Working wrapper script

.dockerignore

@@ -0,0 +1 @@
+temp/

.gitignore

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+temp/

Dockerfile

@@ -64,12 +64,11 @@ ENV PATH="/usr/midas/MIDAS-1.3.2/scripts:${PATH}"
 
 # Add the run script to the PATH
 ADD run.py /usr/midas
-ADD helpers /usr/midas/helpers
+ADD lib /usr/midas/lib
 RUN cd /usr/midas && \
 	chmod +x run.py && \
 	ln -s /usr/midas/run.py /usr/bin/
 
-
 # Run tests and then remove the folder
 ADD tests /usr/midas/tests
 RUN bats /usr/midas/tests/ && rm -r /usr/midas/tests/

lib/exec_helpers.py

@@ -0,0 +1,130 @@
+#!/usr/bin/python
+"""Functions to help with execution of system commands."""
+
+import os
+import sys
+import json
+import shutil
+import logging
+import traceback
+import subprocess
+
+
+def align_reads(read_fp,               # FASTQ file path
+                db_fp,                 # Local path to DB
+                temp_folder,           # Folder for results
+                evalue=0.0001,
+                query_gencode=11,
+                threads=1):
+    """Align a set of reads with Paladin."""
+    pass
+
+
+def run_cmds(commands, retry=0, catchExcept=False):
+    """Run commands and write out the log, combining STDOUT & STDERR."""
+    logging.info("Commands:")
+    logging.info(' '.join(commands))
+    p = subprocess.Popen(commands,
+                         stdout=subprocess.PIPE,
+                         stderr=subprocess.STDOUT)
+    stdout, stderr = p.communicate()
+    exitcode = p.wait()
+    if stdout:
+        logging.info("Standard output of subprocess:")
+        for line in stdout.split('\n'):
+            logging.info(line)
+    if stderr:
+        logging.info("Standard error of subprocess:")
+        for line in stderr.split('\n'):
+            logging.info(line)
+
+    # Check the exit code
+    if exitcode != 0 and retry > 0:
+        msg = "Exit code {}, retrying {} more times".format(exitcode, retry)
+        logging.info(msg)
+        run_cmds(commands, retry=retry - 1)
+    elif exitcode != 0 and catchExcept:
+        msg = "Exit code was {}, but we will continue anyway"
+        logging.info(msg.format(exitcode))
+    else:
+        assert exitcode == 0, "Exit code {}".format(exitcode)
+
+
+def get_reference_database(ref_db, temp_folder):
+    """Get a reference database folder."""
+
+    # Get files from AWS S3
+    if ref_db.startswith('s3://'):
+        logging.info("Getting reference database from S3: " + ref_db)
+
+        # Save the database to the local temp folder
+        local_fp = os.path.join(temp_folder, ref_db.split('/')[-1] + "/")
+
+        assert os.path.exists(local_fp) is False
+
+        logging.info("Saving database to " + local_fp)
+        run_cmds([
+            'aws',
+            's3',
+            'sync',
+            '--quiet',
+            '--sse',
+            'AES256',
+            ref_db,
+            local_fp
+        ])
+
+        return local_fp
+
+    else:
+        # Treat the input as a local path
+        logging.info("Getting reference database from local path: " + ref_db)
+        assert os.path.exists(ref_db)
+
+        return ref_db
+
+
+def return_results(out, read_prefix, output_folder, temp_folder):
+    """Write out the final results as a JSON object."""
+    # Make a temporary file
+    temp_fp = os.path.join(temp_folder, read_prefix + '.json')
+    with open(temp_fp, 'wt') as fo:
+        json.dump(out, fo)
+
+    # Compress the output
+    run_cmds(['gzip', temp_fp])
+    temp_fp = temp_fp + '.gz'
+
+    if output_folder.startswith('s3://'):
+        # Copy to S3
+        run_cmds([
+            'aws',
+            's3',
+            'cp',
+            '--quiet',
+            '--sse',
+            'AES256',
+            temp_fp,
+            output_folder])
+        os.unlink(temp_fp)
+    else:
+        # Copy to local folder
+        run_cmds(['mv', temp_fp, output_folder])
+
+
+def exit_and_clean_up(temp_folder):
+    """Log the error messages and delete the temporary folder."""
+    # Capture the traceback
+    logging.info("There was an unexpected failure")
+    exc_type, exc_value, exc_traceback = sys.exc_info()
+    for line in traceback.format_tb(exc_traceback):
+        logging.info(line)
+
+    # Delete any files that were created for this sample
+    logging.info("Removing temporary folder: " + temp_folder)
+    shutil.rmtree(temp_folder)
+
+    # Exit
+    logging.info("Exit type: {}".format(exc_type))
+    logging.info("Exit code: {}".format(exc_value))
+    sys.exit(exc_value)