diff env/lib/python3.9/site-packages/galaxy/util/checkers.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/util/checkers.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,179 @@
+import bz2
+import gzip
+import re
+import tarfile
+import zipfile
+from io import (
+    BytesIO,
+    StringIO
+)
+
+from galaxy import util
+from galaxy.util.image_util import image_type
+
+HTML_CHECK_LINES = 100
+CHUNK_SIZE = 2 ** 15  # 32Kb
+HTML_REGEXPS = (
+    re.compile(r"<A\s+[^>]*HREF[^>]+>", re.I),
+    re.compile(r"<IFRAME[^>]*>", re.I),
+    re.compile(r"<FRAMESET[^>]*>", re.I),
+    re.compile(r"<META[\W][^>]*>", re.I),
+    re.compile(r"<SCRIPT[^>]*>", re.I),
+)
+
+
+def check_html(name, file_path=True):
+    """
+    Returns True if the file/string contains HTML code.
+    """
+    # Handles files if file_path is True or text if file_path is False
+    if file_path:
+        temp = open(name, encoding='utf-8')
+    else:
+        temp = StringIO(util.unicodify(name))
+    try:
+        for _ in range(HTML_CHECK_LINES):
+            line = temp.readline(CHUNK_SIZE)
+            if not line:
+                break
+            if any(regexp.search(line) for regexp in HTML_REGEXPS):
+                return True
+    except UnicodeDecodeError:
+        return False
+    finally:
+        temp.close()
+    return False
+
+
+def check_binary(name, file_path=True):
+    # Handles files if file_path is True or text if file_path is False
+    if file_path:
+        temp = open(name, "rb")
+    else:
+        temp = BytesIO(name)
+    try:
+        return util.is_binary(temp.read(1024))
+    finally:
+        temp.close()
+
+
+def check_gzip(file_path, check_content=True):
+    # This method returns a tuple of booleans representing ( is_gzipped, is_valid )
+    # Make sure we have a gzipped file
+    try:
+        with open(file_path, "rb") as temp:
+            magic_check = temp.read(2)
+        if magic_check != util.gzip_magic:
+            return (False, False)
+    except Exception:
+        return (False, False)
+    # We support some binary data types, so check if the compressed binary file is valid
+    # If the file is Bam, it should already have been detected as such, so we'll just check
+    # for sff format.
+    try:
+        with gzip.open(file_path, 'rb') as fh:
+            header = fh.read(4)
+        if header == b'.sff':
+            return (True, True)
+    except Exception:
+        return(False, False)
+
+    if not check_content:
+        return (True, True)
+
+    with gzip.open(file_path, mode='rb') as gzipped_file:
+        chunk = gzipped_file.read(CHUNK_SIZE)
+    # See if we have a compressed HTML file
+    if check_html(chunk, file_path=False):
+        return (True, False)
+    return (True, True)
+
+
+def check_bz2(file_path, check_content=True):
+    try:
+        with open(file_path, "rb") as temp:
+            magic_check = temp.read(3)
+        if magic_check != util.bz2_magic:
+            return (False, False)
+    except Exception:
+        return(False, False)
+
+    if not check_content:
+        return (True, True)
+
+    with bz2.BZ2File(file_path, mode='rb') as bzipped_file:
+        chunk = bzipped_file.read(CHUNK_SIZE)
+    # See if we have a compressed HTML file
+    if check_html(chunk, file_path=False):
+        return (True, False)
+    return (True, True)
+
+
+def check_zip(file_path, check_content=True, files=1):
+    if not zipfile.is_zipfile(file_path):
+        return (False, False)
+
+    if not check_content:
+        return (True, True)
+
+    chunk = None
+    for filect, member in enumerate(iter_zip(file_path)):
+        handle, name = member
+        chunk = handle.read(CHUNK_SIZE)
+        if chunk and check_html(chunk, file_path=False):
+            return (True, False)
+        if filect >= files:
+            break
+    return (True, True)
+
+
+def is_bz2(file_path):
+    is_bz2, is_valid = check_bz2(file_path, check_content=False)
+    return is_bz2
+
+
+def is_gzip(file_path):
+    is_gzipped, is_valid = check_gzip(file_path, check_content=False)
+    return is_gzipped
+
+
+def is_zip(file_path):
+    is_zipped, is_valid = check_zip(file_path, check_content=False)
+    return is_zipped
+
+
+def is_single_file_zip(file_path):
+    for i, _ in enumerate(iter_zip(file_path)):
+        if i > 1:
+            return False
+    return True
+
+
+def is_tar(file_path):
+    return tarfile.is_tarfile(file_path)
+
+
+def iter_zip(file_path):
+    with zipfile.ZipFile(file_path) as z:
+        for f in filter(lambda x: not x.endswith('/'), z.namelist()):
+            yield (z.open(f), f)
+
+
+def check_image(file_path):
+    """ Simple wrapper around image_type to yield a True/False verdict """
+    if image_type(file_path):
+        return True
+    return False
+
+
+__all__ = (
+    'check_binary',
+    'check_bz2',
+    'check_gzip',
+    'check_html',
+    'check_image',
+    'check_zip',
+    'is_gzip',
+    'is_bz2',
+    'is_zip',
+)