X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/bd86112ffba029e0f2c29c7d12ae6192e4097e18..441ef97e93a951b349356df96d8a6ef604c6cab7:/sdk/python/arvados/util.py

diff --git a/sdk/python/arvados/util.py b/sdk/python/arvados/util.py
index 0889ffcddd..3f50553c4b 100644
--- a/sdk/python/arvados/util.py
+++ b/sdk/python/arvados/util.py
@@ -1,20 +1,33 @@
 import fcntl
 import hashlib
+import httplib2
 import os
 import re
 import subprocess
 import errno
 import sys
-from arvados.collection import *
+
+import arvados
+from arvados.collection import CollectionReader
 
 HEX_RE = re.compile(r'^[0-9a-fA-F]+$')
 
+keep_locator_pattern = re.compile(r'[0-9a-f]{32}\+\d+(\+\S+)*')
+signed_locator_pattern = re.compile(r'[0-9a-f]{32}\+\d+(\+\S+)*\+A\S+(\+\S+)*')
+portable_data_hash_pattern = re.compile(r'[0-9a-f]{32}\+\d+')
+uuid_pattern = re.compile(r'[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}')
+collection_uuid_pattern = re.compile(r'[a-z0-9]{5}-4zz18-[a-z0-9]{15}')
+group_uuid_pattern = re.compile(r'[a-z0-9]{5}-j7d0g-[a-z0-9]{15}')
+user_uuid_pattern = re.compile(r'[a-z0-9]{5}-tpzed-[a-z0-9]{15}')
+link_uuid_pattern = re.compile(r'[a-z0-9]{5}-o0j2j-[a-z0-9]{15}')
+manifest_pattern = re.compile(r'((\S+)( +[a-f0-9]{32}(\+\d+)(\+\S+)*)+( +\d+:\d+:\S+)+$)+', flags=re.MULTILINE)
+
 def clear_tmpdir(path=None):
     """
     Ensure the given directory (or TASK_TMPDIR if none given)
     exists and is empty.
     """
-    if path == None:
+    if path is None:
         path = arvados.current_task().tmpdir
     if os.path.exists(path):
         p = subprocess.Popen(['rm', '-rf', path])
@@ -32,7 +45,7 @@ def run_command(execargs, **kwargs):
     p = subprocess.Popen(execargs, **kwargs)
     stdoutdata, stderrdata = p.communicate(None)
     if p.returncode != 0:
-        raise errors.CommandFailedError(
+        raise arvados.errors.CommandFailedError(
             "run_command %s exit %d:\n%s" %
             (execargs, p.returncode, stderrdata))
     return stdoutdata, stderrdata
@@ -97,7 +110,7 @@ def tarball_extract(tarball, path):
             elif re.search('\.tar$', f.name()):
                 p = tar_extractor(path, '')
             else:
-                raise errors.AssertionError(
+                raise arvados.errors.AssertionError(
                     "tarball_extract cannot handle filename %s" % f.name())
             while True:
                 buf = f.read(2**20)
@@ -108,10 +121,10 @@ def tarball_extract(tarball, path):
             p.wait()
             if p.returncode != 0:
                 lockfile.close()
-                raise errors.CommandFailedError(
+                raise arvados.errors.CommandFailedError(
                     "tar exited %d" % p.returncode)
         os.symlink(tarball, os.path.join(path, '.locator'))
-    tld_extracts = filter(lambda f: f != '.locator', os.listdir(path))
+    tld_extracts = [f for f in os.listdir(path) if f != '.locator']
     lockfile.close()
     if len(tld_extracts) == 1:
         return os.path.join(path, tld_extracts[0])
@@ -152,7 +165,7 @@ def zipball_extract(zipball, path):
 
         for f in CollectionReader(zipball).all_files():
             if not re.search('\.zip$', f.name()):
-                raise errors.NotImplementedError(
+                raise arvados.errors.NotImplementedError(
                     "zipball_extract cannot handle filename %s" % f.name())
             zip_filename = os.path.join(path, os.path.basename(f.name()))
             zip_file = open(zip_filename, 'wb')
@@ -173,11 +186,11 @@ def zipball_extract(zipball, path):
             p.wait()
             if p.returncode != 0:
                 lockfile.close()
-                raise errors.CommandFailedError(
+                raise arvados.errors.CommandFailedError(
                     "unzip exited %d" % p.returncode)
             os.unlink(zip_filename)
         os.symlink(zipball, os.path.join(path, '.locator'))
-    tld_extracts = filter(lambda f: f != '.locator', os.listdir(path))
+    tld_extracts = [f for f in os.listdir(path) if f != '.locator']
     lockfile.close()
     if len(tld_extracts) == 1:
         return os.path.join(path, tld_extracts[0])
@@ -237,7 +250,7 @@ def collection_extract(collection, path, files=[], decompress=True):
                     outfile.write(buf)
                 outfile.close()
     if len(files_got) < len(files):
-        raise errors.AssertionError(
+        raise arvados.errors.AssertionError(
             "Wanted files %s but only got %s from %s" %
             (files, files_got,
              [z.name() for z in CollectionReader(collection).all_files()]))
@@ -292,19 +305,37 @@ def stream_extract(stream, path, files=[], decompress=True):
                 outfile.write(buf)
             outfile.close()
     if len(files_got) < len(files):
-        raise errors.AssertionError(
+        raise arvados.errors.AssertionError(
             "Wanted files %s but only got %s from %s" %
             (files, files_got, [z.name() for z in stream.all_files()]))
     lockfile.close()
     return path
 
-def listdir_recursive(dirname, base=None):
+def listdir_recursive(dirname, base=None, max_depth=None):
+    """listdir_recursive(dirname, base, max_depth)
+
+    Return a list of file and directory names found under dirname.
+
+    If base is not None, prepend "{base}/" to each returned name.
+
+    If max_depth is None, descend into directories and return only the
+    names of files found in the directory tree.
+
+    If max_depth is a non-negative integer, stop descending into
+    directories at the given depth, and at that point return directory
+    names instead.
+
+    If max_depth==0 (and base is None) this is equivalent to
+    sorted(os.listdir(dirname)).
+    """
     allfiles = []
     for ent in sorted(os.listdir(dirname)):
         ent_path = os.path.join(dirname, ent)
         ent_base = os.path.join(base, ent) if base else ent
-        if os.path.isdir(ent_path):
-            allfiles += listdir_recursive(ent_path, ent_base)
+        if os.path.isdir(ent_path) and max_depth != 0:
+            allfiles += listdir_recursive(
+                ent_path, base=ent_base,
+                max_depth=(max_depth-1 if max_depth else None))
         else:
             allfiles += [ent_base]
     return allfiles
@@ -321,8 +352,8 @@ def is_hex(s, *length_args):
     """
     num_length_args = len(length_args)
     if num_length_args > 2:
-        raise ArgumentError("is_hex accepts up to 3 arguments ({} given)".
-                            format(1 + num_length_args))
+        raise arvados.errors.ArgumentError(
+            "is_hex accepts up to 3 arguments ({} given)".format(1 + num_length_args))
     elif num_length_args == 2:
         good_len = (length_args[0] <= len(s) <= length_args[1])
     elif num_length_args == 1:
@@ -331,13 +362,34 @@ def is_hex(s, *length_args):
         good_len = True
     return bool(good_len and HEX_RE.match(s))
 
-def list_all(fn, **kwargs):
+def list_all(fn, num_retries=0, **kwargs):
+    # Default limit to (effectively) api server's MAX_LIMIT
+    kwargs.setdefault('limit', sys.maxsize)
     items = []
     offset = 0
-    items_available = sys.maxint
+    items_available = sys.maxsize
     while len(items) < items_available:
-        c = fn(offset=offset, **kwargs).execute()
+        c = fn(offset=offset, **kwargs).execute(num_retries=num_retries)
         items += c['items']
         items_available = c['items_available']
         offset = c['offset'] + len(c['items'])
     return items
+
+def ca_certs_path(fallback=httplib2.CA_CERTS):
+    """Return the path of the best available CA certs source.
+
+    This function searches for various distribution sources of CA
+    certificates, and returns the first it finds.  If it doesn't find any,
+    it returns the value of `fallback` (httplib2's CA certs by default).
+    """
+    for ca_certs_path in [
+        # Arvados specific:
+        '/etc/arvados/ca-certificates.crt',
+        # Debian:
+        '/etc/ssl/certs/ca-certificates.crt',
+        # Red Hat:
+        '/etc/pki/tls/certs/ca-bundle.crt',
+        ]:
+        if os.path.exists(ca_certs_path):
+            return ca_certs_path
+    return fallback