6 @@ Some notes:
 - Use option `--java-opts="JAVA_OPTS"` to override the default JAVA_OPTS for the Tomcat process. That's tipically used to set the maximum/initial Heap Memory size (for example: `--java-opts="-Xmx3500m -Xms2500m"`)
 - Use option `--postgis-version=13-3.1-alpine` to specify the PostGIS version to use. By default, 10-2.5-alpine is used.
 - Use option `--debug-port=PORT` to specify the debug port of the Tomcat process.
-- Use option `--glowroot-port=PORT` to specify the APM glowroot port of the Tomcat process.
-- Use option `--glowroot` to use the latest version of glowroot in the Tomcat process.
-- Use option `--glowroot-zip=FILE` to specify the zip file with a version of glowroot to run in the Tomcat process.
 
 #### Custom DHIS2 dhis.conf
 
@@ -381,3 +378,17 @@ $ cp flaskenv.secret ~/.config/d2-docker/
 
 $ curl -sS 'http://localhost:5000/harbor/https://docker.eyeseetea.com/api/v2.0/quotas/1' | jq
 ```
+
+## Glowroot
+
+Glowroot is an open-source Java APM (Application Performance Monitoring) tool. It can help detect and diagnose application performance problems, tracing slow requests, errors, response time breakdowns, SQL capture and more.
+When starting a container, there are a few options to enable glowroot on the Tomcat process:
+- Use option `--glowroot-port=PORT` to specify the APM glowroot port of the Tomcat process.
+- Use option `--glowroot` to use the latest version of glowroot in the Tomcat process.
+- Use option `--glowroot-zip=FILE` to specify the zip file with a version of glowroot to run in the Tomcat process.
+
+### Run d2-docker with glowroot enabled in the default port at the latest version available
+
+```
+$ d2-docker start docker.eyeseetea.com/eyeseetea/dhis2-data:2.37.9-sierra --glowroot
+```
\ No newline at end of file
diff --git a/src/d2_docker/commands/start.py b/src/d2_docker/commands/start.py
index bd6384c..c59a5b8 100644
--- a/src/d2_docker/commands/start.py
+++ b/src/d2_docker/commands/start.py
@@ -41,6 +41,7 @@ def setup(parser):
     parser.add_argument("--postgis-version", type=str, help="Set PostGIS database version")
     parser.add_argument("--enable-postgres-queries-logging", action="store_true",
                         help="Enable Postgres queries logging")
+    
     parser.add_argument("--glowroot", action="store_true", help="Enables glowroot in tomcat in latest version")
     parser.add_argument("--glowroot-zip", metavar="FILE", help="ZIP file with glowroot binaries")
     parser.add_argument("--glowroot-port", metavar="PORT", help="Set glowroot port")
diff --git a/src/d2_docker/config/dhis2-core-entrypoint.sh b/src/d2_docker/config/dhis2-core-entrypoint.sh
index d1756a7..6e01881 100755
--- a/src/d2_docker/config/dhis2-core-entrypoint.sh
+++ b/src/d2_docker/config/dhis2-core-entrypoint.sh
@@ -46,14 +46,14 @@ wait_for_data_container_to_finish_copy() {
 
 }
 
-if [ "$(id -u)" = "0" ]; then
-    if [ -f $WARFILE ]; then
-        unzip -q $WARFILE -d $TOMCATDIR/webapps/ROOT
-        rm -v $WARFILE # just to save space
-    fi
-
+setup_glowroot() {
     if [ -f $GLOWROOT_ZIP ] && [ ! -d $GLOWROOT_DIR ] ; then
-        unzip -q $GLOWROOT_ZIP -d /opt/ || [ $? -le 1 ]
+        status=0
+        unzip -q "$GLOWROOT_ZIP" -d /opt/ || status=$?
+        # Ignore RC=1 that implies only warnings and no errors (like an empty zip file)
+        if [ $status -gt 1 ]; then
+            exit $status
+        fi
         if [ -d $GLOWROOT_DIR ] ; then
             echo '{ "web": { "bindAddress": "0.0.0.0", "port": "4000" }}' > $GLOWROOT_DIR/admin.json
             chown -R tomcat:tomcat $GLOWROOT_DIR
@@ -63,7 +63,15 @@ if [ "$(id -u)" = "0" ]; then
             chown tomcat:tomcat /usr/local/tomcat/bin/setenv.sh
         fi
     fi
+}
+
+if [ "$(id -u)" = "0" ]; then
+    if [ -f $WARFILE ]; then
+        unzip -q $WARFILE -d $TOMCATDIR/webapps/ROOT
+        rm -v $WARFILE # just to save space
+    fi
 
+    setup_glowroot
     wait_for_data_container_to_finish_copy
 
     mkdir -p $DATA_DIR/apps
diff --git a/src/d2_docker/glowroot.py b/src/d2_docker/glowroot.py
new file mode 100644
index 0000000..2b6cda2
--- /dev/null
+++ b/src/d2_docker/glowroot.py
@@ -0,0 +1,46 @@
+import atexit
+import json
+import os
+import shutil
+import tempfile
+import urllib.request
+import zipfile
+from d2_docker import utils
+
+GLOWROOT_DEFAULT_PORT = "4000"
+
+def get_latest_glowroot_url():
+    glowroot_releases_url = "https://api.github.com/repos/glowroot/glowroot/releases/latest"
+    glowroot_download_url = "https://github.com/glowroot/glowroot/releases/download"
+    with urllib.request.urlopen(glowroot_releases_url) as response:
+        data = response.read().decode()
+        release_info = json.loads(data)
+
+    tag_name = release_info["tag_name"]
+    return "{}/{}/glowroot-{}-dist.zip".format(glowroot_download_url, tag_name, tag_name.lstrip("v"))
+
+def get_glowroot_zip(command, glowroot_zip, glowroot):
+    logger = utils.logger
+    glowroot_path=None
+    if command == "up":
+        glowroot_file = tempfile.NamedTemporaryFile(delete=False, prefix="glowroot_", suffix=".zip", dir="/tmp")
+        glowroot_path = glowroot_file.name
+
+        atexit.register(lambda: os.remove(glowroot_path) if os.path.exists(glowroot_path) else None)
+        if glowroot_zip:
+            logger.debug("Copy zip file: {} -> {}".format(glowroot_zip, glowroot_path))
+            shutil.copy(glowroot_zip, glowroot_path)
+        elif glowroot:
+            glowroot_url = get_latest_glowroot_url()
+            logger.info("Download file: {}".format(glowroot_url))
+            urllib.request.urlretrieve(glowroot_url, glowroot_path)
+        else:
+            # empty zipfile
+            with zipfile.ZipFile(glowroot_path, mode="w") as zf:
+                pass
+
+    return utils.get_absfile_for_docker_volume(glowroot_path)
+
+def get_port_glowroot(glowroot_port, glowroot_zip, glowroot):
+    port = glowroot_port if glowroot_port else GLOWROOT_DEFAULT_PORT
+    return "{}:{}".format(port, GLOWROOT_DEFAULT_PORT) if (glowroot_port or glowroot_zip or glowroot) else None
diff --git a/src/d2_docker/utils.py b/src/d2_docker/utils.py
index f95a3b2..0442a6c 100644
--- a/src/d2_docker/utils.py
+++ b/src/d2_docker/utils.py
@@ -10,13 +10,12 @@
 import time
 import yaml
 import urllib.request
-import json
-import zipfile
 from setuptools._distutils import dir_util
 from pathlib import Path
 from typing import Optional
 
 import d2_docker
+from d2_docker.glowroot import get_glowroot_zip, get_port_glowroot
 from .image_name import ImageName
 
 PROJECT_NAME_PREFIX = "d2-docker"
@@ -41,16 +40,6 @@ def get_dhis2_war_url(version):
     )
     return releases_base_url + "/" + path
 
-def get_latest_glowroot_url():
-    glowroot_releases_url = "https://api.github.com/repos/glowroot/glowroot/releases/latest"
-    glowroot_download_url = "https://github.com/glowroot/glowroot/releases/download"
-    with urllib.request.urlopen(glowroot_releases_url) as response:
-        data = response.read().decode()
-        release_info = json.loads(data)
-
-    tag_name = release_info["tag_name"]
-    return "{}/{}/glowroot-{}-dist.zip".format(glowroot_download_url, tag_name, tag_name.lstrip("v"))
-
 
 def docker_build(directory, tag):
     return run(["docker", "build", "--platform", "linux/amd64", "--tag", tag, directory])
@@ -291,24 +280,6 @@ def run_docker_compose(
     core_image_name = core_image or get_core_image_name(data_image)
     post_sql_dir_abs = get_absdir_for_docker_volume(post_sql_dir)
     scripts_dir_abs = get_absdir_for_docker_volume(scripts_dir)
-    glowroot_path=None
-
-    if args[0] == "up":
-        glowroot_file = tempfile.NamedTemporaryFile(delete=False, prefix="glowroot_", suffix=".zip", dir="/tmp")
-        glowroot_path = glowroot_file.name
-
-        atexit.register(lambda: os.remove(glowroot_path) if os.path.exists(glowroot_path) else None)
-        if glowroot_zip:
-            logger.debug("Copy zip file: {} -> {}".format(glowroot_zip, glowroot_path))
-            shutil.copy(glowroot_zip, glowroot_path)
-        elif glowroot:
-            glowroot_url = get_latest_glowroot_url()
-            logger.info("Download file: {}".format(glowroot_url))
-            urllib.request.urlretrieve(glowroot_url, glowroot_path)
-        else:
-            # empty zipfile
-            with zipfile.ZipFile(glowroot_path, mode="w") as zf:
-                pass
 
     env_pairs = [
         ("DHIS2_DATA_IMAGE", final_image_name),
@@ -330,8 +301,8 @@ def run_docker_compose(
         # Add ROOT_PATH from environment (required when run inside a docker)
         ("ROOT_PATH", ROOT_PATH),
         ("PSQL_ENABLE_QUERY_LOGS", "") if not enable_postgres_queries_logging else None,
-        ("GLOWROOT_PORT", "{}:4000".format(glowroot_port) if glowroot_port else "4000:4000") if (glowroot or glowroot_zip) else ("GLOWROOT_PORT", None),
-        ("GLOWROOT_ZIP", get_absfile_for_docker_volume(glowroot_path)),
+        ("GLOWROOT_PORT", get_port_glowroot(glowroot_port, glowroot_zip, glowroot)),
+        ("GLOWROOT_ZIP", get_glowroot_zip(args[0], glowroot_zip, glowroot)),
     ]
     env = dict((k, v) for (k, v) in [pair for pair in env_pairs if pair] if v is not None)
 

From e1ed7a8e3e3304d89bc7cae8b4bae5a7d64e5913 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Tue, 26 Aug 2025 15:15:42 +0200
Subject: [PATCH 03/11] Avoid warning output from unzip

---
 src/d2_docker/config/dhis2-core-entrypoint.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/d2_docker/config/dhis2-core-entrypoint.sh b/src/d2_docker/config/dhis2-core-entrypoint.sh
index 6e01881..4265882 100755
--- a/src/d2_docker/config/dhis2-core-entrypoint.sh
+++ b/src/d2_docker/config/dhis2-core-entrypoint.sh
@@ -49,9 +49,10 @@ wait_for_data_container_to_finish_copy() {
 setup_glowroot() {
     if [ -f $GLOWROOT_ZIP ] && [ ! -d $GLOWROOT_DIR ] ; then
         status=0
-        unzip -q "$GLOWROOT_ZIP" -d /opt/ || status=$?
+        output=$(unzip -q "$GLOWROOT_ZIP" -d /opt/ 2>&1 || status=$?)
         # Ignore RC=1 that implies only warnings and no errors (like an empty zip file)
         if [ $status -gt 1 ]; then
+            echo "$output"
             exit $status
         fi
         if [ -d $GLOWROOT_DIR ] ; then

From 344243a4c6e8009c644a425bcc1d0f9e4b6e9f4c Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Tue, 26 Aug 2025 15:59:36 +0200
Subject: [PATCH 04/11] status was always 0 because incorrect placement of
 parenthesis

---
 src/d2_docker/config/dhis2-core-entrypoint.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/d2_docker/config/dhis2-core-entrypoint.sh b/src/d2_docker/config/dhis2-core-entrypoint.sh
index 4265882..45b9a0a 100755
--- a/src/d2_docker/config/dhis2-core-entrypoint.sh
+++ b/src/d2_docker/config/dhis2-core-entrypoint.sh
@@ -49,7 +49,7 @@ wait_for_data_container_to_finish_copy() {
 setup_glowroot() {
     if [ -f $GLOWROOT_ZIP ] && [ ! -d $GLOWROOT_DIR ] ; then
         status=0
-        output=$(unzip -q "$GLOWROOT_ZIP" -d /opt/ 2>&1 || status=$?)
+	output=$(unzip -q "$GLOWROOT_ZIP" -d /opt/ 2>&1) || status=$?
         # Ignore RC=1 that implies only warnings and no errors (like an empty zip file)
         if [ $status -gt 1 ]; then
             echo "$output"

From 94a3dcec5ab34a13b28b11f6f541db31648b62c5 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Thu, 2 Oct 2025 12:44:27 +0200
Subject: [PATCH 05/11] Fixed an error when `d2-docker logs` was used.

---
 src/d2_docker/glowroot.py | 2 +-
 src/d2_docker/utils.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/d2_docker/glowroot.py b/src/d2_docker/glowroot.py
index 2b6cda2..34a99d7 100644
--- a/src/d2_docker/glowroot.py
+++ b/src/d2_docker/glowroot.py
@@ -22,7 +22,7 @@ def get_latest_glowroot_url():
 def get_glowroot_zip(command, glowroot_zip, glowroot):
     logger = utils.logger
     glowroot_path=None
-    if command == "up":
+    if isinstance(command, list) and command[0] == "up":
         glowroot_file = tempfile.NamedTemporaryFile(delete=False, prefix="glowroot_", suffix=".zip", dir="/tmp")
         glowroot_path = glowroot_file.name
 
diff --git a/src/d2_docker/utils.py b/src/d2_docker/utils.py
index 0442a6c..bc2bf93 100644
--- a/src/d2_docker/utils.py
+++ b/src/d2_docker/utils.py
@@ -302,7 +302,7 @@ def run_docker_compose(
         ("ROOT_PATH", ROOT_PATH),
         ("PSQL_ENABLE_QUERY_LOGS", "") if not enable_postgres_queries_logging else None,
         ("GLOWROOT_PORT", get_port_glowroot(glowroot_port, glowroot_zip, glowroot)),
-        ("GLOWROOT_ZIP", get_glowroot_zip(args[0], glowroot_zip, glowroot)),
+        ("GLOWROOT_ZIP", get_glowroot_zip(args, glowroot_zip, glowroot)),
     ]
     env = dict((k, v) for (k, v) in [pair for pair in env_pairs if pair] if v is not None)
 

From 969633447a3095e898473d4036f9cf3460a27ee2 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Wed, 8 Oct 2025 13:21:22 +0200
Subject: [PATCH 06/11] Added an option in the docker-compose.yml to ensure
 there is no "search" domain in the /etc/resolv.conf copied onto the
 containers This avoids the `core` container trying to determine when the
 `data` container has finished its execution via `curl` to get responses from
 any `data.search_domain` machine that might exist.

---
 src/d2_docker/docker-compose.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/d2_docker/docker-compose.yml b/src/d2_docker/docker-compose.yml
index 36a1ed7..1b8eda2 100644
--- a/src/d2_docker/docker-compose.yml
+++ b/src/d2_docker/docker-compose.yml
@@ -29,6 +29,7 @@ services:
         ports:
             - "${DHIS2_CORE_DEBUG_PORT}"
             - "${GLOWROOT_PORT}"
+        dns_search: .
     db:
         image: "postgis/postgis:${POSTGIS_VERSION:-14-3.2-alpine}"
         shm_size: 1gb

From 9baa64e88f07277a11dbfe8acd672977e0dcf1f0 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Fri, 10 Oct 2025 17:22:17 +0200
Subject: [PATCH 07/11] Moved 4 functions inside a condition to avoid reseting
 container folders to the original content (it didn't erase contents, but
 overwrote any change on those folders with the files' previous version)

---
 src/d2_docker/config/dhis2-core-start.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/d2_docker/config/dhis2-core-start.sh b/src/d2_docker/config/dhis2-core-start.sh
index 4a55c5b..691af21 100755
--- a/src/d2_docker/config/dhis2-core-start.sh
+++ b/src/d2_docker/config/dhis2-core-start.sh
@@ -162,14 +162,14 @@ init_done() {
 run() {
     local host=$1 psql_port=$2
 
-    setup_tomcat
-    copy_apps
-    copy_documents
-    copy_datavalues
-
     if is_init_done; then
-        debug "Container: already configured. Skip DB load"
+        debug "Container: already configured. Skip DB load and keeping other changes"
     else
+	debug "Container: clean. Copying tomcat files and dhis folders"
+        setup_tomcat
+        copy_apps
+        copy_documents
+        copy_datavalues
         debug "Container: clean. Load DB"
         wait_for_postgres
         run_sql_files

From a4b64328e752cd2001cd96d6d33c42435701a6e0 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Mon, 20 Oct 2025 10:40:43 +0200
Subject: [PATCH 08/11] extracted setup_tomcat, since it will copy any
 dhis.conf or server.xml that is passed as arguments

---
 src/d2_docker/config/dhis2-core-start.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/d2_docker/config/dhis2-core-start.sh b/src/d2_docker/config/dhis2-core-start.sh
index 691af21..83d9beb 100755
--- a/src/d2_docker/config/dhis2-core-start.sh
+++ b/src/d2_docker/config/dhis2-core-start.sh
@@ -162,11 +162,11 @@ init_done() {
 run() {
     local host=$1 psql_port=$2
 
+    setup_tomcat
     if is_init_done; then
         debug "Container: already configured. Skip DB load and keeping other changes"
     else
 	debug "Container: clean. Copying tomcat files and dhis folders"
-        setup_tomcat
         copy_apps
         copy_documents
         copy_datavalues

From 029174ba9a9b07ebb76a5c8df1b44bb5eb1d0c73 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Mon, 20 Oct 2025 12:55:23 +0200
Subject: [PATCH 09/11] Fix in tabs

---
 src/d2_docker/config/dhis2-core-start.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/d2_docker/config/dhis2-core-start.sh b/src/d2_docker/config/dhis2-core-start.sh
index 83d9beb..508fcde 100755
--- a/src/d2_docker/config/dhis2-core-start.sh
+++ b/src/d2_docker/config/dhis2-core-start.sh
@@ -166,7 +166,7 @@ run() {
     if is_init_done; then
         debug "Container: already configured. Skip DB load and keeping other changes"
     else
-	debug "Container: clean. Copying tomcat files and dhis folders"
+        debug "Container: clean. Copying tomcat files and dhis folders"
         copy_apps
         copy_documents
         copy_datavalues

From 07bc6a91d829c7d43e02fba0059a10144bb44bef Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Mon, 20 Oct 2025 15:18:54 +0200
Subject: [PATCH 10/11] After stopping the running containers, the command
 "docker compose ps -q" did not return any container, so a "-a" parameter is
 added to ensure all processes (even stopped) are returned

---
 src/d2_docker/commands/rm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/d2_docker/commands/rm.py b/src/d2_docker/commands/rm.py
index a645f52..b619d26 100644
--- a/src/d2_docker/commands/rm.py
+++ b/src/d2_docker/commands/rm.py
@@ -15,7 +15,7 @@ def run(args):
 def remove_image(image):
     utils.logger.info("Delete image/containers: {}".format(image))
     utils.run_docker_compose(["stop"], image)
-    result = utils.run_docker_compose(["ps", "-q"], data_image=image, capture_output=True)
+    result = utils.run_docker_compose(["ps", "-aq"], data_image=image, capture_output=True)
     container_ids = result.stdout.decode("utf-8").splitlines()
     utils.logger.debug("Container IDs: {}".format(container_ids))
     if container_ids:

From c394814452c96bba8a9f5af2a74c1d5926ceab89 Mon Sep 17 00:00:00 2001
From: cgbautista <carlos@eyeseetea.com>
Date: Thu, 23 Oct 2025 10:56:52 +0200
Subject: [PATCH 11/11] Fixed formatting and Readme

---
 README.md                                     | 11 ++++++-----
 src/d2_docker/config/dhis2-core-entrypoint.sh |  2 +-
 src/d2_docker/glowroot.py                     |  3 ++-
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 08db6a6..77db90d 100644
--- a/README.md
+++ b/README.md
@@ -382,13 +382,14 @@ $ curl -sS 'http://localhost:5000/harbor/https://docker.eyeseetea.com/api/v2.0/q
 ## Glowroot
 
 Glowroot is an open-source Java APM (Application Performance Monitoring) tool. It can help detect and diagnose application performance problems, tracing slow requests, errors, response time breakdowns, SQL capture and more.
-When starting a container, there are a few options to enable glowroot on the Tomcat process:
-- Use option `--glowroot-port=PORT` to specify the APM glowroot port of the Tomcat process.
-- Use option `--glowroot` to use the latest version of glowroot in the Tomcat process.
-- Use option `--glowroot-zip=FILE` to specify the zip file with a version of glowroot to run in the Tomcat process.
+When starting a container, there are two options to enable glowroot on the Tomcat process:
+- Use option `--glowroot` to use the latest version of glowroot in the Tomcat process. This requires internet access to be able to retrieve the file.
+- Use option `--glowroot-zip=FILE` to specify the zip file with the version of glowroot to run in the Tomcat process. This takes precedence over the other option.
+When enabling glowroot, it will start listening on port 4000/tcp so you can connect via browser to its interface. You may override this port with:
+- `--glowroot-port=PORT` to specify the APM glowroot port.
 
 ### Run d2-docker with glowroot enabled in the default port at the latest version available
 
 ```
 $ d2-docker start docker.eyeseetea.com/eyeseetea/dhis2-data:2.37.9-sierra --glowroot
-```
\ No newline at end of file
+```
diff --git a/src/d2_docker/config/dhis2-core-entrypoint.sh b/src/d2_docker/config/dhis2-core-entrypoint.sh
index 45b9a0a..ffc3a3f 100755
--- a/src/d2_docker/config/dhis2-core-entrypoint.sh
+++ b/src/d2_docker/config/dhis2-core-entrypoint.sh
@@ -49,7 +49,7 @@ wait_for_data_container_to_finish_copy() {
 setup_glowroot() {
     if [ -f $GLOWROOT_ZIP ] && [ ! -d $GLOWROOT_DIR ] ; then
         status=0
-	output=$(unzip -q "$GLOWROOT_ZIP" -d /opt/ 2>&1) || status=$?
+        output=$(unzip -q "$GLOWROOT_ZIP" -d /opt/ 2>&1) || status=$?
         # Ignore RC=1 that implies only warnings and no errors (like an empty zip file)
         if [ $status -gt 1 ]; then
             echo "$output"
diff --git a/src/d2_docker/glowroot.py b/src/d2_docker/glowroot.py
index 34a99d7..a5a542f 100644
--- a/src/d2_docker/glowroot.py
+++ b/src/d2_docker/glowroot.py
@@ -21,7 +21,6 @@ def get_latest_glowroot_url():
 
 def get_glowroot_zip(command, glowroot_zip, glowroot):
     logger = utils.logger
-    glowroot_path=None
     if isinstance(command, list) and command[0] == "up":
         glowroot_file = tempfile.NamedTemporaryFile(delete=False, prefix="glowroot_", suffix=".zip", dir="/tmp")
         glowroot_path = glowroot_file.name
@@ -38,6 +37,8 @@ def get_glowroot_zip(command, glowroot_zip, glowroot):
             # empty zipfile
             with zipfile.ZipFile(glowroot_path, mode="w") as zf:
                 pass
+    else:
+        glowroot_path = None
 
     return utils.get_absfile_for_docker_volume(glowroot_path)