diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index ffd31ea3ffee3df947d1e97f80a49c66acfa182b..0000000000000000000000000000000000000000 --- a/Dockerfile +++ /dev/null @@ -1,4 +0,0 @@ -FROM bitnami/apache:2.4 -COPY ./webserver/htdocs/NOMAD/ /opt/bitnami/apache/htdocs/NOMAD/ -COPY ./webserver/cgi-bin/NOMAD/ /opt/bitnami/apache/cgi-bin/NOMAD/ - diff --git a/README.md b/README.md index adb848541b7b46d34720ab921b0c9df1b32c21c7..802e7362debed87ee26d04743f9ecaa34c92866f 100644 --- a/README.md +++ b/README.md @@ -43,6 +43,15 @@ Subdirectories: htdocs: Web pages containing the VR software and documentation. cgi-bin: cgi scripts to create suitable config files from a material number. + Docker container running the VR webservices + # install docker + # add your NOMAD username and password in webserver/pass + # build container + sudo docker build -t nomadvr . + # run container + sudo docker run -d -p 8080:8080 nomadvr + # Test e.g. with you.rip.add.res:8080/cgi-bin/NOMAD/material?109702 + RemoteVisualization: NOMAD2xyz app Transforms a json from encyclopedia or archive into an XYZ file Useful for the remote visualization infrastructure @@ -54,6 +63,7 @@ Subdirectories: MD-Driver/SimpleMove and MD-Driver/PeriodicTable: see MD-Driver/Readme Support for atom drag-and-drop functionality in OpenVR NOMAD VR. + More platforms will be added in the future. The code is distributed under the Apache 2.0 License (See LICENSE file). diff --git a/containerization/Dockerfile b/containerization/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..f3552baae4ee5abf60d6c53e02430934a6127975 --- /dev/null +++ b/containerization/Dockerfile @@ -0,0 +1,19 @@ +# note, copy this file to VR-demos folder first +FROM bitnami/apache:2.4 + +# copy NOMAD webservices +COPY ./webserver/htdocs/NOMAD/ /opt/bitnami/apache/htdocs/NOMAD/ +COPY ./webserver/cgi-bin/NOMAD/ /opt/bitnami/apache/cgi-bin/NOMAD/ +COPY ./webserver/pass /opt/bitnami/apache/ + +# allow cgi-bin +RUN sed -i 's%#LoadModule cgid_module modules/mod_cgid.so%LoadModule cgid_module modules/mod_cgid.so%' /opt/bitnami/apache/conf/httpd.conf + +# add wget. gzip, curl, tar are there by default +USER root +RUN apt-get update \ + && apt-get install -y wget \ + && apt-get install -y zip \ + && rm -rf /var/lib/apt/lists/* + + diff --git a/containerization/README.md b/containerization/README.md new file mode 100644 index 0000000000000000000000000000000000000000..4a164b2d7250e0a68a3bbb3cd1edc01109daccda --- /dev/null +++ b/containerization/README.md @@ -0,0 +1,13 @@ +Docker file to build a container to perform the VR conversion webservices + +* copy the Dockerfile to .. (VR-demos -folder) +* install docker +* add your NOMAD username and password in webserver/pass +* build container + sudo docker build -t nomadvr . +* run container + sudo docker run -d -p 8080:8080 nomadvr +* Test e.g. with you.rip.add.res:8080/cgi-bin/NOMAD/material?109702 +* stop container + sudo docker stop + diff --git a/webserver/cgi-bin/NOMAD/configuredmaterial b/webserver/cgi-bin/NOMAD/configuredmaterial old mode 100644 new mode 100755 diff --git a/webserver/cgi-bin/NOMAD/configurematerial b/webserver/cgi-bin/NOMAD/configurematerial old mode 100644 new mode 100755 diff --git a/webserver/cgi-bin/NOMAD/material b/webserver/cgi-bin/NOMAD/material old mode 100644 new mode 100755 index 14c55e18430cff9299fa0e33528809c7cfa10af3..d1e276ea4204631d01aaaa45e2392aefb6735b33 --- a/webserver/cgi-bin/NOMAD/material +++ b/webserver/cgi-bin/NOMAD/material @@ -1,104 +1,104 @@ -#!/bin/bash - - # Copyright 2016-2018 Ruben Jesus Garcia Hernandez - # - # Licensed under the Apache License, Version 2.0 (the "License"); - # you may not use this file except in compliance with the License. - # You may obtain a copy of the License at - # - # http://www.apache.org/licenses/LICENSE-2.0 - # - # Unless required by applicable law or agreed to in writing, software - # distributed under the License is distributed on an "AS IS" BASIS, - # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - # See the License for the specific language governing permissions and - # limitations under the License. - -source ../../pass - -if [[ "$QUERY_STRING" = "" ]] -then - #echo Location: /NOMAD/ - echo Location:https://www.nomad-coe.eu/the-project/graphics/VR-prototype - echo '' -else -#rgh: text/plain works in pc but android chrome saves it as .txt, removing the extension - -# export TOKEN=`cat t.b64` - export MAT=$QUERY_STRING - export RAND=$RANDOM -#rgh: before end of september 2017, use /var/tmp, after, use /tmp (apache update) - cd /tmp - /usr/bin/mkdir $RAND - cd $RAND - -#pre 2018: http://encyclopedia-api.nomad-coe.eu/v1.0/saml/ -#post 2018: -SAMLURL=https://encyclopedia.nomad-coe.eu/api/v1.0/saml/ - -wget --save-cookies cookies.txt \ - --keep-session-cookies \ - --no-check-certificate $SAMLURL -O login.html >/dev/null 2>&1 -URL=`grep "form action" login.html |cut -f 2 -d \" |head -n 1` -wget --save-cookies cookies2.txt --keep-session-cookies --load-cookies cookies.txt --no-check-certificate \ - "https://idp.nomad-coe.eu$URL&j_username=$USER&j_password=$PASS&_eventId_proceed" -O a.html >/dev/null 2>&1 -URL=`grep "form action" a.html |cut -f 2 -d \" |head -n 1` -wget --save-cookies cookies3.txt --keep-session-cookies --load-cookies cookies2.txt --no-check-certificate \ - "https://idp.nomad-coe.eu$URL&_shib_idp_consentOptions=_shib_idp_globalConsent&_eventId_proceed" \ - -O b.html >/dev/null 2>&1 - -#now continue, as we don't support javascript :o) -URL2=`echo $URL |cut -f 1 -d \?` -DEST=`grep action b.html |cut -f 2 -d \"` -RELAY=`grep RelayState b.html |cut -f6 -d \"` -SAML=`grep SAMLResponse b.html |cut -f6 -d \"` -#rgh: since 25-09-2017, this line gives "invalid url" (possibly curl update) -#RELAY="https%3A%2F%2Fencyclopedia-api.nomad-coe.eu%2Fv1.0%2Fsaml%2F" -#pre-2018 -#RELAY="https://encyclopedia-api.nomad-coe.eu/v1.0/saml/" -RELAY=$SAMLURL - -#echo relay is $RELAY - - -MATERIALSURL=https://encyclopedia.nomad-coe.eu/api/v1.0/materials - -curl -L -c cookies3.txt -X GET -F "RelayState=$RELAY" -F "SAMLResponse=$SAML" "$SAMLURL?acs" -o resp.json >/dev/null 2>&1 -TOKEN=`grep data resp.json |cut -f 4 -d \"` - - - mkdir $MAT - cd $MAT - wget --no-check-certificate --user "$TOKEN" --password "" $MATERIALSURL/$MAT/cells?pagination=off -O material_cells.json >/dev/null 2>&1 - wget --no-check-certificate --user "$TOKEN" --password "" $MATERIALSURL/$MAT/elements?pagination=off -O material_elements.json >/dev/null 2>&1 - echo \# Material $QUERY_STRING >> $MAT.ncfg - echo background 0 0 0 >> $MAT.ncfg - echo atomscaling 0.5 >> $MAT.ncfg - echo json material >> $MAT.ncfg - echo displaybonds >> $MAT.ncfg - echo displayunitcell >> $MAT.ncfg - echo showcontrollers >> $MAT.ncfg - cd .. - - if grep html $MAT/material_cells.json > /dev/null ; then - echo "CGI backend for NOMAD VR: Encyclopedia API issue. Material $MAT" | - mailx -s 'CGI backend for NOMAD VR: Encyclopedia API issue' $EMAIL - echo "Content-type: text/html" - echo '' - echo "" - echo "VR backend currently being updated" - echo "" - echo "VR backend currently being updated." - echo "Please contact us if the problem persists." - echo "" - else - zip -r $MAT $MAT >/dev/null 2>&1 - - echo "Content-type: application/octet-stream" - echo "Content-disposition: attachment; filename=${QUERY_STRING}.zip" - echo '' - cat $MAT.zip - fi - cd .. - \rm -r $RAND -fi +#!/bin/bash + + # Copyright 2016-2018 Ruben Jesus Garcia Hernandez + # + # Licensed under the Apache License, Version 2.0 (the "License"); + # you may not use this file except in compliance with the License. + # You may obtain a copy of the License at + # + # http://www.apache.org/licenses/LICENSE-2.0 + # + # Unless required by applicable law or agreed to in writing, software + # distributed under the License is distributed on an "AS IS" BASIS, + # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + # See the License for the specific language governing permissions and + # limitations under the License. + +source ../../pass + +if [[ "$QUERY_STRING" = "" ]] +then + #echo Location: /NOMAD/ + echo Location:https://www.nomad-coe.eu/the-project/graphics/VR-prototype + echo '' +else +#rgh: text/plain works in pc but android chrome saves it as .txt, removing the extension + +# export TOKEN=`cat t.b64` + export MAT=$QUERY_STRING + export RAND=$RANDOM +#rgh: before end of september 2017, use /var/tmp, after, use /tmp (apache update) + cd /tmp + /usr/bin/mkdir $RAND + cd $RAND + +#pre 2018: http://encyclopedia-api.nomad-coe.eu/v1.0/saml/ +#post 2018: +SAMLURL=https://encyclopedia.nomad-coe.eu/api/v1.0/saml/ + +wget --save-cookies cookies.txt \ + --keep-session-cookies \ + --no-check-certificate $SAMLURL -O login.html >/dev/null 2>&1 +URL=`grep "form action" login.html |cut -f 2 -d \" |head -n 1` +wget --save-cookies cookies2.txt --keep-session-cookies --load-cookies cookies.txt --no-check-certificate \ + "https://idp.nomad-coe.eu$URL&j_username=$USER&j_password=$PASS&_eventId_proceed" -O a.html >/dev/null 2>&1 +URL=`grep "form action" a.html |cut -f 2 -d \" |head -n 1` +wget --save-cookies cookies3.txt --keep-session-cookies --load-cookies cookies2.txt --no-check-certificate \ + "https://idp.nomad-coe.eu$URL&_shib_idp_consentOptions=_shib_idp_globalConsent&_eventId_proceed" \ + -O b.html >/dev/null 2>&1 + +#now continue, as we don't support javascript :o) +URL2=`echo $URL |cut -f 1 -d \?` +DEST=`grep action b.html |cut -f 2 -d \"` +RELAY=`grep RelayState b.html |cut -f6 -d \"` +SAML=`grep SAMLResponse b.html |cut -f6 -d \"` +#rgh: since 25-09-2017, this line gives "invalid url" (possibly curl update) +#RELAY="https%3A%2F%2Fencyclopedia-api.nomad-coe.eu%2Fv1.0%2Fsaml%2F" +#pre-2018 +#RELAY="https://encyclopedia-api.nomad-coe.eu/v1.0/saml/" +RELAY=$SAMLURL + +#echo relay is $RELAY + + +MATERIALSURL=https://encyclopedia.nomad-coe.eu/api/v1.0/materials + +curl -L -c cookies3.txt -X GET -F "RelayState=$RELAY" -F "SAMLResponse=$SAML" "$SAMLURL?acs" -o resp.json >/dev/null 2>&1 +TOKEN=`grep data resp.json |cut -f 4 -d \"` + + + mkdir $MAT + cd $MAT + wget --no-check-certificate --user "$TOKEN" --password "" $MATERIALSURL/$MAT/cells?pagination=off -O material_cells.json >/dev/null 2>&1 + wget --no-check-certificate --user "$TOKEN" --password "" $MATERIALSURL/$MAT/elements?pagination=off -O material_elements.json >/dev/null 2>&1 + echo \# Material $QUERY_STRING >> $MAT.ncfg + echo background 0 0 0 >> $MAT.ncfg + echo atomscaling 0.5 >> $MAT.ncfg + echo json material >> $MAT.ncfg + echo displaybonds >> $MAT.ncfg + echo displayunitcell >> $MAT.ncfg + echo showcontrollers >> $MAT.ncfg + cd .. + + if grep html $MAT/material_cells.json > /dev/null ; then + echo "CGI backend for NOMAD VR: Encyclopedia API issue. Material $MAT" | + mailx -s 'CGI backend for NOMAD VR: Encyclopedia API issue' $EMAIL + echo "Content-type: text/html" + echo '' + echo "" + echo "VR backend currently being updated" + echo "" + echo "VR backend currently being updated." + echo "Please contact us if the problem persists." + echo "" + else + zip -r $MAT $MAT >/dev/null 2>&1 + + echo "Content-type: application/octet-stream" + echo "Content-disposition: attachment; filename=${QUERY_STRING}.zip" + echo '' + cat $MAT.zip + fi + cd .. +# \rm -r $RAND +fi diff --git a/webserver/cgi-bin/NOMAD/materialAnalytics b/webserver/cgi-bin/NOMAD/materialAnalytics old mode 100644 new mode 100755 diff --git a/webserver/pass b/webserver/pass index 35953d707aac3f28b25ae139b7e6cd58d65a66ae..541d45fab6c4645974ae7f02b34ccea7bf47a7b8 100644 --- a/webserver/pass +++ b/webserver/pass @@ -3,5 +3,5 @@ export USER= export PASS= #Notification email -export EMAIL= +export EMAIL