Merge pull request #25 from common-workflow-language/ftp

Initial support for ftp locations

.travis.yml

@@ -16,5 +16,8 @@ script:
 after_failure:
   - echo "FUNNEL LOGS ----------"
   - cat ./tests/test_tmp/conformance_test_v1.0_*/funnel_log.txt
+branches:
+  only:
+    - master
 notifications:
   email: false

cwl_tes/ftp.py

@@ -0,0 +1,231 @@
+"""FTP support"""
+from __future__ import absolute_import
+
+import contextlib
+import fnmatch
+import ftplib
+import logging
+import netrc
+import glob
+import os
+from typing import List, Text  # noqa F401 # pylint: disable=unused-import
+
+from six import PY2
+from six.moves import urllib
+from schema_salad.ref_resolver import uri_file_path
+
+from cwltool.stdfsaccess import StdFsAccess
+from cwltool.loghandler import _logger
+
+
+def abspath(src, basedir):  # type: (Text, Text) -> Text
+    """http(s):, file:, ftp:, and plain path aware absolute path"""
+    scheme = urllib.parse.urlparse(src).scheme
+    if scheme == u"file":
+        apath = Text(uri_file_path(str(src)))
+    elif scheme:
+        return src
+    else:
+        if basedir.startswith(u"file://"):
+            apath = src if os.path.isabs(src) else basedir + '/' + src
+        else:
+            apath = src if os.path.isabs(src) else os.path.join(basedir, src)
+    return apath
+
+
+class FtpFsAccess(StdFsAccess):
+    """FTP access with upload."""
+    def __init__(self, basedir, cache=None):  # type: (Text) -> None
+        super(FtpFsAccess, self).__init__(basedir)
+        self.cache = cache or {}
+        self.netrc = None
+        try:
+            if 'HOME' in os.environ:
+                if os.path.exists(os.path.join(os.environ['HOME'], '.netrc')):
+                    self.netrc = netrc.netrc(
+                        os.path.join(os.environ['HOME'], '.netrc'))
+            elif os.path.exists(os.path.join(os.curdir, '.netrc')):
+                self.netrc = netrc.netrc(os.path.join(os.curdir, '.netrc'))
+        except netrc.NetrcParseError as err:
+            _logger.debug(err)
+
+    def _parse_url(self, url):
+        # type: (Text) -> Tuple[Optional[Text], Optional[Text]]
+        parse = urllib.parse.urlparse(url)
+        user = parse.username
+        passwd = parse.password
+        host = parse.netloc
+        path = parse.path
+        if parse.scheme == 'ftp':
+            if not user and self.netrc:
+                creds = self.netrc.authenticators(host)
+                if creds:
+                    user, _, passwd = creds
+        if not user:
+            user = "anonymous"
+            passwd = "anonymous@"
+        return host, user, passwd, path
+
+    def _connect(self, url):  # type: (Text) -> Optional[ftplib.FTP]
+        parse = urllib.parse.urlparse(url)
+        if parse.scheme == 'ftp':
+            host, user, passwd, _ = self._parse_url(url)
+            if (host, user, passwd) in self.cache:
+                if self.cache[(host, user, passwd)].pwd():
+                    return self.cache[(host, user, passwd)]
+            ftp = ftplib.FTP_TLS()
+            ftp.set_debuglevel(1 if _logger.isEnabledFor(logging.DEBUG) else 0)
+            ftp.connect(host)
+            ftp.login(user, passwd)
+            self.cache[(host, user, passwd)] = ftp
+            return ftp
+        return None
+
+    def _abs(self, p):  # type: (Text) -> Text
+        return abspath(p, self.basedir)
+
+    def glob(self, pattern):  # type: (Text) -> List[Text]
+        if not self.basedir.startswith("ftp:"):
+            return super(FtpFsAccess, self).glob(pattern)
+        return self._glob(pattern)
+
+    def _glob0(self, basename, basepath):
+        if basename == '':
+            if self.isdir(basepath):
+                return [basename]
+        else:
+            if self.isfile(self.join(basepath, basename)):
+                return [basename]
+        return []
+
+    def _glob1(self, pattern, basepath=None):
+        try:
+            names = self.listdir(basepath)
+        except ftplib.all_errors:
+            return []
+        if pattern[0] != '.':
+            names = filter(lambda x: x[0] != '.', names)
+        return fnmatch.filter(names, pattern)
+
+    def _glob(self, pattern):  # type: (Text) -> List[Text]
+        if pattern.endswith("/."):
+            pattern = pattern[:-1]
+        dirname, basename = pattern.rsplit('/', 1)
+        if not glob.has_magic(pattern):
+            if basename:
+                if self.exists(pattern):
+                    return [pattern]
+            else:  # Patterns ending in slash should match only directories
+                if self.isdir(dirname):
+                    return [pattern]
+            return []
+        if not dirname:
+            return self._glob1(basename)
+
+        dirs = self._glob(dirname)
+        if glob.has_magic(basename):
+            glob_in_dir = self._glob1
+        else:
+            glob_in_dir = self._glob0
+        results = []
+        for dirname in dirs:
+            results.extend(glob_in_dir(basename, dirname))
+        return results
+
+    def open(self, fn, mode):
+        if not fn.startswith("ftp:"):
+            return super(FtpFsAccess, self).open(fn, mode)
+        if 'r' in mode:
+            host, user, passwd, path = self._parse_url(fn)
+            handle = urllib.request.urlopen(
+                "ftp://{}:{}@{}/{}".format(user, passwd, host, path))
+            if PY2:
+                return contextlib.closing(handle)
+            return handle
+        raise Exception('Write mode FTP not implemented')
+
+    def exists(self, fn):  # type: (Text) -> bool
+        if not self.basedir.startswith("ftp:"):
+            return super(FtpFsAccess, self).exists(fn)
+        return self.isfile(fn) or self.isdir(fn)
+
+    def isfile(self, fn):  # type: (Text) -> bool
+        ftp = self._connect(fn)
+        if ftp:
+            try:
+                self.size(fn)
+                return True
+            except ftplib.all_errors:
+                return False
+        return super(FtpFsAccess, self).isfile(fn)