Permissions bugfix for guide design (#7)

* ensuring permissions for web access are set

* slightly more helpful error message

(fixes issue with tmp.fa not being written)

Author: helrick

Diff for: docker-compose.yaml

@@ -17,5 +17,7 @@ services:
             && ./setup.sh
             && python3 /var/www/html/src/setup/setup.py -r /var/www/html -g ${ORGANISM} -v ${ASSEMBLY} -fa2bit /var/www/html/bin/faToTwoBit -b /var/www/html/bin/ncbi-blast-2.7.1+/bin
             && /var/www/html/src/setup/enable_dicey.sh ${ORGANISM} ${ASSEMBLY}
+            && cd /var/www/html/src/installation
+            && sudo ./setPermissions.sh
             && sudo service apache2 start
             && tail -f /dev/null"

Diff for: src/guide-finder/core/get_sequence.py

@@ -33,7 +33,8 @@ def fetch_sequence(twobit_to_fa, chrom_coord, genome_twobit, output_fasta):
     except Exception as err:
         print(err)
 
-    if os.path.getsize(tmp_fasta) == 0:
+    if not os.path.isfile(tmp_fasta) or os.path.getsize(tmp_fasta) == 0:
+        print("twobitToFasta failed: "+" ".join([twobit_to_fa, seq_param, start_param, end_param, genome_twobit, tmp_fasta]))
         sys.exit("sequence is empty for given parameters. Please check your parameters again")
 
     with open(tmp_fasta,"r") as inp_fa, open(output_fasta,"w") as out_fa:

Diff for: src/installation/setPermissions.sh

@@ -1,5 +1,13 @@
-# need to make sure these files and directories can be run from the web
-cd ../..
+#!/bin/bash
+# script to ensure these files and directories can be run from the web
+
+curr_dir=${PWD##*/}
+if [ $curr_dir == "installation" ]; then
+    cd ../..
+else
+    echo "this script must be run from the installation folder"
+    exit
+fi
 
 sudo chgrp -R www-data config
 sudo chmod -R 755 config