Add method to check a BinaryCIF file

Author: benmwebb

doc/modules/frontend.rst

@@ -41,6 +41,8 @@ The :mod:`saliweb.frontend` Python module
 
 .. autofunction:: check_mmcif
 
+.. autofunction:: check_bcif
+
 .. autofunction:: check_pdb
 
 .. autofunction:: pdb_code_exists

python/saliweb/frontend/__init__.py

@@ -516,7 +516,7 @@ class _AtomSiteHandler:
     def __init__(self):
         self.num_rows = 0
 
-    def __call__(self):
+    def __call__(self, cartn_x, cartn_y, cartn_z):
         self.num_rows += 1
 
 
@@ -547,6 +547,33 @@ def check_mmcif(filename, show_filename=None):
             "%s contains no _atom_site entries!" % cif_file)
 
 
+def check_bcif(filename, show_filename=None):
+    """Check that a BinaryCIF file really looks like an (atomic) BinaryCIF
+       file. If it does not, raise an :exc:`InputValidationError` exception.
+
+       :param str filename: The BinaryCIF file to check.
+       :param str show_filename: If provided, include this filename in any
+              error message to identify the BinaryCIF file (useful for services
+              that allow upload of multiple BinaryCIF files).
+    """
+    if show_filename:
+        bcif_file = "BinaryCIF file %s" % show_filename
+    else:
+        bcif_file = "BinaryCIF file"
+    ash = _AtomSiteHandler()
+    with open(filename, 'rb') as fh:
+        c = ihm.format_bcif.BinaryCifReader(
+            fh, category_handler={'_atom_site': ash})
+        try:
+            c.read_file()  # read first block
+        except Exception as err:
+            raise InputValidationError(
+                "Invalid %s uploaded: %s" % (bcif_file, str(err)))
+    if ash.num_rows == 0:
+        raise InputValidationError(
+            "%s contains no _atom_site entries!" % bcif_file)
+
+
 def check_pdb_or_mmcif(filename, show_filename=None):
     """Check that a PDB or mmCIF file really looks like an (atomic) PDB
        or mmCIF file.

test/pyfrontend/test_frontend.py

@@ -6,6 +6,8 @@
 import os
 import gzip
 import tempfile
+import struct
+import ihm.format_bcif
 import flask
 
 
@@ -27,6 +29,32 @@ def __init__(self):
     del flask.request
 
 
+def _add_msgpack(d, fh):
+    """Add `d` to filelike object `fh` in msgpack format"""
+    if isinstance(d, dict):
+        fh.write(struct.pack('>Bi', 0xdf, len(d)))
+        for key, val in d.items():
+            _add_msgpack(key, fh)
+            _add_msgpack(val, fh)
+    elif isinstance(d, list):
+        fh.write(struct.pack('>Bi', 0xdd, len(d)))
+        for val in d:
+            _add_msgpack(val, fh)
+    elif isinstance(d, str):
+        b = d.encode('utf8')
+        fh.write(struct.pack('>Bi', 0xdb, len(b)))
+        fh.write(b)
+    elif isinstance(d, bytes):
+        fh.write(struct.pack('>Bi', 0xc6, len(d)))
+        fh.write(d)
+    elif isinstance(d, int):
+        fh.write(struct.pack('>Bi', 0xce, d))
+    elif d is None:
+        fh.write(b'\xc0')
+    else:
+        raise TypeError("Cannot handle %s" % type(d))
+
+
 def make_test_pdb(tmpdir):
     os.mkdir(os.path.join(tmpdir, 'xy'))
     with gzip.open(os.path.join(tmpdir, 'xy', 'pdb1xyz.ent.gz'), 'wt') as fh:
@@ -265,6 +293,32 @@ def test_check_mmcif(self):
             self.assertRaises(saliweb.frontend.InputValidationError,
                               saliweb.frontend.check_pdb_or_mmcif, bad_cif)
 
+    def test_check_bcif(self):
+        """Test check_bcif"""
+        c = {'name': 'Cartn_x',
+             'mask': None,
+             'data': {'data': struct.pack('<2d', 1.0, 2.0),
+                      'encoding':
+                      [{'kind': 'ByteArray',
+                        'type': ihm.format_bcif._Float64}]}}
+        d = {'dataBlocks': [{'categories': [{'name': '_atom_site',
+                                             'columns': [c]}]}]}
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            good_bcif = os.path.join(tmpdir, 'good.bcif')
+            with open(good_bcif, 'wb') as fh:
+                _add_msgpack(d, fh)
+            bad_bcif = os.path.join(tmpdir, 'bad.bcif')
+            with open(bad_bcif, 'w') as fh:
+                fh.write('garbage')
+            saliweb.frontend.check_bcif(good_bcif)
+            saliweb.frontend.check_bcif(good_bcif, show_filename='good.bcif')
+            self.assertRaises(saliweb.frontend.InputValidationError,
+                              saliweb.frontend.check_bcif, bad_bcif)
+            self.assertRaises(saliweb.frontend.InputValidationError,
+                              saliweb.frontend.check_bcif, bad_bcif,
+                              show_filename='bad.bcif')
+
     def test_check_modeller_key(self):
         """Test check_modeller_key function"""
         class MockApp(object):