update output file handling

.osparc/metadata.yml

@@ -33,5 +33,5 @@ outputs:
     description: path to the converted file
     type: data:*/*
     fileToKeyMap:
-      data.json: output_1
+      output.zip: output_1
 

docker-compose.yml

@@ -20,8 +20,8 @@ services:
           file","description":"path of file to be converted","type":"data:*/*"},"input_2":{"displayOrder":2.0,"label":"target
           format","description":"required format of the output file","type":"ref_contentSchema","contentSchema":{"title":"target_format","default":"json","enum":["csv","json","yaml","xls","xlsx","nwb","parquet","feather","pkl","xml","toml","h5","hdf5"]}}}}'
         io.simcore.outputs: '{"outputs":{"output_1":{"displayOrder":1.0,"label":"converted
-          file","description":"path to the converted file","type":"data:*/*","fileToKeyMap":{"data.json":"output_1"}}}}'
-        org.label-schema.build-date: 2024-08-11T20:55:08+0000
+          file","description":"path to the converted file","type":"data:*/*","fileToKeyMap":{"output.zip":"output_1"}}}}'
+        org.label-schema.build-date: 2024-08-12T07:47:35+0000
         org.label-schema.schema-version: '1.0'
         org.label-schema.vcs-ref: ''
         org.label-schema.vcs-url: ''

service.cli/execute.sh

@@ -44,15 +44,17 @@ echo "PWD folder content:"
 ls -al
 
 # display the contents of log_output_filepath.txt
-echo "Content of log_output_filepath.txt:"
-echo "$(cat log_output_filepath.txt)"
+# echo "Content of log_output_filepath.txt:"
+# echo "$(cat log_output_filepath.txt)"
 
-cp "$(cat log_output_filepath.txt)" $OUTPUT_FOLDER
+# cp "$(cat log_output_filepath.txt)" $OUTPUT_FOLDER
 # echo "TEST DATA" > $OUTPUT_FOLDER/outputs.txt
 
+cp output.zip $OUTPUT_FOLDER
+
 #TODO: Replace following
-cat > "${OUTPUT_FOLDER}"/outputs.json << EOF
-{
-    "output_1":"$(cat log_output_filepath.txt)"
-}
-EOF
+# cat > "${OUTPUT_FOLDER}"/outputs.json << EOF
+# {
+#     "output_1":"$(cat log_output_filepath.txt)"
+# }
+# EOF

src/file_format_converter/main.py

@@ -1,4 +1,6 @@
 import argparse
+import os
+import zipfile
 
 import pandas as pd
 import json
@@ -9,7 +11,6 @@
 import pickle
 import xml.etree.ElementTree as ET
 import toml
-import os
 
 class FileConverter:
     def __init__(self, input_file):
@@ -108,9 +109,13 @@ def convert(self, output_file):
         self.read_file()
         self.write_file(output_file)
         print(f"Converted {self.input_file} to {output_file} successfully.")
-        # write output file path to a file
-        with open('log_output_filepath.txt', 'w') as f:
-            f.write(output_file)
+        # now create a zip of the output file as output.zip
+        with zipfile.ZipFile('output.zip', 'w') as z:
+            z.write(output_file)
+        print(f"Zipped {output_file} to output.zip successfully.")
+        # # write output file path to a file
+        # with open('log_output_filepath.txt', 'w') as f:
+        #     f.write(output_file)
 
 # Example Usage
 if __name__ == "__main__":