Merge branch 'java' into java-release

Author: Nick Bargnesi

java/scripts/create-webroot.sh

@@ -0,0 +1,101 @@
+#!/usr/bin/env bash
+DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"/../../
+. "$DIR"/env.sh || exit 1
+
+if [ $# -ne 2 ]; then
+    echo "Usage: $0 [PATH] [WEB ROOT]"
+    echo "E.g. '$0 $(date +%Y-%m-%d) \"http://localhost:8000\"'"
+    exit 1
+fi
+
+assert-env-or-die RG_NS_OUTPUT
+assert-env-or-die RG_EQ_OUTPUT
+assert-env-or-die RG_ANNO_OUTPUT
+
+output_dir="$1"
+if [ -d "$output_dir" ]; then
+    echo "Output directory \"$output_dir\" already exists." >&2
+    exit 1
+fi
+webroot="$2"
+
+mkdir "$output_dir" && cd "$output_dir"
+
+echo -en "Mirroring latest BEL framework resources... "
+wget --quiet --mirror --no-parent --cut-dirs=2 "http://resource.belframework.org/belframework/latest-release/"
+mv resource.belframework.org/* .
+rmdir resource.belframework.org
+echo "done"
+
+rm -fr namespace annotation equivalence index.xml*
+
+cp -a "$RG_NS_OUTPUT" .
+cp -a "$RG_EQ_OUTPUT" .
+cp -a "$RG_ANNO_OUTPUT" .
+
+echo '<idx:index
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://www.belscript.org/schema/index index.xsd"
+    xmlns:idx="http://www.belscript.org/schema/index"
+    idx:belframework_version="2.0">
+
+    <idx:annotationdefinitions>' > index.xml
+
+find -name "*.belanno" | while read belanno; do
+    belanno=annotation/$(basename $belanno)
+    echo "    <idx:annotationdefinition idx:resourceLocation=\"$webroot/$belanno\" />" >> index.xml
+done
+
+echo '    </idx:annotationdefinitions>
+
+    <idx:namespaces>' >> index.xml
+
+find -name "*.belns" | while read belns; do
+    belns=namespace/$(basename $belns)
+    echo "       <idx:namespace idx:resourceLocation=\"$webroot/$belns\" />" >> index.xml
+done
+
+echo '    </idx:namespaces>
+
+    <idx:equivalences>' >> index.xml
+
+find -name "*.beleq" | while read beleq; do
+    beleq=equivalence/$(basename $beleq)
+    belns=namespace/$(basename $beleq | sed 's/beleq/belns/')
+    echo "        <idx:equivalence idx:resourceLocation=\"$webroot/$beleq\" >" >> index.xml
+    echo "            <idx:namespace-ref idx:resourceLocation=\"$webroot/$belns\" />" >> index.xml
+    echo "        </idx:equivalence>" >> index.xml
+done
+
+echo "    </idx:equivalences>
+
+    <idx:knowledge>
+        <idx:protein-families idx:resourceLocation=\"$webroot/resource/protein-families.bel\" />
+        <idx:named-complexes idx:resourceLocation=\"$webroot/resource/named-complexes.bel\" />
+        <idx:gene-scaffolding idx:resourceLocation=\"$webroot/resource/gene_scaffolding_document_9606_10090_10116.bel\" />
+        <idx:orthologies>
+            <idx:orthology idx:resourceLocation=\"$webroot/resource/gene-orthology.bel\" />
+        </idx:orthologies>
+    </idx:knowledge>
+</idx:index>" >> index.xml
+
+sha256sum index.xml > index.xml.sha256
+
+base=$(pwd)
+# create sha256 hashes for each namespace
+cd namespace || exit 1
+for x in *.belns; do sha256sum "$x" > "$x.sha256"; done
+cd "$base"
+
+# create sha256 hashes for each equivalence
+cd equivalence || exit 1
+for x in *.beleq; do sha256sum "$x" > "$x.sha256"; done
+cd "$base"
+
+# create sha256 hashes for each annotation
+cd annotation || exit 1
+for x in *.belanno; do sha256sum "$x" > "$x.sha256"; done
+cd "$base"
+
+echo "Done!"
+