--- a/create_or_update_organism.py	Mon Dec 02 05:49:03 2019 -0500
+++ b/create_or_update_organism.py	Tue Apr 14 10:43:00 2020 -0400
@@ -2,10 +2,10 @@
 from __future__ import print_function
 
 import argparse
-import glob
 import json
 import logging
 import os
+import re
 import shutil
 import stat
 import subprocess
@@ -13,6 +13,7 @@
 import tarfile
 import tempfile
 import time
+from pathlib import Path
 
 from apollo import accessible_organisms
 from apollo.util import GuessOrg, OrgOrGuess
@@ -49,6 +50,23 @@
     return 'GALAXY_SHARED_DIR' not in os.environ or len(os.environ['GALAXY_SHARED_DIR'].lower().strip()) == 0
 
 
+def zip_data_dir(dataset_data_dir, tar):
+    tar.add(dataset_data_dir, arcname='./', recursive=False)
+    for r, d, f in os.walk(dataset_data_dir):
+        for file_name in f:
+            abs_file = os.path.join(r, file_name)
+            rel_dir = os.path.relpath(r, dataset_data_dir)
+            rel_file = os.path.join(rel_dir, file_name)
+            if not rel_file.startswith('./'):
+                rel_file = './' + rel_file
+            if os.path.islink(abs_file):
+                target = Path(abs_file).resolve().absolute().as_posix()
+                if re.match(r'.*/_metadata_files/[0-9]+/metadata_[0-9]+.dat', target):
+                    # This is a metadata file generated by galaxy, symlink would certainly be dead on remote host, resolve it
+                    abs_file = target
+            tar.add(abs_file, arcname=rel_file)
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
     parser.add_argument('jbrowse_src', help='Source JBrowse Data Directory')
@@ -136,8 +154,7 @@
             with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
                 with tarfile.open(archive.name, mode="w:gz") as tar:
                     dataset_data_dir = args.jbrowse_src
-                    for file in glob.glob(dataset_data_dir):
-                        tar.add(file, arcname=file.replace(dataset_data_dir, './'))
+                    zip_data_dir(dataset_data_dir, tar)
                     if IsBlatEnabled():
                         tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
                 data = wa.remote.update_organism(
@@ -177,8 +194,7 @@
             with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
                 with tarfile.open(archive.name, mode="w:gz") as tar:
                     dataset_data_dir = args.jbrowse_src
-                    for file in glob.glob(dataset_data_dir):
-                        tar.add(file, arcname=file.replace(dataset_data_dir, './'))
+                    zip_data_dir(dataset_data_dir, tar)
                     if IsBlatEnabled():
                         with tempfile.TemporaryDirectory() as empty_dir:
                             os.chmod(empty_dir, stat.S_IRUSR | stat.S_IXUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)