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Monash Biomedical Imaging MonashBI

MonashBI/arcana 3

Abstraction of Repository-Centric ANAlysis - a Python framework

MonashBI/banana 1

Brain imAgiNg Analysis iN Arcana (Banana): brain imaging analysis workflows implemented in the Arcana framework

MonashBI/nipype_arcana_workshop 1

Materials (slides, notebooks, Dockerfile) for a one day workshop on the use of Nipype and Arcana for neuroimaging analysis (https://nbviewer.jupyter.org/github/MonashBI/nipype_arcana_workshop/blob/master/program.ipynb)

MonashBI/xnat-docker-compose 1

Build an XNAT server configuration with Docker Compose

MonashBI/arcana-xnat-plugin 0

XNAT plugin containing datatypes required for the Arcana package

MonashBI/Monash_rsPET-MR_prep 0

Scripts used to prepare the Monash rsPET-MR dataset

MonashBI/xnat-eeg-upload 0

A simple interactive script for uploading EEG/COG data to XNAT

MonashBI/xnat-nif-qc-analysis 0

A Dockerized XNAT pipeline that extracts key metrics from quality control scans acquired in accordance with the NIF-TDRS SOP

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Tom Close

commit sha d89747951e2af587cc8c5ba16dd298a62fccaa83

added neurodocker dockerfile generation

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commit sha 21611bb0f33d2bff6391374c55dfdc5f60321f64

touch up formatting

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commit sha e57e317802ecd586ec94b07ee1b48d0fd3b3e8e1

developing generated command JSON method

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commit sha 715393a055000393cc9ecb7e47754ff56fa98a6c

streamlining command JSON so that it is specialised for derivatives

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Tom Close

commit sha 5b309642d28a6943d5d578857630a4b304675681

moved xnat_cs to banana

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commit sha d69c38eed52ae557a849889930cd659cdb3c6401

added all options to mrthreshold

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Tom Close

commit sha 7c867ef62b26d3997854a8d54d4f32215cc95fc6

moved xnat_cs repository from arcana to banana

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commit sha 1737b0651c4af0bda4041c868d71367ab003b173

made output spec of mergetuple general to avoid bug in nipype

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Tom Close

commit sha 909312e6fe426a45bfabe642bfe657672bfd47f2

implemented multi-shell tensor residual calculation

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issue openedMonashBI/arcana

Construct "directory" formats from nested file formats

Should be able to specify file-group formats in rich manner such that the contents of the directory are specified as collections of their constituent file formats (analogous to the way you can build up complex types/traits)

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created tagMonashBI/xnatutils

tag0.7.0

A collection of CLI scripts for conveniently up/downloading and listing data on/from XNAT repositories.

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commit sha 0a3e8dc2064a99386f7e5f45ce4ae656fd5f2835

Fixes bugs with generalisation of xnat-get/ls to arbitrary subject/session naming conventions

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commit sha 0362c06c8ad195681599a105e60c8a481d80233e

added residual calculation to the tensor

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commit sha 2c739a47dee0ad9c8b28e90820e5d0fcb7f0ed7d

fixed up handling of reprocessing of protected artefacts

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commit sha 92e2e7a1a566dad815004e0c39f75d4ba5b10ac7

added scan id option

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commit sha fbf29280800fc0eafdb50e944ee5fd970a1709f1

fixed subject_id switch

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commit sha 908eb4efc742b41d2c0d8d2d21b6546ae1eeec7f

added project and subject ID to the argument parser for xnat-put

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commit sha 90394f88794e2f829c10c48c753ae7663c151f7e

upped version to 0.6.5

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commit sha e0e04b1954db31ee94075e9faab6ae7b14b3f775

add project and subject ID to xnat-put

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Tom Close

commit sha 20795cec5ef037b1349afbeb63fda88c43abfdf4

added DS_Store to gitignore

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issue closedMonashBI/xnat-docker-compose

Project License - License.md ?

Hi! Is this project also open-source like the rest of XNAT? Thanks!

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ktunallux

issue commentMonashBI/xnat-docker-compose

Project License - License.md ?

done

ktunallux

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commit sha 34abb2cf426ac054663663b050e42f886622ab3f

added licence and authors

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issue commentMonashBI/xnat-docker-compose

Project License - License.md ?

@tclose can you add in the license too? thanks

ktunallux

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issue closedMonashBI/xnat-docker-compose

Production XNAT deployment leading to 404

I first tested configure-basic.sh and everything worked for me. I was able to access XNAT on http://localhost.

I want to run production xnat on a domain. I ran configure.sh and set up my SSL and domain. However, when i go to https://domain I get a 404. The SSL cert is valid according to the lock icon and when I run openssl s_client -showcerts -connect domainname I get the certificate chain.

image

I have attached my docker-compose startup log, everything looks good there I have also attached my nginx and web logs which I got from exec into the docker containers. It looks to me like something is wrong with Tomcat where it isn't redirecting to XNAT correctly. I can't quite figure this out, any help will be greatly appreciated :)

This is what nginx says when I try to access my domain. This comes after i run docker-compose up

xnat-web_1     | INFO: Server startup in 14676 ms
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:20:23 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:41:17 +0000] "GET / HTTP/1.1" 400 173 "-" "-"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:41:55 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:42:17 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:43:58 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:58:46 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:22:00:07 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:22:00:14 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"

Logs from xnatweb container web/var/localhost_access_log.log


172.23.0.7 - - [27/Aug/2020:16:15:56 -0500] "GET / HTTP/1.0" 404 1036
172.23.0.7 - - [27/Aug/2020:16:15:57 -0500] "GET /favicon.ico HTTP/1.0" 404 1047
172.23.0.7 - - [27/Aug/2020:16:16:32 -0500] "GET / HTTP/1.0" 404 1036
172.23.0.7 - - [27/Aug/2020:16:22:29 -0500] "GET / HTTP/1.0" 404 1036

var.log.nginx.customsite_access_ssl.log


172.23.0.1 - - [27/Aug/2020:21:15:56 +0000] "GET / HTTP/1.1" 404 470 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
172.23.0.1 - - [27/Aug/2020:21:15:57 +0000] "GET /favicon.ico HTTP/1.1" 404 478 "https://localhost/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
172.23.0.1 - - [27/Aug/2020:21:16:32 +0000] "GET / HTTP/1.1" 404 470 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
172.23.0.1 - - [27/Aug/2020:21:22:29 +0000] "GET / HTTP/1.1" 404 470 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
172.23.0.1 - - [27/Aug/2020:21:22:29 +0000] "GET /favicon.ico HTTP/1.1" 404 478 "https://nuxnattestweb.xyz/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"

startup.log

Starting xnat-docker-compose_xnat-db_1  ... done
Starting xnat-docker-compose_cadvisor_1    ... done
Starting xnat-docker-compose_xnat-web_1    ... done
Starting xnat-docker-compose_xnat-backup_1 ... done
Starting xnat-docker-compose_prometheus_1  ... done
Starting xnat-docker-compose_xnat-nginx_1  ... done
Attaching to xnat-docker-compose_xnat-db_1, xnat-docker-compose_cadvisor_1, xnat-docker-compose_xnat-backup_1, xnat-docker-compose_xnat-web_1, xnat-docker-compose_prometheus_1, xnat-docker-compose_xnat-nginx_1
prometheus_1   | level=info ts=2020-08-27T21:19:11.770Z caller=main.go:308 msg="No time or size retention was set so using the default time retention" duration=15d
prometheus_1   | level=info ts=2020-08-27T21:19:11.770Z caller=main.go:343 msg="Starting Prometheus" version="(version=2.20.1, branch=HEAD, revision=983ebb4a513302315a8117932ab832815f85e3d2)"
prometheus_1   | level=info ts=2020-08-27T21:19:11.771Z caller=main.go:344 build_context="(go=go1.14.6, user=root@7cbd4d1c15e0, date=20200805-17:26:58)"
prometheus_1   | level=info ts=2020-08-27T21:19:11.771Z caller=main.go:345 host_details="(Linux 4.19.76-linuxkit #1 SMP Tue May 26 11:42:35 UTC 2020 x86_64 1f62d585304c (none))"
prometheus_1   | level=info ts=2020-08-27T21:19:11.771Z caller=main.go:346 fd_limits="(soft=1048576, hard=1048576)"
prometheus_1   | level=info ts=2020-08-27T21:19:11.771Z caller=main.go:347 vm_limits="(soft=unlimited, hard=unlimited)"
prometheus_1   | level=info ts=2020-08-27T21:19:11.774Z caller=web.go:524 component=web msg="Start listening for connections" address=0.0.0.0:9090
prometheus_1   | level=info ts=2020-08-27T21:19:11.774Z caller=main.go:684 msg="Starting TSDB ..."
cadvisor_1     | W0827 21:19:11.215905       1 manager.go:349] Could not configure a source for OOM detection, disabling OOM events: open /dev/kmsg: no such file or directory
prometheus_1   | level=info ts=2020-08-27T21:19:11.786Z caller=head.go:641 component=tsdb msg="Replaying on-disk memory mappable chunks if any"
prometheus_1   | level=info ts=2020-08-27T21:19:11.790Z caller=head.go:655 component=tsdb msg="On-disk memory mappable chunks replay completed" duration=3.786119ms
prometheus_1   | level=info ts=2020-08-27T21:19:11.790Z caller=head.go:661 component=tsdb msg="Replaying WAL, this may take a while"
xnat-web_1     | Listening for transport dt_socket at address: 8000
prometheus_1   | level=info ts=2020-08-27T21:19:11.814Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=0 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.822Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=1 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.838Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=2 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.848Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=3 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.850Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=4 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.855Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=5 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.970Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=6 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.971Z caller=head.go:713 component=tsdb msg="WAL segment loaded" segment=7 maxSegment=7
prometheus_1   | level=info ts=2020-08-27T21:19:11.971Z caller=head.go:716 component=tsdb msg="WAL replay completed" checkpoint_replay_duration=95.955µs wal_replay_duration=180.419406ms total_replay_duration=184.377282ms
prometheus_1   | level=info ts=2020-08-27T21:19:11.977Z caller=main.go:700 fs_type=EXT4_SUPER_MAGIC
prometheus_1   | level=info ts=2020-08-27T21:19:11.977Z caller=main.go:701 msg="TSDB started"
prometheus_1   | level=info ts=2020-08-27T21:19:11.977Z caller=main.go:805 msg="Loading configuration file" filename=/etc/prometheus/prometheus.yaml
prometheus_1   | level=info ts=2020-08-27T21:19:11.980Z caller=main.go:833 msg="Completed loading of configuration file" filename=/etc/prometheus/prometheus.yaml
prometheus_1   | level=info ts=2020-08-27T21:19:11.980Z caller=main.go:652 msg="Server is ready to receive web requests."
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Server version:        Apache Tomcat/7.0.94
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Server built:          Apr 10 2019 16:56:40 UTC
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Server number:         7.0.94.0
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: OS Name:               Linux
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: OS Version:            4.19.76-linuxkit
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Architecture:          amd64
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Java Home:             /usr/lib/jvm/java-1.8-openjdk/jre
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: JVM Version:           1.8.0_212-b04
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: JVM Vendor:            IcedTea
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: CATALINA_BASE:         /usr/local/tomcat
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: CATALINA_HOME:         /usr/local/tomcat
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Xms2g
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Xmx4g
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Dxnat.home=/data/xnat/home
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=8000
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Dignore.endorsed.dirs=
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Dcatalina.base=/usr/local/tomcat
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Dcatalina.home=/usr/local/tomcat
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
xnat-web_1     | INFO: Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
xnat-web_1     | INFO: Loaded APR based Apache Tomcat Native library 1.2.21 using APR version 1.6.5.
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
xnat-web_1     | INFO: APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.core.AprLifecycleListener initializeSSL
xnat-web_1     | INFO: OpenSSL successfully initialized (OpenSSL 1.1.1b  26 Feb 2019)
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.coyote.AbstractProtocol init
xnat-web_1     | INFO: Initializing ProtocolHandler ["http-apr-8080"]
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.coyote.AbstractProtocol init
xnat-web_1     | INFO: Initializing ProtocolHandler ["ajp-apr-8009"]
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.Catalina load
xnat-web_1     | INFO: Initialization processed in 807 ms
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.core.StandardService startInternal
xnat-web_1     | INFO: Starting service Catalina
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.core.StandardEngine startInternal
xnat-web_1     | INFO: Starting Servlet Engine: Apache Tomcat/7.0.94
xnat-web_1     | Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.HostConfig deployWAR
xnat-web_1     | INFO: Deploying web application archive /usr/local/tomcat/webapps/ROOT.war
xnat-db_1      | 
xnat-db_1      | PostgreSQL Database directory appears to contain a database; Skipping initialization
xnat-db_1      | 
xnat-db_1      | LOG:  database system was shut down at 2020-08-27 21:18:25 UTC
xnat-db_1      | LOG:  MultiXact member wraparound protections are now enabled
xnat-db_1      | LOG:  autovacuum launcher started
xnat-db_1      | LOG:  database system is ready to accept connections
xnat-web_1     | Aug 27, 2020 4:19:27 PM org.apache.catalina.startup.TldConfig execute
xnat-web_1     | INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
xnat-web_1     | Aug 27, 2020 4:19:27 PM org.apache.catalina.startup.HostConfig deployWAR
xnat-web_1     | INFO: Deployment of web application archive /usr/local/tomcat/webapps/ROOT.war has finished in 14,515 ms
xnat-web_1     | Aug 27, 2020 4:19:27 PM org.apache.coyote.AbstractProtocol start
xnat-web_1     | INFO: Starting ProtocolHandler ["http-apr-8080"]
xnat-web_1     | Aug 27, 2020 4:19:27 PM org.apache.coyote.AbstractProtocol start
xnat-web_1     | INFO: Starting ProtocolHandler ["ajp-apr-8009"]
xnat-web_1     | Aug 27, 2020 4:19:27 PM org.apache.catalina.startup.Catalina start
xnat-web_1     | INFO: Server startup in 14676 ms
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:20:23 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:41:17 +0000] "GET / HTTP/1.1" 400 173 "-" "-"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:41:55 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:42:17 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:43:58 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:21:58:46 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:22:00:07 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"
xnat-nginx_1   | 172.23.0.1 - - [27/Aug/2020:22:00:14 +0000] "GET / HTTP/1.1" 301 185 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/85.0.4183.83 Safari/537.36"

Catalina logs from apache web.catalina.log

Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.94
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Apr 10 2019 16:56:40 UTC
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.94.0
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.19.76-linuxkit
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-1.8-openjdk/jre
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_212-b04
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            IcedTea
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /usr/local/tomcat
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/local/tomcat
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms2g
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx4g
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dxnat.home=/data/xnat/home
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=8000
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dignore.endorsed.dirs=
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/usr/local/tomcat
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/local/tomcat
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
Aug 27, 2020 4:05:02 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: Loaded APR based Apache Tomcat Native library 1.2.21 using APR version 1.6.5.
Aug 27, 2020 4:05:02 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
Aug 27, 2020 4:05:02 PM org.apache.catalina.core.AprLifecycleListener initializeSSL
INFO: OpenSSL successfully initialized (OpenSSL 1.1.1b  26 Feb 2019)
Aug 27, 2020 4:05:02 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-apr-8080"]
Aug 27, 2020 4:05:02 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-apr-8009"]
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 969 ms
Aug 27, 2020 4:05:02 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Aug 27, 2020 4:05:02 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.94
Aug 27, 2020 4:05:02 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /usr/local/tomcat/webapps/ROOT.war
Aug 27, 2020 4:05:17 PM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
Aug 27, 2020 4:05:17 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /usr/local/tomcat/webapps/ROOT.war has finished in 14,531 ms
Aug 27, 2020 4:05:17 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-apr-8080"]
Aug 27, 2020 4:05:17 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-apr-8009"]
Aug 27, 2020 4:05:17 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14676 ms
Aug 27, 2020 4:18:15 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-apr-8080"]
Aug 27, 2020 4:18:15 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-apr-8009"]
Aug 27, 2020 4:18:15 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Aug 27, 2020 4:18:15 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-apr-8080"]
Aug 27, 2020 4:18:15 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-apr-8009"]
Aug 27, 2020 4:18:15 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-apr-8080"]
Aug 27, 2020 4:18:15 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-apr-8009"]
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.94
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Apr 10 2019 16:56:40 UTC
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.94.0
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.19.76-linuxkit
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-1.8-openjdk/jre
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_212-b04
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            IcedTea
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /usr/local/tomcat
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/local/tomcat
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms2g
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx4g
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dxnat.home=/data/xnat/home
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=8000
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dignore.endorsed.dirs=
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/usr/local/tomcat
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/local/tomcat
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
Aug 27, 2020 4:19:12 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: Loaded APR based Apache Tomcat Native library 1.2.21 using APR version 1.6.5.
Aug 27, 2020 4:19:12 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
Aug 27, 2020 4:19:12 PM org.apache.catalina.core.AprLifecycleListener initializeSSL
INFO: OpenSSL successfully initialized (OpenSSL 1.1.1b  26 Feb 2019)
Aug 27, 2020 4:19:12 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-apr-8080"]
Aug 27, 2020 4:19:12 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-apr-8009"]
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 807 ms
Aug 27, 2020 4:19:12 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Aug 27, 2020 4:19:12 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.94
Aug 27, 2020 4:19:12 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /usr/local/tomcat/webapps/ROOT.war
Aug 27, 2020 4:19:27 PM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
Aug 27, 2020 4:19:27 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /usr/local/tomcat/webapps/ROOT.war has finished in 14,515 ms
Aug 27, 2020 4:19:27 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-apr-8080"]
Aug 27, 2020 4:19:27 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-apr-8009"]
Aug 27, 2020 4:19:27 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14676 ms

closed time in 2 months

aditsanghvi94

issue commentMonashBI/xnat-docker-compose

Production XNAT deployment leading to 404

Solved. Default XNAT version 1.7.5.6 leads to this error. During config setup, i selected XNAT version as 1.7.6 (latest as of time of this comment) and my website spun up.

aditsanghvi94

comment created time in 2 months

issue commentMonashBI/xnat-docker-compose

Project License - License.md ?

Thank you good sir, should I close the issue after you add in the license file?

ktunallux

comment created time in 2 months

issue openedMonashBI/xnat-docker-compose

Production XNAT deployment leading to 404

I first tested configure-basic.sh and everything worked for me. I was able to access XNAT on http://localhost.

I want to run production xnat on a domain. I ran configure.sh and set up my SSL and domain. However, when i go to https://domain I get a 404. The SSL cert is valid according to the lock icon.

image

I have attached my docker-compose startup log, everything looks good there I have also attached my nginx and web logs which I got from exec into the docker containers. It looks to me like something is wrong with Tomcat where it isn't redirecting to XNAT correctly. I can't quite figure this out, any help will be greatly appreciated :)

web.catalina.log web.var.localhost_access_log.log var.log.nginx.customsite_access_ssl.log startup.log

created time in 2 months

issue commentMonashBI/xnat-docker-compose

Help configuring SSL certs

closed - not related to project + figured it out

aditsanghvi94

comment created time in 2 months

issue closedMonashBI/xnat-docker-compose

Help configuring SSL certs

I'm using https://gethttpsforfree.com/ to get SSL certs for my domain -

I can't figure out this step image

Where would I run this command? Is it inside the xnat-web docker container after installing python?

closed time in 2 months

aditsanghvi94

issue openedMonashBI/xnat-docker-compose

Help configuring SSL certs

I'm using https://gethttpsforfree.com/ to get SSL certs for my domain -

I can't figure out this step image

Where would I run this command? Is it inside the xnat-web docker container after installing python?

created time in 2 months

issue openedMonashBI/xnat-docker-compose

HTTPS over Localhost - Redirecting back to http?

I am trying to deploy XNAT on https://localhost because I have other dependencies that need SSL (and I need to test on localhost).

When I try to navigate to https://localhost, it redirects me to http://localhost/app/template/Login.vm.

image

image

Then, I can add the s and go to https://localhost/app/template/Login.vm and view the login page image

Once I login, I am redirected again to http://localhost I can just type in the url https://localhost/app/template/Index.vm?login=true and then xnat works fine. Once logged in, I can navigate XNAT without any redirections image

Can somebody help me figure out what is wrong with my nginx config? Or should I be looking at xnat-web ?

#user www-data;
worker_processes auto;
events {
  worker_connections 1024;
  # multi_accept on;
}
http {
  ##
  # Basic Settings
  ##
  sendfile on;
  tcp_nopush on;
  tcp_nodelay on;
  keepalive_timeout 65;
  types_hash_max_size 2048;
  # server_tokens off;
  # server_names_hash_bucket_size 64;
  # server_name_in_redirect off;
  #include /etc/nginx/mime.types;
  default_type application/octet-stream;
  ##
  # SSL Settings
  ##
  #ssl_protocols TLSv1 TLSv1.1 TLSv1.2; # Dropping SSLv3, ref: POODLE
  #ssl_prefer_server_ciphers on;
  ##
  # Logging Settings
  ##
  access_log /var/log/nginx/access.log;
  error_log /var/log/nginx/error.log;
  ##
  # Gzip Settings
  ##
  gzip on;
  gzip_disable "msie6";
  ##
  # Virtual Host Configs
  ##
  #include /etc/nginx/conf.d/*.conf;
  #include /etc/nginx/sites-enabled/*;
server {
  listen 80 default_server;
  listen [::]:80 default_server;
  server_name xnat-web;
  return 301 https://$server_name$request_uri;
}
  server {

        listen 443 ssl;
        server_name xnat-web;
        ssl on;
        ssl_protocols TLSv1 TLSv1.1 TLSv1.2;

        ssl_certificate     /etc/ssl/xnat/localhost.pem;
        ssl_certificate_key /etc/ssl/xnat/localhost-key.pem;

        root /var/lib/tomcat7/webapps/ROOT;

        proxy_set_header Host $host;

        location / {

        proxy_pass                          http://xnat-web:8080;
        proxy_redirect                      http://xnat-web:8080 $scheme://localhost;
        proxy_set_header Host               $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-Host $host;
        proxy_set_header X-Forwarded-Server $host;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto  $scheme;

        #proxy_intercept_errors  on;
        proxy_connect_timeout 3000;
        proxy_send_timeout 2000;
        proxy_read_timeout 2000;
        proxy_buffers 4 32k;
        client_max_body_size 0;
        client_body_buffer_size 128k;
    }

    large_client_header_buffers 8 80k;

    access_log /var/log/nginx/xnat.access.log;
    error_log /var/log/nginx/xnat.error.log;
}
}

created time in 2 months

issue commentMonashBI/xnat-docker-compose

Project License - License.md ?

Hi,

Yes, it should be licenced under the MIT licence. I will add in the licence file.

Cheers,

Tom

On Tue, 25 Aug 2020 at 09:27, ktunallux notifications@github.com wrote:

Hi! Is this project also open-source like the rest of XNAT? Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MonashBI/xnat-docker-compose/issues/21, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBRFSQOAB57AVFFOYTTILSCLZP7ANCNFSM4QKATRYA .

-- THOMAS G. CLOSE, PHD Imaging Informatics Officer

Monash Biomedical Imaging Monash University Room 139, 770 Blackburn Rd Clayton Campus, Clayton VIC 3800 Australia

T: +61 3 9902 9804 M: +61 491 141 390 E: tom.close@monash.edu mbi.monash.edu.au

ktunallux

comment created time in 2 months

issue openedMonashBI/xnat-docker-compose

Project License - License.md ?

Hi! Is this project also open-source like the rest of XNAT? Thanks!

created time in 2 months

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commit sha d0b46aa59ef8918514f693e73c4acd1ca8e25a4b

added mif.gz conversion format

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commit sha f5b25d32988c5cc1754b53258775ce032a8c8526

fixed up the error message when mrtrix isn't installed

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commit sha 327f2ca52414a889c049b63806897c688a1a71d1

added Python 3.7 and 3.8 to the valid languages of the package description

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commit sha 122ae6334cddfbd7e9c4f8b53501ead5bae2f835

fixed issues with types in xml option upped version to 0.6.3

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removed strip

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commit sha 0867e4362a1add7c33459c2f1e28219ff3f88b32

update to 0.6.2 and fixed bug in scan type

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