diff --git a/parse/compare.py b/parse/compare.py
index 902eed3..44d9db4 100755
--- a/parse/compare.py
+++ b/parse/compare.py
@@ -49,23 +49,41 @@ def open_file(p):
 if __name__ == '__main__':
 	if len(sys.argv) < 2:
 		sys.exit('No input file... Aborting.')
-	fp1 = open_file(sys.argv[1])
+	try:
+		fp1 = open_file(sys.argv[1])
+	except:
+		sys.exit("Can't open file " + sys.argv[1] + ". Aborting.")
 	if len(sys.argv) < 3:
 		fp2 = sys.stdin
 	else:
-		fp2 = open_file(sys.argv[2])
+		try:
+			fp2 = open_file(sys.argv[2])
+		except:
+			sys.exit("Can't open file " + sys.argv[2] + ". Aborting.")
 
-	data1 = json.load(fp1)
-	data2 = json.load(fp2)
-
-	# print "----"
-	# print data1
-	# print "----"
-	# print data2
-	# print "----"
-
-	fp1.close()
-	fp2.close()
+	try:
+		sdata = fp1.read()
+		data1 = json.loads(sdata)
+	except:
+		e = "<compare> Error loading data from" + sys.argv[1] + ". Aborting.\n"
+		if sdata:
+			e += "Traceback: " + sdata1
+		fp2.close()
+		sys.exit(e)		
+	finally:
+		fp1.close()
+		
+	try:
+		sdata = fp2.read()
+		data2 = json.loads(sdata)
+	except:
+		e = "<compare> Error loading data. Aborting.\n"
+		if sdata:
+			e += "Traceback: " + sdata
+		fp1.close()
+		sys.exit(e)
+	finally:
+		fp2.close()
 
 	data = difference(data1, data2)
 
diff --git a/parse/inject.py b/parse/inject.py
index 035d5ab..3e16018 100755
--- a/parse/inject.py
+++ b/parse/inject.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 from statemachine import StateMachine
-import sys, os, string, json, shutil, codecs
+import sys, os, string, json, shutil, codecs, traceback
 
 quote_nbr = sys.maxint
 fileout = ''
@@ -170,17 +170,35 @@ if __name__ == '__main__':
 	if len(sys.argv) < 2:
 		sys.exit('No input file... Aborting.')
 	# fp1 should be the incoming .mmd file
-	fileref = backupfile(sys.argv[1])
-	fileout = open_fileoutput(sys.argv[1])
-	fileout.seek(0)
+	try:
+		fileref = backupfile(sys.argv[1])
+		fileout = open_fileoutput(sys.argv[1])
+		fileout.seek(0)
+	except:
+		sys.exit("Can't open file " + sys.argv[1] + ". Aborting.")
+
 	if len(sys.argv) < 3:
 		fp2 = sys.stdin
 	else:
-		fp2 = open_file(sys.argv[2])
+		try:
+			fp2 = open_file(sys.argv[2])
+		except:
+			sys.exit("Can't open file " + sys.argv[2] + ". Aborting.")
 
 	# fp2 should be the incoming (json) data to inject in fp1
-	data = json.load(fp2)
-	fp2.close()
+
+	try:
+		sdata = fp2.read()
+		data = json.loads(sdata)
+	except:
+		e = "<inject> Error loading data. Aborting\n"
+		if sdata:
+			e += "Traceback: " + sdata
+		fileout.close()
+		fileref.close()
+		sys.exit(e)
+	finally:
+		fp2.close()
 
 	if not data['QUOTES'] and not data['NOTES']:
 		print "Document up-to-date."
@@ -192,18 +210,27 @@ if __name__ == '__main__':
 
 	notes_cnt = 0
 
-	m = StateMachine();
-	m.add_state(parse)
-	m.add_state(NOTES)
-	m.add_state(QUOTES)
-	m.add_state(process_quote)
-	m.add_state(process_note)
-	m.add_state(error, end_state=1)
-	m.add_state(eof, end_state=1)
-	m.set_start(parse)
-	m.run((fileref, ''))
-
-	fileout.close()
-	fileref.close()
+	try:
+		m = StateMachine();
+		m.add_state(parse)
+		m.add_state(NOTES)
+		m.add_state(QUOTES)
+		m.add_state(process_quote)
+		m.add_state(process_note)
+		m.add_state(error, end_state=1)
+		m.add_state(eof, end_state=1)
+		m.set_start(parse)
+		m.run((fileref, ''))
+	except:
+		trace = "Error injecting.\n\nTrace: \n"
+		trace += traceback.format_exc()
+	else:
+		trace = "Done injection."
+	finally:
+		fileout.close()
+		fileref.close()
+		sys.exit(trace)
+
+
 
 
diff --git a/parse/parse-skim.sh b/parse/parse-skim.sh
index 370a459..83e64ba 100755
--- a/parse/parse-skim.sh
+++ b/parse/parse-skim.sh
@@ -4,8 +4,8 @@ for i in *.pdf; do
     f=$i
 done
 
-if [[ -z '$f' ]]; then
-	echo "No pdf file in directory... Aborting.";
+if [[ -d '$f' ]]; then
+	echo "$f No pdf file in directory... Aborting.";
 	exit;
 fi
 
@@ -13,6 +13,11 @@ filename="${f%.*}"
 
 skimnotes get -format txt $f
 
+if [[ ! -f '$filename.txt' ]]; then
+	echo "No skim notes in pdf $f. Aborting.";
+	exit;
+fi
+
 parse-skim.py < "$filename.txt"
 
 rm $filename.txt
\ No newline at end of file