Add platform check in atoms.cpp

Add archive-NomadVR link and readme in web backend.

Add platform check in atoms.cpp
Add archive-NomadVR link and readme in web backend.
ff82d8ec · Ruben Jesus Garcia Hernandez · 003a9fd9 · ff82d8ec · ff82d8ec · ff82d8ec
Commit ff82d8ec authored Nov 02, 2018 by Ruben Jesus Garcia Hernandez
--- a/NOMADVRLib/atoms.cpp
+++ b/NOMADVRLib/atoms.cpp
@@ -279,6 +279,7 @@ int readAtomsXYZ(const char *const file, int **numatoms, int *timesteps, float *
 {
 	const char *myfile=nullptr;
 	const char *webdownload="material.xyz";
+#if !defined(OCULUSMOBILE) && !defined(__ANDROID__)
 	//add http support
 	if (!strncmp(file, "http:", 5) || !strncmp(file, "https:", 6)) {
 		char cmd[2048];
@@ -294,6 +295,9 @@ int readAtomsXYZ(const char *const file, int **numatoms, int *timesteps, float *
 	} else {
 		myfile = file;
 	}
+#else
+	myfile=file;
+#endif
 	int mynumatoms;
 	std::vector<float*> mypos;
 	std::vector<int> mynum;

--- a/webserver/Readme.md
+++ b/webserver/Readme.md
+This directory contains the support files for the CGI backend to obtain 
+NOMAD VR files from the Encyclopedia and Archive.
+
+Directories:
+	htdocs: Example files related to NOMAD VR
+	cgi-bin: CGI-backend
+
+Files:
+	Readme.md: This document
+	pass: Information on the NOMAD user under which the data is accessed.
+	
+	cgi-bin/NOMAD/material: 
+	
+	Entry point for NOMAD Encyclopedia.
+	See also the VR tutorial at
+	https://www.nomad-coe.eu/the-project/graphics/vrtutorial6
+	In the Encyclopedia webpage for a given material:
+		https://encyclopedia.nomad-coe.eu/gui/#/material/<mat id>
+	the link "Virtual Reality files" -> "Get VR file" points to
+		http://nomad.srv.lrz.de/cgi-bin/NOMAD/material?<mat_id>
+	This entry point creates a zip file with a the crystal structure of mat_id.
+	
+	cgi-bin/NOMAD/materialAnalytics:
+	
+	Entry point for NOMAD Archive / Analytics.
+	See also the VR tutorial at
+	https://www.nomad-coe.eu/the-project/graphics/vrtutorial5
+	In the analytics toolkit tutorial webpage, the tutorial
+		"Querying and visualizing the content of the NOMAD Archive" at
+	https://analytics-toolkit.nomad-coe.eu/notebook-edit/data/shared/tutorialsNew/nomad-query/nomad-query.bkr
+	The results of the queries have the form:
+	nmd://<string>
+	with the link "Virtual Reality" pointing to
+	http://nomad.srv.lrz.de/cgi-bin/NOMAD/materialAnalytics?<string>
+	This entry point creates a zip file with the structure or molecular dynamics
+	for <string>.
+	
+		
\ No newline at end of file
--- a/webserver/cgi-bin/NOMAD/materialAnalytics
+++ b/webserver/cgi-bin/NOMAD/materialAnalytics
+#!/bin/bash
+
+export DATASOURCE=https://analytics-toolkit.nomad-coe.eu/api/resolve
+
+if [[ "$QUERY_STRING" = "" ]]
+then
+	#echo Location: /NOMAD/
+	echo Location:https://www.nomad-coe.eu/the-project/graphics/VR-prototype
+	echo ''
+else
+#rgh: text/plain works in pc but android chrome saves it as .txt, removing the extension
+
+#	export TOKEN=`cat t.b64`
+	export RAND=$RANDOM
+#rgh: before end of september 2017, use /var/tmp, after, use /tmp (apache update)
+	cd /tmp
+	/usr/bin/mkdir $RAND
+	cd $RAND
+
+	export MAT=`echo $QUERY_STRING|cut -f 2 -d/`
+
+	mkdir $MAT
+	cd $MAT
+#Some systems have atomic positions in section_system:0
+#Others don't; they start at section_system:1
+#Better to download all and test this in NOMADVR.
+#        wget --no-check-certificate https://analytics-toolkit.nomad-coe.eu/api/resolve/$QUERY_STRING/section_run/0c/section_system/0c?format=recursiveJson -O material.json
+
+	if [[ $QUERY_STRING = *"section_run"* ]]
+	then
+		QS=$QUERY_STRING
+	else
+		QS=$QUERY_STRING/section_run/0c
+	fi
+
+	wget --no-check-certificate $DATASOURCE/$QS?format=recursiveJson -O \
+		materialtmp.json
+
+	if [[ $QUERY_STRING = *"section_run"* ]]
+        then
+		echo "{ "section_system" : [" >>material.json
+		cat materialtmp.json >> material.json
+		echo "] }" >> material.json
+		rm materialtmp.json
+	else
+		mv materialtmp.json material.json
+        fi
+
+	export FORMULA=`grep system_composition material.json|head -n 1 |cut -f 4 -d\"`
+
+	if [[ "$FORMULA" = "" ]]
+	then
+		echo "Content-type: text/html"
+		echo ''
+		echo "<html><body>"
+		echo "No system_composition found in json: no information to display in VR"
+		echo "</body></html>"
+	else
+
+		echo \# Material $QUERY_STRING >> $FORMULA.ncfg
+		echo background 0 0 0 >> $FORMULA.ncfg
+		echo atomscaling 0.5 >> $FORMULA.ncfg
+		echo analyticsjson material.json >> $FORMULA.ncfg
+		echo displaybonds >> $FORMULA.ncfg
+		echo displayunitcell >> $FORMULA.ncfg
+		echo showcontrollers >> $FORMULA.ncfg
+		cd ..
+	
+		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