From 105e2dc70688d2fffc05da9124303b713fab9b1e Mon Sep 17 00:00:00 2001 From: Emilian Date: Wed, 10 Apr 2024 15:15:41 +0200 Subject: [PATCH 1/2] chore: upgrade openspecimen to v10.1.RC1 --- appinfo.json | 7 +- configs/openspecimen/scripts/adduser.jar | Bin 5230 -> 0 bytes configs/openspecimen/scripts/defaultvar.sh | 15 -- configs/openspecimen/scripts/entrypoint.sh | 17 -- configs/openspecimen/scripts/waitforit.sh | 182 --------------------- docker-compose.yml | 8 +- docker-compose.yml.template | 7 +- 7 files changed, 10 insertions(+), 226 deletions(-) delete mode 100755 configs/openspecimen/scripts/adduser.jar delete mode 100755 configs/openspecimen/scripts/defaultvar.sh delete mode 100755 configs/openspecimen/scripts/entrypoint.sh delete mode 100755 configs/openspecimen/scripts/waitforit.sh diff --git a/appinfo.json b/appinfo.json index cf7d484..8ec44fe 100644 --- a/appinfo.json +++ b/appinfo.json @@ -1,13 +1,12 @@ { "name": "OpenSpecimen", "short_name": "OpenSpecimen", - "version": "v9.0.RC2", - "description": "OpenSpecimen Version 9.0.RC2", + "version": "v10.1.RC1", + "description": "OpenSpecimen Version 10.1.RC1", "catalogue_url": "http://biobankapps.com/software/view?id=26", "application_url": "https://www.openspecimen.org/", "tags": ["Sample Management", "BIMS"], "application_documentation_url": "https://openspecimen.atlassian.net/wiki/spaces/CAT", - - "instance_information": "

OpenSpecimen is a highly Configurable Biospecimen Management System, which enables to track the Complete Lifecycle of your Biospecimen Inventory from Collection to Utilization.
user: admin

password: Login@123>br/>

" + "instance_information": "

OpenSpecimen is a highly Configurable Biospecimen Management System, which enables to track the Complete Lifecycle of your Biospecimen Inventory from Collection to Utilization.

To login use:

user:admin

password:Login@123

" } diff --git a/configs/openspecimen/scripts/adduser.jar b/configs/openspecimen/scripts/adduser.jar deleted file mode 100755 index 220a4ad93fd928e4e922a133445ac341a3bd9832..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5230 zcmai&1yodP*T+YY5{7i>6mUd3q(fAi85&2C1`!x?Xof*RL>i=9x*H?~1f(P+qE5?|r@ZyUY9Sv(8%Qth4|7Jp0*apSAW+RSEOvZ2&GVE+7}Cp#b=c-3HtQKx8zf zITfI?+z@G~f~<^&CKp8ZvI_v9>y{>LW+VnQxszQs;lNni@Sm#CQ$vFEdepV2vN&*u za*C^VZtzRon#mDFq^gVf50Ve(O+aAzB1Z1QK``m2D3H{FNF0;@w{Pma%nje* zpPSp7-^n;il*KkWQ`1c1qnOlVeLt5UtpNR$?YjhQSd!oG0RXrFz`BXr-}1ox`P9&X`}Yn%HP;Si_J(f%;zjfqFDp|MM{Dzc zaVGz#vyr)xk&VkAnm_kD_5bWQ__rE}tA?8LQyY6rQ+qCBxFG_O1jBc^J>qy-Oy4aZ z^pJ>UnnyfH@2jFgkd?v`>rIY=umTV+k0AX9q0x?oGrt(VcZFS|u>YPDsZhui3)HB+ zjF)Nj^LyT+saF4q>XniG3;BqK_gPj0f*!RHn!2k`{AXb>`G(z8_rA%Rqu!by=Rc%= zY_8cf9P_<~G!LlWE$OlsYolF*w^!4By^E$x-|6okdLnlf*Re4d9*GFuc$Gt(BVnFY zCQ7PpUtnyopF!vNpqnIzJBZLULcvnN5MNVHqm#v~RYSq6tt9@vt4>;CG-!$N)P}jH>V^8^XdJw`XEd?)1COJ8uq<4}6bj#m4J)XY+Dezd zTWgIlM(WVf^t^16LWUx&LA4+a`g%0X>V%x z$pCQ3vr@`~4qG3z9Tk^RI3kTgpz?gRkSOeEqi3LHc1&sqwnAQ2UkkP=0|PDsx*m+MzCvsZ9u>t6>?QXB zH_Xc9A;S;75rULCM;SCg0ha*?Ho40{4>q;LiZ&)BdC1Bj6+HFQARKJk z6=SbuC*zZpn52bR3qAd6OKwh-@GB9!lXW8PYVf>3SNwLLF9Y4vO_K<%QJ+uLkN7`O zibODp6RbauEmwagL{#k(Kp6nm6`lFmR_C}*!NVGli-lmc0yCS7QG?66G2gtQqK=u) zZDV{ZFv;~z)rbs}gkUh;TqH7V)VhY+v=ArXJje%Iwj@ZdFKfkE2W6DKWl86U6|Jv? z$sesaZto{XKpQ32jgB$)f!?ICkLv9K&m17&%U-B60@WwZ50B z>oS~Y4SaLeJVxehg7%NySQh3|b>$PJ-pG@^4Q3(s%XAoMk}!zvDIE~Ub%tFbBn6Fi z+FcW?wG&b(h704q+H{Cx;3O5jF} z%Wfxvdb-Be9J=zU={u6E+^Ngld;`zlw>#APoXYs;Dc`kZV7~)gX>q2mR=JZkUddn7 z>>=A;m#cyD%3v1Rlfa&4HyZ}MJj@~;+hL&)XCwx0gzf`@38@z?m@jjS<2ZLH75Gr% z)?zm__*9xIa^`cZ-IrobM&ViC#j7QdAGnP^wyvYesrU`7fw4UkiyU<|mF`@UuZhf$ z4G7QpRV-#(j&UFNnQh2>RfrXDoD4jXq#&9{Q%l}0Sr{)TKt4+IL+DEwNR`A2oA~(AKBkhUu#!e}WRrfhoT=KTo||{nl_dd>Ap{PEkG@Kw z#f8F&lBQe@o{9>f5XZA)I^d6TNnZW@*+xPkzV0U*FL%}X(0j1*Y}i7R!3^;YR=hJ_ z%oL3wxEMr+}%AibtBri;h)TQb4&1FXFvsnr!$^ za=)jdR}($Rc7hUWWP8P%UuiS!TioSGUWA4@HOee1jkhuPso%9I`o3c|EH@&F&{VVT zPsKv@HEk&!!g8=BpxSbHtbP*Q7ffr~QWz62v64+lWt=_Xvnt!!9LGq)S_w-rK15|j z^nK$W^J2$EZ>9R8M);?xkLfQT8E_3gZ`^pkJL#a<8En5*w+$qwyVC}^!T2IeM#t!RRtdhDM zX?=n3Q$l=eVfTx%#KB4=rHKzI*kNoGkHsh!T`hY-S+GKXEsVfokxpXE*5~8i!rL9v zv!hq#xb^7T%-$ee@->2fj=1zY<|@^-uUO;Ux8FN3_eWtWlT59qB{hHxED%C17d4VC&8;~A=f@V!$~ zh#MWg1IIuqtesR>ww<~!wjs+57TJ#~y`3u+XCF7L(Er(@H1wHL$t6q=d7M8`$>k#Q zLU2%wUvLTPW1l@AX!zy6AbTS|oH1&-lkv$G&u#N~=6zj$qC>^t-j@#@+AM+8dmC z8|qe}7F9V;6XlA2bnv5HmRWr)74=MLzkII08&|8Mg$HJ)lSQ4E+q5#oCOzvD%!_!2 zu&MRN_#R=wl4(OS`oqBxUJ04UI+oL-N>!hfE*deaJ0s=m^^uJ>Y?rAE%QxeGlW1*b zTtcO4=5Sgt%^pqYf*{x0Qh+_-!6002oQvrgW0Tgr&U<;z&7Inqc1+OM*tVf%c%@iHdc&PL~=F3YZwR&Z^`nQDvMXTOWJpdl#qmVBx= zbfnQ1IiNF=@z)$!L*SaGnd^ENtD(25-A)?UnoH+xLM+B@HL$U3#%0 zK1pNL!JObZ<;1heb>gUHkk%-hcDhPIiyq4H=Rd%@l*;`HMM@Pji&M#ruZI!Q8Bg;q z+AJIZ5$&X*2-o~GT&4%L?|$G$7T@$OZ%Kz8DXI-(ZIM+}Q(N7554 z+6o5Heo_4GW_%aB_u_Xp4%TS#l;LA zB;HQ3XJ6&17-NY*0PJQn zt0F%(>Sk|j8vPX!+LEgcyDsI^beoH z~zxbzCeOxt^Jx`!$i-T!ewow&c{F*)^QkH}77Z!nmZ0WA8kA zTisOLg>Ygk3y$bkdH-N@uBKhVg3aL$1dxS$$8V3{K`lBTIw(U{(M;94?c{g}33Dz( zUyhBC%-YOzo&-L?DDaGB#k-11Q;ytA^s^5m14&xCmf!cl=al=BuspPl84R+RQc>d; zB8?w;G0URou6lP#{?Wp_{i7=3=WUlAp!0?8if=6&z%&cRZaPD$zO5f;9)&X_CmudC zLZ=sx8uizYlr%kg8G2~6F6&}KkYL2LM>k+AZEXf}ry*s@jmVmbuxid@)CcF?_R(H7 zgX&$2U4eZ_hOsc%v0a|G z>Zne!r2KX%iB2es+tf)IsX7Jp(iPv>7wKl6ue&<3b)nuqi065LloPE`j@Ud`>&=!! 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IN NO EVENT SHALL THE -#AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -#LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -#OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -#SOFTWARE. -# -cmdname=$(basename $0) - -echoerr() { if [[ $QUIET -ne 1 ]]; then echo "$@" 1>&2; fi } - -usage() -{ - cat << USAGE >&2 -Usage: - $cmdname host:port [-s] [-t timeout] [-- command args] - -h HOST | --host=HOST Host or IP under test - -p PORT | --port=PORT TCP port under test - Alternatively, you specify the host and port as host:port - -s | --strict Only execute subcommand if the test succeeds - -q | --quiet Don't output any status messages - -t TIMEOUT | --timeout=TIMEOUT - Timeout in seconds, zero for no timeout - -- COMMAND ARGS Execute command with args after the test finishes -USAGE - exit 1 -} - -wait_for() -{ - if [[ $TIMEOUT -gt 0 ]]; then - echoerr "$cmdname: waiting $TIMEOUT seconds for $HOST:$PORT" - else - echoerr "$cmdname: waiting for $HOST:$PORT without a timeout" - fi - start_ts=$(date +%s) - while : - do - (echo > /dev/tcp/$HOST/$PORT) >/dev/null 2>&1 - result=$? - if [[ $result -eq 0 ]]; then - end_ts=$(date +%s) - echoerr "$cmdname: $HOST:$PORT is available after $((end_ts - start_ts)) seconds" - break - fi - sleep 1 - done - return $result -} - -wait_for_wrapper() -{ - # In order to support SIGINT during timeout: http://unix.stackexchange.com/a/57692 - if [[ $QUIET -eq 1 ]]; then - timeout $TIMEOUT $0 --quiet --child --host=$HOST --port=$PORT --timeout=$TIMEOUT & - else - timeout $TIMEOUT $0 --child --host=$HOST --port=$PORT --timeout=$TIMEOUT & - fi - PID=$! - trap "kill -INT -$PID" INT - wait $PID - RESULT=$? - if [[ $RESULT -ne 0 ]]; then - echoerr "$cmdname: timeout occurred after waiting $TIMEOUT seconds for $HOST:$PORT" - fi - return $RESULT -} - -# process arguments -while [[ $# -gt 0 ]] -do - case "$1" in - *:* ) - hostport=(${1//:/ }) - HOST=${hostport[0]} - PORT=${hostport[1]} - shift 1 - ;; - --child) - CHILD=1 - shift 1 - ;; - -q | --quiet) - QUIET=1 - shift 1 - ;; - -s | --strict) - STRICT=1 - shift 1 - ;; - -h) - HOST="$2" - if [[ $HOST == "" ]]; then break; fi - shift 2 - ;; - --host=*) - HOST="${1#*=}" - shift 1 - ;; - -p) - PORT="$2" - if [[ $PORT == "" ]]; then break; fi - shift 2 - ;; - --port=*) - PORT="${1#*=}" - shift 1 - ;; - -t) - TIMEOUT="$2" - if [[ $TIMEOUT == "" ]]; then break; fi - shift 2 - ;; - --timeout=*) - TIMEOUT="${1#*=}" - shift 1 - ;; - --) - shift - CLI="$@" - break - ;; - --help) - usage - ;; - *) - echoerr "Unknown argument: $1" - usage - ;; - esac -done - -if [[ "$HOST" == "" || "$PORT" == "" ]]; then - echoerr "Error: you need to provide a host and port to test." - usage -fi - -TIMEOUT=${TIMEOUT:-1000} -STRICT=${STRICT:-0} -CHILD=${CHILD:-0} -QUIET=${QUIET:-0} - -if [[ $CHILD -gt 0 ]]; then - wait_for - RESULT=$? - exit $RESULT -else - if [[ $TIMEOUT -gt 0 ]]; then - wait_for_wrapper - RESULT=$? - else - wait_for - RESULT=$? - fi -fi - -if [[ $CLI != "" ]]; then - if [[ $RESULT -ne 0 && $STRICT -eq 1 ]]; then - echoerr "$cmdname: strict mode, refusing to execute subprocess" - exit $RESULT - fi - exec $CLI -else - exit $RESULT -fi diff --git a/docker-compose.yml b/docker-compose.yml index 3cf3f1c..f2c3612 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -24,7 +24,7 @@ services: - SYS_NICE local-openspecimen-web: - image: bibbox/openspecimen:9-0-RC2 + image: bibbox/openspecimen:v10.1.RC1pre container_name: local-openspecimen-web user: tomcat restart: unless-stopped @@ -34,6 +34,7 @@ services: - local-openspecimen-db:openspecimen-db environment: - DATABASE_HOST=openspecimen-db + - DATABASE_PORT=3306 - MYSQL_ROOT_PASSWORD=openspecimen - MYSQL_DATABASE=openspecimen - MYSQL_USER=openspecimen @@ -41,9 +42,8 @@ services: depends_on: - local-openspecimen-db volumes: - - ./data/os-data:/var/lib/tomcat9/openspecimen/data - - ./data/os-plugins:/var/lib/tomcat9/openspecimen/plugins + - ./data/os-data:/var/lib/openspecimen/data + - ./data/os-plugins:/var/lib/openspecimen/plugins - ./configs/openspecimen/ROOT:/var/lib/tomcat9/webapps/ROOT - - ./configs/openspecimen/scripts/entrypoint.sh:/opt/scripts/entrypoint.sh ports: - "9000:8080" diff --git a/docker-compose.yml.template b/docker-compose.yml.template index 5d6ecab..c3fc046 100644 --- a/docker-compose.yml.template +++ b/docker-compose.yml.template @@ -22,7 +22,7 @@ services: - ./configs/openspecimen.cnf:/etc/mysql/conf.d/openspecimen.cnf:ro §§INSTANCE-openspecimen-web: - image: bibbox/openspecimen:9-0-RC2 + image: bibbox/openspecimen:v10.1.RC1pre container_name: §§INSTANCE-openspecimen-web restart: unless-stopped user: tomcat @@ -44,9 +44,8 @@ services: depends_on: - §§INSTANCE-openspecimen-db volumes: - - ./data/os-data:/var/lib/tomcat9/openspecimen/data - - ./data/os-plugins:/var/lib/tomcat9/openspecimen/plugins + - ./data/os-data:/var/lib/openspecimen/data + - ./data/os-plugins:/var/lib/openspecimen/plugins - ./configs/openspecimen/ROOT:/var/lib/tomcat9/webapps/ROOT - - ./configs/openspecimen/scripts/entrypoint.sh:/opt/scripts/entrypoint.sh ports: - "9000:8080" From 803416611fef0502c61e09b17ab5d7ffe119f65f Mon Sep 17 00:00:00 2001 From: Emilian Date: Thu, 11 Apr 2024 14:34:39 +0200 Subject: [PATCH 2/2] chore: switch from prerelease of dockeer img to normal --- docker-compose.yml | 2 +- docker-compose.yml.template | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index f2c3612..646b8a7 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -24,7 +24,7 @@ services: - SYS_NICE local-openspecimen-web: - image: bibbox/openspecimen:v10.1.RC1pre + image: bibbox/openspecimen:v10.1.RC1 container_name: local-openspecimen-web user: tomcat restart: unless-stopped diff --git a/docker-compose.yml.template b/docker-compose.yml.template index c3fc046..85c4b46 100644 --- a/docker-compose.yml.template +++ b/docker-compose.yml.template @@ -22,7 +22,7 @@ services: - ./configs/openspecimen.cnf:/etc/mysql/conf.d/openspecimen.cnf:ro §§INSTANCE-openspecimen-web: - image: bibbox/openspecimen:v10.1.RC1pre + image: bibbox/openspecimen:v10.1.RC1 container_name: §§INSTANCE-openspecimen-web restart: unless-stopped user: tomcat @@ -32,6 +32,7 @@ services: - §§INSTANCE-openspecimen-db:openspecimen-db environment: - DATABASE_HOST=openspecimen-db + - DATABASE_PORT=3306 - MYSQL_ROOT_PASSWORD=thispasswordisneverusededoutsidethecontainer - MYSQL_DATABASE=openspecimen - MYSQL_USER=§§MYSQL_DATABASE_USER