[med-svn] r18686 - trunk/community/edam

[Steffen Möller]

Author: moeller
Date: 2015-01-31 21:03:19 +0000 (Sat, 31 Jan 2015)
New Revision: 18686

Modified:
   trunk/community/edam/README.txt
   trunk/community/edam/debian2edam
Log:
Session with Herve - initial commit.

Modified: trunk/community/edam/README.txt
===================================================================
--- trunk/community/edam/README.txt	2015-01-31 18:22:26 UTC (rev 18685)
+++ trunk/community/edam/README.txt	2015-01-31 21:03:19 UTC (rev 18686)
@@ -10,3 +10,4 @@
 
 [1] http://edamontology.org/
 [2] http://www.yaml.org/
+[3] https://elixir-registry.cbs.dtu.dk

Modified: trunk/community/edam/debian2edam
===================================================================
--- trunk/community/edam/debian2edam	2015-01-31 18:22:26 UTC (rev 18685)
+++ trunk/community/edam/debian2edam	2015-01-31 21:03:19 UTC (rev 18686)
@@ -6,23 +6,29 @@
 	cat - 1>&2
 }
 
+# echoindent outputs a series of blanks to STDOUT. An optional
+# second argument is echoed after those blanks if present.
 function echoindent () {
 	for i in $(seq 1 $1)
 	do
 		echo -n " "
 	done
+	if [ "" != "$2" ]; then
+		echo $2
+	fi
 }
 
+level=0
 # helper to properly close an open paranthesis
 function closeParenthesis () {
-			level=$((level-1))
-			echoindent $level
-			echo -n ")"
-			if [ -n "$1" ]; then
-				echo "# $1"
-			else
-				echo
-			fi
+	level=$(($level-1))
+	echoindent $level
+	echo -n ")"
+	if [ -n "$1" ]; then
+		echo "# $1"
+	else
+		echo
+	fi
 }
 
 # Key argument indicating the debian directory from which to retrieve all the
@@ -33,7 +39,13 @@
 
 # Variable keeping usage information
 USAGE=<<EOUSAGE
-debian2edam <path to 'debian' directory>
+debian2edam [--upload] <path to 'debian' directory> 
+
+server=https://
+Environment variables:
+elixir_cat_username
+elixir_cat_password 
+
 EOUSAGE
 
 filename=$(basename "$pathToDebian")
@@ -77,12 +89,10 @@
 
 if [ -n "$debug" ]; then cat debian/control; fi
 
-while read desc; do
-	d=$(echo "$desc"|sed -e 's/^[^:]*: *//')
-	echo Package: $d
-	#packages="$d"
-	#packages[1]="$d"
-	packages[${#packages[*]}]="$d"
+while read pack; do
+	p=$(echo "$pack"|sed -e 's/^[^:]*: *//')
+	echo Package: $p
+	packages[${#packages[*]}]="$p"
 done < <(grep "^Package:" debian/control )
 
 while read desc; do
@@ -122,7 +132,6 @@
 openfunction=0
 openscope=0
 indentlen=0
-level=0
 
 # Core part of the program
 # It reads every line of the EDAM file (see end of loop for the redirection)
@@ -199,7 +208,7 @@
 			openfunction=0
 		fi
 		echoindent $level
-		echo "(function";
+		echo "(function $val";
 		level=$((level+1))
 		openfunction=1
 	elif [ "input" = "$type" -o "output" = "$type" ]; then