[elixir-cloud-aai#12] FileTransput.download_file()

TODO It's still using the host path. This has to be translated to a path inside the container.

tesk_core/transput_filer.py

@@ -13,6 +13,7 @@
 import logging
 import requests
 from exception import UnknownProtocol
+import shutil
 
 try:
     from urllib.parse import urlparse
@@ -127,21 +128,25 @@ def download_dir(self):
         return 1
 
 
+def getPath(url):
+
+    parsed_url = urlparse(url)
+
+    return parsed_url.path
+
+
 class FileTransput(Transput):
     def __init__(self, path, url, ftype):
         Transput.__init__(self, path, url, ftype)
 
     def download_file(self):
-        req = requests.get(self.url)
+
+        src = getPath(self.url)        
+        dst = self.path
 
-        if req.status_code < 200 or req.status_code >= 300:
-            logging.error('Got status code: %d', req.status_code)
-            logging.error(req.text)
-            return 1
-        logging.debug('OK, got status code: %d', req.status_code)
+        logging.debug(f"Copying {src} to {dst}")
+        shutil.copy(src, dst)
 
-        with open(self.path, 'wb') as file:
-            file.write(req.content)
         return 0
 
     def upload_file(self):
@@ -449,7 +454,7 @@ def process_file(ttype, filedata):
         logging.error('Could not determine protocol for url: "%s"', filedata['url'])
         return 1
 
-    trans = newTransput(filedata, scheme)
+    trans = newTransput(scheme)
 
     with trans(filedata['path'], filedata['url'], Type(filedata['type'])) as transfer:
         if ttype == 'inputs':
@@ -461,6 +466,14 @@ def process_file(ttype, filedata):
     return 0
 
 
+
+def logConfig(loglevel):
+
+    logging.basicConfig(format='%(asctime)s %(levelname)s: %(message)s', 
+                        datefmt='%m/%d/%Y %I:%M:%S', 
+                        level=loglevel,
+                        stream=sys.stdout)
+
 def main():
     parser = argparse.ArgumentParser(
         description='Filer script for down- and uploading files')
@@ -482,10 +495,7 @@ def main():
     else:
         loglevel = logging.ERROR
 
-    logging.basicConfig(
-        format='%(asctime)s %(levelname)s: %(message)s',
-        datefmt='%m/%d/%Y %I:%M:%S',
-        level=loglevel)
+    logConfig(loglevel)
 
     logging.info('Starting %s filer...', args.transputtype)
 

tests/FilerTest.py

@@ -1,11 +1,50 @@
 import unittest
-from transput_filer import newTransput, FTPTransput, HTTPTransput, FileTransput
+from transput_filer import newTransput, FTPTransput, HTTPTransput, FileTransput,\
+    process_file, logConfig, getPath
 from exception import UnknownProtocol
 from assertThrows import AssertThrowsMixin
+import logging
+from unittest.mock import patch
+
 
 
 class FilerTest(unittest.TestCase, AssertThrowsMixin):
+
+
+    @classmethod
+    def setUpClass(cls):
+
+        logConfig(logging.DEBUG)        # Doesn't work...
 
+
+    @patch('transput_filer.shutil.copy')
+    def test_process_file(self, copyMock):
+
+        filedata = {
+
+            "url": "file:///home/tfga/workspace/cwl-tes/tmphrtip1o8/md5",
+            "path": "/var/lib/cwl/stgda974802-fa81-4f0b-8fe4-341d5655af4b/md5",
+
+            "type": "FILE",  # File      = 'FILE'
+                             # Directory = 'DIRECTORY'
+
+            "name": "md5",
+            "description": "cwl_input:md5"
+        }
+
+        process_file('inputs', filedata)
+
+        copyMock.assert_called_once_with( '/home/tfga/workspace/cwl-tes/tmphrtip1o8/md5'
+                                        , '/var/lib/cwl/stgda974802-fa81-4f0b-8fe4-341d5655af4b/md5')
+
+
+    def test_getPath(self):
+
+        self.assertEquals( getPath('file:///home/tfga/workspace/cwl-tes/tmphrtip1o8/md5')
+                         ,                '/home/tfga/workspace/cwl-tes/tmphrtip1o8/md5')
+
+
+
     def test_newTransput(self):
 
         self.assertEquals(newTransput('ftp')   , FTPTransput)