diff data_manager/data_manager_cat.py @ 0:f59e7e242bde draft

planemo upload commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_cat.py	Sun Nov 24 21:54:57 2019 -0500
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import json
+import os.path
+import subprocess
+import tarfile
+import tempfile
+import zipfile
+try:
+    # For Python 3.0 and later
+    from urllib.request import urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import urlopen
+
+
+def url_download(url, workdir):
+    file_path = os.path.join(workdir, 'download.dat')
+    src = None
+    dst = None
+    try:
+        src = urlopen(url)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    finally:
+        if src:
+            src.close()
+    if tarfile.is_tarfile(file_path):
+        fh = tarfile.open(file_path, 'r:*')
+    elif zipfile.is_zipfile(file_path):
+        fh = zipfile.ZipFile(file_path, 'r')
+    else:
+        return
+    fh.extractall(workdir)
+    os.remove(file_path)
+
+
+def cat_prepare(install_dir):
+    cmd = ['CAT', 'prepare' '--fresh', '-q']
+    cmd_stdout = tempfile.NamedTemporaryFile()
+    cmd_stderr = tempfile.NamedTemporaryFile()
+    return_code = subprocess.call(cmd, shell=True, cwd=install_dir,
+                                  stdout=cmd_stdout, stderr=cmd_stderr)
+    if return_code:
+        msg = "stdout:\n%s\nstderr:\n%s" % (cmd_stdout.read(),
+                                            cmd_stderr.read())
+        cmd_stdout.close()
+        cmd_stderr.close()
+        raise Exception('Error: (%s), returncode=%s %s'
+                        % (' '.join(cmd), return_code, msg))
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--config_file')
+    parser.add_argument('--install_path')
+    parser.add_argument('--db_url', default=None)
+    args = parser.parse_args()
+
+    if not os.path.exists(args.install_path):
+        os.makedirs(args.install_path)
+    if args.db_url:
+        url_download(args.db_url, args.install_path)
+    else:
+        cat_prepare(args.install_path)
+
+    cat_path = None
+    cat_db = None
+    tax_db = None
+    for root, dirs, files in os.walk(args.install_path):
+        for dname in dirs:
+            if dname.endswith('CAT_database'):
+                cat_db = dname
+            elif dname.endswith('taxonomy'):
+                tax_db = dname
+        if cat_db and tax_db:
+            cat_path = root
+            break
+
+    cat_dir = os.path.basename(cat_path)
+    # params = json.loads(open(args.config_file).read())
+    dm_dict = {}
+    dm_dict['data_tables'] = dm_dict.get('data_tables', {})
+    data_table = 'cat_database'
+    dm_dict['data_tables'][data_table]\
+        = dm_dict['data_tables'].get(data_table, [])
+    data_table_entry = dict(value=cat_dir, name=cat_dir,
+                            database_folder=os.path.join(cat_dir, cat_db),
+                            taxonomy_folder=os.path.join(cat_dir, tax_db))
+    dm_dict['data_tables'][data_table].append(data_table_entry)
+    # save info to json file
+    open(args.config_file, 'wb').write(json.dumps(dm_dict))
+
+
+if __name__ == "__main__":
+    main()