From caef1023737cc56c717dcfdf5dd84918d2a0fc5d Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Tue, 3 Sep 2024 13:48:13 +0200 Subject: [PATCH 01/12] docker: add custom httpd.conf to iva docker #TASK-6559 --- docker/iva-app/Dockerfile | 4 +- docker/iva-app/custom-httpd.conf | 551 +++++++++++++++++++++++++++++++ 2 files changed, 554 insertions(+), 1 deletion(-) create mode 100644 docker/iva-app/custom-httpd.conf diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 6923534ff7..765bc8db35 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -1,8 +1,10 @@ FROM httpd:2.4-bullseye +COPY ./docker/Dockerfile/custom-httpd.conf /usr/local/apache2/conf/httpd.conf + ## To run the docker use: ## docker build -f ./docker/iva-app/Dockerfile -t iva-httpd . -## docker run --name jsorolla -p 8888:80 opencb/iva-app +## docker run --name jsorolla -p 8888:8080 opencb/iva-app ## Then open: http://localhost:8888/iva o http://localhost:8888/api LABEL org.label-schema.vendor="OpenCB" \ diff --git a/docker/iva-app/custom-httpd.conf b/docker/iva-app/custom-httpd.conf new file mode 100644 index 0000000000..b00c511372 --- /dev/null +++ b/docker/iva-app/custom-httpd.conf @@ -0,0 +1,551 @@ +# +# This is the main Apache HTTP server configuration file. It contains the +# configuration directives that give the server its instructions. +# See for detailed information. +# In particular, see +# +# for a discussion of each configuration directive. +# +# Do NOT simply read the instructions in here without understanding +# what they do. They're here only as hints or reminders. If you are unsure +# consult the online docs. You have been warned. +# +# Configuration and logfile names: If the filenames you specify for many +# of the server's control files begin with "/" (or "drive:/" for Win32), the +# server will use that explicit path. If the filenames do *not* begin +# with "/", the value of ServerRoot is prepended -- so "logs/access_log" +# with ServerRoot set to "/usr/local/apache2" will be interpreted by the +# server as "/usr/local/apache2/logs/access_log", whereas "/logs/access_log" +# will be interpreted as '/logs/access_log'. + +# +# ServerRoot: The top of the directory tree under which the server's +# configuration, error, and log files are kept. +# +# Do not add a slash at the end of the directory path. If you point +# ServerRoot at a non-local disk, be sure to specify a local disk on the +# Mutex directive, if file-based mutexes are used. If you wish to share the +# same ServerRoot for multiple httpd daemons, you will need to change at +# least PidFile. +# +ServerRoot "/usr/local/apache2" + +# +# Mutex: Allows you to set the mutex mechanism and mutex file directory +# for individual mutexes, or change the global defaults +# +# Uncomment and change the directory if mutexes are file-based and the default +# mutex file directory is not on a local disk or is not appropriate for some +# other reason. +# +# Mutex default:logs + +# +# Listen: Allows you to bind Apache to specific IP addresses and/or +# ports, instead of the default. See also the +# directive. +# +# Change this to Listen on specific IP addresses as shown below to +# prevent Apache from glomming onto all bound IP addresses. +# +#Listen 12.34.56.78:80 +Listen 8080 + +# +# Dynamic Shared Object (DSO) Support +# +# To be able to use the functionality of a module which was built as a DSO you +# have to place corresponding `LoadModule' lines at this location so the +# directives contained in it are actually available _before_ they are used. +# Statically compiled modules (those listed by `httpd -l') do not need +# to be loaded here. +# +# Example: +# LoadModule foo_module modules/mod_foo.so +# +LoadModule mpm_event_module modules/mod_mpm_event.so +#LoadModule mpm_prefork_module modules/mod_mpm_prefork.so +#LoadModule mpm_worker_module modules/mod_mpm_worker.so +LoadModule authn_file_module modules/mod_authn_file.so +#LoadModule authn_dbm_module modules/mod_authn_dbm.so +#LoadModule authn_anon_module modules/mod_authn_anon.so +#LoadModule authn_dbd_module modules/mod_authn_dbd.so +#LoadModule authn_socache_module modules/mod_authn_socache.so +LoadModule authn_core_module modules/mod_authn_core.so +LoadModule authz_host_module modules/mod_authz_host.so +LoadModule authz_groupfile_module modules/mod_authz_groupfile.so +LoadModule authz_user_module modules/mod_authz_user.so +#LoadModule authz_dbm_module modules/mod_authz_dbm.so +#LoadModule authz_owner_module modules/mod_authz_owner.so +#LoadModule authz_dbd_module modules/mod_authz_dbd.so +LoadModule authz_core_module modules/mod_authz_core.so +#LoadModule authnz_ldap_module modules/mod_authnz_ldap.so +#LoadModule authnz_fcgi_module modules/mod_authnz_fcgi.so +LoadModule access_compat_module modules/mod_access_compat.so +LoadModule auth_basic_module modules/mod_auth_basic.so +#LoadModule auth_form_module modules/mod_auth_form.so +#LoadModule auth_digest_module modules/mod_auth_digest.so +#LoadModule allowmethods_module modules/mod_allowmethods.so +#LoadModule isapi_module modules/mod_isapi.so +#LoadModule file_cache_module modules/mod_file_cache.so +#LoadModule cache_module modules/mod_cache.so +#LoadModule cache_disk_module modules/mod_cache_disk.so +#LoadModule cache_socache_module modules/mod_cache_socache.so +#LoadModule socache_shmcb_module modules/mod_socache_shmcb.so +#LoadModule socache_dbm_module modules/mod_socache_dbm.so +#LoadModule socache_memcache_module modules/mod_socache_memcache.so +#LoadModule socache_redis_module modules/mod_socache_redis.so +#LoadModule watchdog_module modules/mod_watchdog.so +#LoadModule macro_module modules/mod_macro.so +#LoadModule dbd_module modules/mod_dbd.so +#LoadModule bucketeer_module modules/mod_bucketeer.so +#LoadModule dumpio_module modules/mod_dumpio.so +#LoadModule echo_module modules/mod_echo.so +#LoadModule example_hooks_module modules/mod_example_hooks.so +#LoadModule case_filter_module modules/mod_case_filter.so +#LoadModule case_filter_in_module modules/mod_case_filter_in.so +#LoadModule example_ipc_module modules/mod_example_ipc.so +#LoadModule buffer_module modules/mod_buffer.so +#LoadModule data_module modules/mod_data.so +#LoadModule ratelimit_module modules/mod_ratelimit.so +LoadModule reqtimeout_module modules/mod_reqtimeout.so +#LoadModule ext_filter_module modules/mod_ext_filter.so +#LoadModule request_module modules/mod_request.so +#LoadModule include_module modules/mod_include.so +LoadModule filter_module modules/mod_filter.so +#LoadModule reflector_module modules/mod_reflector.so +#LoadModule substitute_module modules/mod_substitute.so +#LoadModule sed_module modules/mod_sed.so +#LoadModule charset_lite_module modules/mod_charset_lite.so +#LoadModule deflate_module modules/mod_deflate.so +#LoadModule xml2enc_module modules/mod_xml2enc.so +#LoadModule proxy_html_module modules/mod_proxy_html.so +#LoadModule brotli_module modules/mod_brotli.so +LoadModule mime_module modules/mod_mime.so +#LoadModule ldap_module modules/mod_ldap.so +LoadModule log_config_module modules/mod_log_config.so +#LoadModule log_debug_module modules/mod_log_debug.so +#LoadModule log_forensic_module modules/mod_log_forensic.so +#LoadModule logio_module modules/mod_logio.so +#LoadModule lua_module modules/mod_lua.so +LoadModule env_module modules/mod_env.so +#LoadModule mime_magic_module modules/mod_mime_magic.so +#LoadModule cern_meta_module modules/mod_cern_meta.so +#LoadModule expires_module modules/mod_expires.so +LoadModule headers_module modules/mod_headers.so +#LoadModule ident_module modules/mod_ident.so +#LoadModule usertrack_module modules/mod_usertrack.so +#LoadModule unique_id_module modules/mod_unique_id.so +LoadModule setenvif_module modules/mod_setenvif.so +LoadModule version_module modules/mod_version.so +#LoadModule remoteip_module modules/mod_remoteip.so +#LoadModule proxy_module modules/mod_proxy.so +#LoadModule proxy_connect_module modules/mod_proxy_connect.so +#LoadModule proxy_ftp_module modules/mod_proxy_ftp.so +#LoadModule proxy_http_module modules/mod_proxy_http.so +#LoadModule proxy_fcgi_module modules/mod_proxy_fcgi.so +#LoadModule proxy_scgi_module modules/mod_proxy_scgi.so +#LoadModule proxy_uwsgi_module modules/mod_proxy_uwsgi.so +#LoadModule proxy_fdpass_module modules/mod_proxy_fdpass.so +#LoadModule proxy_wstunnel_module modules/mod_proxy_wstunnel.so +#LoadModule proxy_ajp_module modules/mod_proxy_ajp.so +#LoadModule proxy_balancer_module modules/mod_proxy_balancer.so +#LoadModule proxy_express_module modules/mod_proxy_express.so +#LoadModule proxy_hcheck_module modules/mod_proxy_hcheck.so +#LoadModule session_module modules/mod_session.so +#LoadModule session_cookie_module modules/mod_session_cookie.so +#LoadModule session_crypto_module modules/mod_session_crypto.so +#LoadModule session_dbd_module modules/mod_session_dbd.so +#LoadModule slotmem_shm_module modules/mod_slotmem_shm.so +#LoadModule slotmem_plain_module modules/mod_slotmem_plain.so +#LoadModule ssl_module modules/mod_ssl.so +#LoadModule optional_hook_export_module modules/mod_optional_hook_export.so +#LoadModule optional_hook_import_module modules/mod_optional_hook_import.so +#LoadModule optional_fn_import_module modules/mod_optional_fn_import.so +#LoadModule optional_fn_export_module modules/mod_optional_fn_export.so +#LoadModule dialup_module modules/mod_dialup.so +#LoadModule http2_module modules/mod_http2.so +#LoadModule proxy_http2_module modules/mod_proxy_http2.so +#LoadModule md_module modules/mod_md.so +#LoadModule lbmethod_byrequests_module modules/mod_lbmethod_byrequests.so +#LoadModule lbmethod_bytraffic_module modules/mod_lbmethod_bytraffic.so +#LoadModule lbmethod_bybusyness_module modules/mod_lbmethod_bybusyness.so +#LoadModule lbmethod_heartbeat_module modules/mod_lbmethod_heartbeat.so +LoadModule unixd_module modules/mod_unixd.so +#LoadModule heartbeat_module modules/mod_heartbeat.so +#LoadModule heartmonitor_module modules/mod_heartmonitor.so +#LoadModule dav_module modules/mod_dav.so +LoadModule status_module modules/mod_status.so +LoadModule autoindex_module modules/mod_autoindex.so +#LoadModule asis_module modules/mod_asis.so +#LoadModule info_module modules/mod_info.so +#LoadModule suexec_module modules/mod_suexec.so + + #LoadModule cgid_module modules/mod_cgid.so + + + #LoadModule cgi_module modules/mod_cgi.so + +#LoadModule dav_fs_module modules/mod_dav_fs.so +#LoadModule dav_lock_module modules/mod_dav_lock.so +#LoadModule vhost_alias_module modules/mod_vhost_alias.so +#LoadModule negotiation_module modules/mod_negotiation.so +LoadModule dir_module modules/mod_dir.so +#LoadModule imagemap_module modules/mod_imagemap.so +#LoadModule actions_module modules/mod_actions.so +#LoadModule speling_module modules/mod_speling.so +#LoadModule userdir_module modules/mod_userdir.so +LoadModule alias_module modules/mod_alias.so +#LoadModule rewrite_module modules/mod_rewrite.so + + +# +# If you wish httpd to run as a different user or group, you must run +# httpd as root initially and it will switch. +# +# User/Group: The name (or #number) of the user/group to run httpd as. +# It is usually good practice to create a dedicated user and group for +# running httpd, as with most system services. +# +User www-data +Group www-data + + + +# 'Main' server configuration +# +# The directives in this section set up the values used by the 'main' +# server, which responds to any requests that aren't handled by a +# definition. These values also provide defaults for +# any containers you may define later in the file. +# +# All of these directives may appear inside containers, +# in which case these default settings will be overridden for the +# virtual host being defined. +# + +# +# ServerAdmin: Your address, where problems with the server should be +# e-mailed. This address appears on some server-generated pages, such +# as error documents. e.g. admin@your-domain.com +# +ServerAdmin you@example.com + +# +# ServerName gives the name and port that the server uses to identify itself. +# This can often be determined automatically, but we recommend you specify +# it explicitly to prevent problems during startup. +# +# If your host doesn't have a registered DNS name, enter its IP address here. +# +#ServerName www.example.com:80 + +# +# Deny access to the entirety of your server's filesystem. You must +# explicitly permit access to web content directories in other +# blocks below. +# + + AllowOverride none + Require all denied + + +# +# Note that from this point forward you must specifically allow +# particular features to be enabled - so if something's not working as +# you might expect, make sure that you have specifically enabled it +# below. +# + +# +# DocumentRoot: The directory out of which you will serve your +# documents. By default, all requests are taken from this directory, but +# symbolic links and aliases may be used to point to other locations. +# +DocumentRoot "/usr/local/apache2/htdocs" + + # + # Possible values for the Options directive are "None", "All", + # or any combination of: + # Indexes Includes FollowSymLinks SymLinksifOwnerMatch ExecCGI MultiViews + # + # Note that "MultiViews" must be named *explicitly* --- "Options All" + # doesn't give it to you. + # + # The Options directive is both complicated and important. Please see + # http://httpd.apache.org/docs/2.4/mod/core.html#options + # for more information. + # + Options Indexes FollowSymLinks + + # + # AllowOverride controls what directives may be placed in .htaccess files. + # It can be "All", "None", or any combination of the keywords: + # AllowOverride FileInfo AuthConfig Limit + # + AllowOverride None + + # + # Controls who can get stuff from this server. + # + Require all granted + + +# +# DirectoryIndex: sets the file that Apache will serve if a directory +# is requested. +# + + DirectoryIndex index.html + + +# +# The following lines prevent .htaccess and .htpasswd files from being +# viewed by Web clients. +# + + Require all denied + + +# +# ErrorLog: The location of the error log file. +# If you do not specify an ErrorLog directive within a +# container, error messages relating to that virtual host will be +# logged here. If you *do* define an error logfile for a +# container, that host's errors will be logged there and not here. +# +ErrorLog /proc/self/fd/2 + +# +# LogLevel: Control the number of messages logged to the error_log. +# Possible values include: debug, info, notice, warn, error, crit, +# alert, emerg. +# +LogLevel warn + + + # + # The following directives define some format nicknames for use with + # a CustomLog directive (see below). + # + LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\"" combined + LogFormat "%h %l %u %t \"%r\" %>s %b" common + + + # You need to enable mod_logio.c to use %I and %O + LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %I %O" combinedio + + + # + # The location and format of the access logfile (Common Logfile Format). + # If you do not define any access logfiles within a + # container, they will be logged here. Contrariwise, if you *do* + # define per- access logfiles, transactions will be + # logged therein and *not* in this file. + # + CustomLog /proc/self/fd/1 common + + # + # If you prefer a logfile with access, agent, and referer information + # (Combined Logfile Format) you can use the following directive. + # + #CustomLog "logs/access_log" combined + + + + # + # Redirect: Allows you to tell clients about documents that used to + # exist in your server's namespace, but do not anymore. The client + # will make a new request for the document at its new location. + # Example: + # Redirect permanent /foo http://www.example.com/bar + + # + # Alias: Maps web paths into filesystem paths and is used to + # access content that does not live under the DocumentRoot. + # Example: + # Alias /webpath /full/filesystem/path + # + # If you include a trailing / on /webpath then the server will + # require it to be present in the URL. You will also likely + # need to provide a section to allow access to + # the filesystem path. + + # + # ScriptAlias: This controls which directories contain server scripts. + # ScriptAliases are essentially the same as Aliases, except that + # documents in the target directory are treated as applications and + # run by the server when requested rather than as documents sent to the + # client. The same rules about trailing "/" apply to ScriptAlias + # directives as to Alias. + # + ScriptAlias /cgi-bin/ "/usr/local/apache2/cgi-bin/" + + + + + # + # ScriptSock: On threaded servers, designate the path to the UNIX + # socket used to communicate with the CGI daemon of mod_cgid. + # + #Scriptsock cgisock + + +# +# "/usr/local/apache2/cgi-bin" should be changed to whatever your ScriptAliased +# CGI directory exists, if you have that configured. +# + + AllowOverride None + Options None + Require all granted + + + + # + # Avoid passing HTTP_PROXY environment to CGI's on this or any proxied + # backend servers which have lingering "httpoxy" defects. + # 'Proxy' request header is undefined by the IETF, not listed by IANA + # + RequestHeader unset Proxy early + + + + # + # TypesConfig points to the file containing the list of mappings from + # filename extension to MIME-type. + # + TypesConfig conf/mime.types + + # + # AddType allows you to add to or override the MIME configuration + # file specified in TypesConfig for specific file types. + # + #AddType application/x-gzip .tgz + # + # AddEncoding allows you to have certain browsers uncompress + # information on the fly. Note: Not all browsers support this. + # + #AddEncoding x-compress .Z + #AddEncoding x-gzip .gz .tgz + # + # If the AddEncoding directives above are commented-out, then you + # probably should define those extensions to indicate media types: + # + AddType application/x-compress .Z + AddType application/x-gzip .gz .tgz + + # + # AddHandler allows you to map certain file extensions to "handlers": + # actions unrelated to filetype. These can be either built into the server + # or added with the Action directive (see below) + # + # To use CGI scripts outside of ScriptAliased directories: + # (You will also need to add "ExecCGI" to the "Options" directive.) + # + #AddHandler cgi-script .cgi + + # For type maps (negotiated resources): + #AddHandler type-map var + + # + # Filters allow you to process content before it is sent to the client. + # + # To parse .shtml files for server-side includes (SSI): + # (You will also need to add "Includes" to the "Options" directive.) + # + #AddType text/html .shtml + #AddOutputFilter INCLUDES .shtml + + +# +# The mod_mime_magic module allows the server to use various hints from the +# contents of the file itself to determine its type. The MIMEMagicFile +# directive tells the module where the hint definitions are located. +# +#MIMEMagicFile conf/magic + +# +# Customizable error responses come in three flavors: +# 1) plain text 2) local redirects 3) external redirects +# +# Some examples: +#ErrorDocument 500 "The server made a boo boo." +#ErrorDocument 404 /missing.html +#ErrorDocument 404 "/cgi-bin/missing_handler.pl" +#ErrorDocument 402 http://www.example.com/subscription_info.html +# + +# +# MaxRanges: Maximum number of Ranges in a request before +# returning the entire resource, or one of the special +# values 'default', 'none' or 'unlimited'. +# Default setting is to accept 200 Ranges. +#MaxRanges unlimited + +# +# EnableMMAP and EnableSendfile: On systems that support it, +# memory-mapping or the sendfile syscall may be used to deliver +# files. This usually improves server performance, but must +# be turned off when serving from networked-mounted +# filesystems or if support for these functions is otherwise +# broken on your system. +# Defaults: EnableMMAP On, EnableSendfile Off +# +#EnableMMAP off +#EnableSendfile on + +# Supplemental configuration +# +# The configuration files in the conf/extra/ directory can be +# included to add extra features or to modify the default configuration of +# the server, or you may simply copy their contents here and change as +# necessary. + +# Server-pool management (MPM specific) +#Include conf/extra/httpd-mpm.conf + +# Multi-language error messages +#Include conf/extra/httpd-multilang-errordoc.conf + +# Fancy directory listings +#Include conf/extra/httpd-autoindex.conf + +# Language settings +#Include conf/extra/httpd-languages.conf + +# User home directories +#Include conf/extra/httpd-userdir.conf + +# Real-time info on requests and configuration +#Include conf/extra/httpd-info.conf + +# Virtual hosts +#Include conf/extra/httpd-vhosts.conf + +# Local access to the Apache HTTP Server Manual +#Include conf/extra/httpd-manual.conf + +# Distributed authoring and versioning (WebDAV) +#Include conf/extra/httpd-dav.conf + +# Various default settings +#Include conf/extra/httpd-default.conf + +# Configure mod_proxy_html to understand HTML4/XHTML1 + +Include conf/extra/proxy-html.conf + + +# Secure (SSL/TLS) connections +#Include conf/extra/httpd-ssl.conf +# +# Note: The following must must be present to support +# starting without SSL on platforms with no /dev/random equivalent +# but a statically compiled-in mod_ssl. +# + +SSLRandomSeed startup builtin +SSLRandomSeed connect builtin + + From 314871e4de7848a71dd07cf582d0a7f933a716a6 Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Tue, 3 Sep 2024 14:37:41 +0200 Subject: [PATCH 02/12] docker: Fix custom httpd path in Dockerfile #TASK-6559 --- docker/iva-app/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 765bc8db35..610fb71148 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -1,5 +1,5 @@ FROM httpd:2.4-bullseye -COPY ./docker/Dockerfile/custom-httpd.conf /usr/local/apache2/conf/httpd.conf +COPY ./docker/iva-app/custom-httpd.conf /usr/local/apache2/conf/httpd.conf ## To run the docker use: From defe8a1a0ff6ae5374e73b078c545de2c8345165 Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Tue, 3 Sep 2024 16:03:12 +0200 Subject: [PATCH 03/12] docker: change run user to avoid root #TASK-6559 --- docker/iva-app/Dockerfile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 610fb71148..c4c7045f70 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -1,7 +1,6 @@ FROM httpd:2.4-bullseye COPY ./docker/iva-app/custom-httpd.conf /usr/local/apache2/conf/httpd.conf - ## To run the docker use: ## docker build -f ./docker/iva-app/Dockerfile -t iva-httpd . ## docker run --name jsorolla -p 8888:8080 opencb/iva-app @@ -35,6 +34,10 @@ COPY ./build/api /usr/local/apache2/htdocs/api COPY ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ +## Run Docker images as non root +RUN opencga -m -u 1001 myuser +USER opencga + ## Genome Maps (Coming soon :-) ) #COPY ./build/genome-maps /usr/local/apache2/htdocs/genome-maps From b61a323bfe7c5c63d1dec1e5e7f172bdff49aece Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Tue, 3 Sep 2024 16:27:20 +0200 Subject: [PATCH 04/12] docker: fix docker user #TASK-6559 --- docker/iva-app/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index c4c7045f70..eb9bec9450 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -35,7 +35,7 @@ COPY ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ ## Run Docker images as non root -RUN opencga -m -u 1001 myuser +RUN useradd -m -u 1001 opencga USER opencga ## Genome Maps (Coming soon :-) ) From 8871fba534e0ee4e47f9500e44067ceb41090c8f Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Tue, 3 Sep 2024 17:20:26 +0200 Subject: [PATCH 05/12] docker: change docker user to www-data #TASK-6559 --- docker/iva-app/Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index eb9bec9450..1083f65bf6 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -18,6 +18,9 @@ RUN apt-get update && apt-get -y upgrade && \ apt-get install -y vim jq && \ rm -rf /var/lib/apt/lists/* +## Run Docker images as non root +USER www-data + ## Allow to build different images by passing the path to the SITE ARG SITE=src/sites @@ -34,9 +37,6 @@ COPY ./build/api /usr/local/apache2/htdocs/api COPY ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ -## Run Docker images as non root -RUN useradd -m -u 1001 opencga -USER opencga ## Genome Maps (Coming soon :-) ) #COPY ./build/genome-maps /usr/local/apache2/htdocs/genome-maps From 2c917c33294cc077d323368620e045e6d3e33497 Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Wed, 4 Sep 2024 11:35:02 +0200 Subject: [PATCH 06/12] docker: change owner path htdocs to www-data #TASK-6559 --- docker/iva-app/Dockerfile | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 1083f65bf6..fda3506712 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -18,9 +18,6 @@ RUN apt-get update && apt-get -y upgrade && \ apt-get install -y vim jq && \ rm -rf /var/lib/apt/lists/* -## Run Docker images as non root -USER www-data - ## Allow to build different images by passing the path to the SITE ARG SITE=src/sites @@ -37,6 +34,10 @@ COPY ./build/api /usr/local/apache2/htdocs/api COPY ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ +## Change owner +RUN chown -R www-date /usr/local/apache2/htdocs/ +## Run Docker images as non root +USER www-data ## Genome Maps (Coming soon :-) ) #COPY ./build/genome-maps /usr/local/apache2/htdocs/genome-maps From 53c4edda65f0876f1b481090b1d4f87fb905c04c Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Wed, 4 Sep 2024 11:50:18 +0200 Subject: [PATCH 07/12] docker: cfix owner path htdocs to www-data #TASK-6559 --- docker/iva-app/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index fda3506712..0db1c54436 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -35,7 +35,7 @@ COPY ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ ## Change owner -RUN chown -R www-date /usr/local/apache2/htdocs/ +RUN chown -R www-data /usr/local/apache2/htdocs/ ## Run Docker images as non root USER www-data From 3bed704e7a76bb87fa8a17d2c2bb0adc6613a2a3 Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Wed, 4 Sep 2024 12:21:47 +0200 Subject: [PATCH 08/12] docker: change owner apache2/logs to www-data #TASK-6559 --- docker/iva-app/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 0db1c54436..9c2ac16971 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -36,6 +36,7 @@ COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ ## Change owner RUN chown -R www-data /usr/local/apache2/htdocs/ +RUN chown -R www-data /usr/local/apache2/logs/ ## Run Docker images as non root USER www-data From ba103a8282e39a3a384dfc4a47edbfc6a13258bf Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Thu, 5 Sep 2024 15:08:47 +0200 Subject: [PATCH 09/12] docker: edit docker steps and add README file #TASK-6559 --- docker/iva-app/Dockerfile | 19 +++++++++---------- docker/iva-app/README.md | 17 +++++++++++++++++ 2 files changed, 26 insertions(+), 10 deletions(-) create mode 100644 docker/iva-app/README.md diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 9c2ac16971..6768e4fc9f 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -1,4 +1,5 @@ FROM httpd:2.4-bullseye +## Custom httpd.conf file to update exposed port from 80 to 8080 COPY ./docker/iva-app/custom-httpd.conf /usr/local/apache2/conf/httpd.conf ## To run the docker use: @@ -16,27 +17,25 @@ LABEL org.label-schema.vendor="OpenCB" \ ## Update and create iva user RUN apt-get update && apt-get -y upgrade && \ apt-get install -y vim jq && \ - rm -rf /var/lib/apt/lists/* + rm -rf /var/lib/apt/lists/* && \ + chown -R www-data /usr/local/apache2/logs/ ## Allow to build different images by passing the path to the SITE ARG SITE=src/sites ## Copy files ## IVA -COPY ./build/iva /usr/local/apache2/htdocs/iva -COPY ./${SITE}/iva/conf /usr/local/apache2/htdocs/iva/conf/ -COPY ./${SITE}/iva/img /usr/local/apache2/htdocs/iva/img/ +COPY --chown=www-data ./build/iva /usr/local/apache2/htdocs/iva +COPY --chown=www-data ./${SITE}/iva/conf /usr/local/apache2/htdocs/iva/conf/ +COPY --chown=www-data ./${SITE}/iva/img /usr/local/apache2/htdocs/iva/img/ RUN true ## API -COPY ./build/api /usr/local/apache2/htdocs/api -COPY ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ -COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ +COPY --chown=www-data ./build/api /usr/local/apache2/htdocs/api +COPY --chown=www-data ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ +COPY --chown=www-data ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ -## Change owner -RUN chown -R www-data /usr/local/apache2/htdocs/ -RUN chown -R www-data /usr/local/apache2/logs/ ## Run Docker images as non root USER www-data diff --git a/docker/iva-app/README.md b/docker/iva-app/README.md new file mode 100644 index 0000000000..28e20ee353 --- /dev/null +++ b/docker/iva-app/README.md @@ -0,0 +1,17 @@ +# How to update this docker + +If you want to update the base image https://hub.docker.com/_/httpd , it is necesary repeat this steps + +To customize the configuration of the httpd server, first obtain the upstream default configuration from the container: + +```bash +docker run --rm httpd:2.4-bullseye cat /usr/local/apache2/conf/httpd.conf > ./docker/iva-app/custom-httpd.conf +``` + +And then change custom-httpd.conf + +``` +Listen 8080 +``` + + From 87d0ad343243fc16ece4ec778516c32ca2191d44 Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Tue, 10 Dec 2024 15:47:46 +0100 Subject: [PATCH 10/12] docker: solve conflicts api folder #TASK-6559 --- docker/iva-app/Dockerfile | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 6923534ff7..74ca581685 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -28,12 +28,7 @@ COPY ./${SITE}/iva/img /usr/local/apache2/htdocs/iva/img/ RUN true -## API -COPY ./build/api /usr/local/apache2/htdocs/api -COPY ./${SITE}/api/conf /usr/local/apache2/htdocs/api/conf/ -COPY ./${SITE}/api/img /usr/local/apache2/htdocs/api/img/ - ## Genome Maps (Coming soon :-) ) #COPY ./build/genome-maps /usr/local/apache2/htdocs/genome-maps -ENTRYPOINT ["httpd-foreground"] +ENTRYPOINT ["httpd-foreground"] \ No newline at end of file From ea69f080be4ed7512fd8dc4bbc3bc2b5e8e5532a Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Wed, 11 Dec 2024 11:58:16 +0100 Subject: [PATCH 11/12] docker: fix reverted changes solving conflicts #TASK-6559 --- docker/iva-app/Dockerfile | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index 74ca581685..beca1bff66 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -1,8 +1,10 @@ FROM httpd:2.4-bullseye +## Custom httpd.conf file to update exposed port from 80 to 8080 +COPY ./docker/iva-app/custom-httpd.conf /usr/local/apache2/conf/httpd.conf ## To run the docker use: ## docker build -f ./docker/iva-app/Dockerfile -t iva-httpd . -## docker run --name jsorolla -p 8888:80 opencb/iva-app +## docker run --name jsorolla -p 8888:8080 opencb/iva-app ## Then open: http://localhost:8888/iva o http://localhost:8888/api LABEL org.label-schema.vendor="OpenCB" \ @@ -15,19 +17,23 @@ LABEL org.label-schema.vendor="OpenCB" \ ## Update and create iva user RUN apt-get update && apt-get -y upgrade && \ apt-get install -y vim jq && \ - rm -rf /var/lib/apt/lists/* + rm -rf /var/lib/apt/lists/* \ + chown -R www-data /usr/local/apache2/logs/ ## Allow to build different images by passing the path to the SITE ARG SITE=src/sites ## Copy files ## IVA -COPY ./build/iva /usr/local/apache2/htdocs/iva -COPY ./${SITE}/iva/conf /usr/local/apache2/htdocs/iva/conf/ -COPY ./${SITE}/iva/img /usr/local/apache2/htdocs/iva/img/ +COPY --chown=www-data ./build/iva /usr/local/apache2/htdocs/iva +COPY --chown=www-data ./${SITE}/iva/conf /usr/local/apache2/htdocs/iva/conf/ +COPY --chown=www-data ./${SITE}/iva/img /usr/local/apache2/htdocs/iva/img/ RUN true +## Run Docker images as non root +USER www-data + ## Genome Maps (Coming soon :-) ) #COPY ./build/genome-maps /usr/local/apache2/htdocs/genome-maps From e2bb047ae8adb057e8dbdfa6d2ab7984cde34712 Mon Sep 17 00:00:00 2001 From: juanrizetta Date: Wed, 11 Dec 2024 12:25:27 +0100 Subject: [PATCH 12/12] docker: fix concat run chown command #TASK-6559 --- docker/iva-app/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile index beca1bff66..3df181f758 100644 --- a/docker/iva-app/Dockerfile +++ b/docker/iva-app/Dockerfile @@ -17,7 +17,7 @@ LABEL org.label-schema.vendor="OpenCB" \ ## Update and create iva user RUN apt-get update && apt-get -y upgrade && \ apt-get install -y vim jq && \ - rm -rf /var/lib/apt/lists/* \ + rm -rf /var/lib/apt/lists/* && \ chown -R www-data /usr/local/apache2/logs/ ## Allow to build different images by passing the path to the SITE