Fixed relative imports for 'read_files' method.

nmrstarlib/__init__.py

@@ -40,6 +40,14 @@
     :class:`~nmrstarlib.translator.StarFileToPeakList` for conversion of NMR-STAR
     formatted files into peak list files using chemical shift values and assignment
     information.
+
+``fileio``
+    This module provides the :func:`~nmrstarlib.fileio.read_files` generator
+    to open files from different sources (single file/multiple files on a local 
+    machine, directory/archive of files, URL address of a file).
 """
 
-__version__ = "2.0.3"
+__version__ = "2.0.4"
+
+
+from .fileio import read_files

nmrstarlib/cli.py

@@ -8,13 +8,14 @@
     nmrstarlib -h | --help
     nmrstarlib --version
     nmrstarlib convert (<from_path> <to_path>) [--from_format=<format>] [--to_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose]
-    nmrstarlib csview <starfile_path> [--amino_acids=<aa>] [--atoms=<at>] [--csview_outfile=<path>] [--csview_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose]
+    nmrstarlib csview <starfile_path> [--amino_acids=<aa>] [--atoms=<at>] [--csview_outfile=<path>] [--csview_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose] [--show]
     nmrstarlib plsimulate (<from_path> <to_path> <spectrum>) [--from_format=<format>] [--to_format=<format>] [--plsplit=<%>] [--distribution=<func>] [--H=<value>] [--C=<value>] [--N=<value>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--spectrum_descriptions=<path>] [--verbose]
 
 Options:
     -h, --help                      Show this screen.
     --version                       Show version.
     --verbose                       Print what files are processing.
+    --show                          Display chemical shifts image generated by 'csview' command by default image viewer.
     --from_format=<format>          Input file format, available formats: nmrstar, json [default: nmrstar].
     --to_format=<format>            Output file format, available formats: nmrstar, json [default: json].
     --nmrstar_version=<version>     Version of NMR-STAR format to use, available: 2, 3 [default: 3].
@@ -64,8 +65,9 @@ def cli(cmdargs):
                                              amino_acids=aminoacids,
                                              atoms=atoms,
                                              filename=cmdargs["--csview_outfile"],
-                                             csview_format=cmdargs["--csview_format"])
-        chemshift_viewer.csview(view=True)
+                                             csview_format=cmdargs["--csview_format"],
+                                             nmrstar_version=cmdargs["--nmrstar_version"])
+        chemshift_viewer.csview(view=cmdargs["--show"])
 
     elif cmdargs["plsimulate"]:
         if cmdargs["--spectrum_descriptions"]:

nmrstarlib/converter.py

@@ -108,8 +108,7 @@
 import bz2
 import gzip
 
-from . import nmrstarlib
-
+from . import fileio
 
 class Converter(object):
     """Converter class to convert BMRB NMR-STAR files from NMR-STAR to JSON or from JSON to NMR-STAR format."""
@@ -135,7 +134,7 @@ def convert(self):
 
         if os.path.isdir(self.file_generator.from_path):
             self._many_to_many()
-        elif os.path.isfile(self.file_generator.from_path) or nmrstarlib.GenericFilePath.is_url(self.file_generator.from_path):
+        elif os.path.isfile(self.file_generator.from_path) or fileio.GenericFilePath.is_url(self.file_generator.from_path):
             if self.file_generator.from_path_compression in ("zip", "tar", "tar.gz", "tar.bz2"):
                 self._many_to_many()
             elif self.file_generator.from_path_compression in ("gz", "bz2"):

nmrstarlib/csviewer.py

@@ -10,8 +10,7 @@
 """
 
 from graphviz import Source
-from . import nmrstarlib
-
+from . import fileio
 
 class CSViewer(object):
     """Chemical Shifts Viewer uses :meth:`~nmrstarlib.nmrstarlib.StarFile.chem_shifts_by_residue`
@@ -74,7 +73,7 @@ def csview(self, view=False):
         :return: None
         :rtype: :py:obj:`None`
         """
-        for starfile in nmrstarlib.read_files(self.from_path):
+        for starfile in fileio.read_files(self.from_path):
             chains = starfile.chem_shifts_by_residue(amino_acids=self.amino_acids,
                                                      atoms=self.atoms,
                                                      nmrstar_version=self.nmrstar_version)

nmrstarlib/nmrstarlib.py

@@ -28,10 +28,6 @@
 import sys
 import os
 import io
-import zipfile
-import bz2
-import gzip
-import tarfile
 import pprint
 
 
@@ -47,13 +43,6 @@
 else:
     import json
 
-if sys.version_info.major == 3:
-    from urllib.request import urlopen
-    from urllib.parse import urlparse
-else:
-    from urllib2 import urlopen
-    from urlparse import urlparse
-
 try:
     from .cbmrblex import bmrblex
 except ImportError:
@@ -238,6 +227,7 @@ def _build_starfile(self, nmrstar_str):
                 print("Error: Invalid token {}".format(token), file=sys.stderr)
                 print("In _build_starfile except block", file=sys.stderr)
                 raise
+
             finally:
                 token = next(lexer)
         return self
@@ -317,7 +307,7 @@ def _build_loop(self, lexer):
         values = [OrderedDict(zip(fields, values[i:i + len(fields)])) for i in range(0, len(values), len(fields))]
         return fields, values
 
-    def print_starfile(self, f=sys.stdout, file_format="nmrstar", tw=3):
+    def print_file(self, f=sys.stdout, file_format="nmrstar", tw=3):
         """Print :class:`~nmrstarlib.nmrstarlib.StarFile` into a file or stdout.
 
         :param io.StringIO f: writable file-like stream.
@@ -420,7 +410,7 @@ def _to_nmrstar(self):
         :rtype: :py:class:`str`
         """
         nmrstar_str = io.StringIO()
-        self.print_starfile(nmrstar_str)
+        self.print_file(nmrstar_str)
         return nmrstar_str.getvalue()
 
     def _skip_saveframe(self, lexer):
@@ -540,169 +530,6 @@ def chem_shifts_by_residue(self, amino_acids=None, atoms=None, amino_acids_and_a
         return chains
 
 
-def _generate_filenames(sources):
-    """Generate filenames.
-
-    :param tuple sources: Sequence of strings representing path to file(s).
-    :return: Path to file(s).
-    :rtype: :py:class:`str`
-    """
-    for source in sources:
-        if os.path.isdir(source):
-            for path, dirlist, filelist in os.walk(source):
-                for fname in filelist:
-                    print("Processing...", fname)
-                    if GenericFilePath.is_compressed(fname):
-                        if VERBOSE:
-                            print("Skipping compressed file: {}".format(os.path.abspath(fname)))
-                        continue
-                    else:
-                        yield os.path.join(path, fname)
-        elif os.path.isfile(source):
-            yield source
-        elif source.isdigit():
-            yield BMRB_REST + source
-        elif GenericFilePath.is_url(source):
-            yield source
-        else:
-            raise TypeError("Unknown file source.")
-
-
-def _generate_handles(filenames):
-    """Open a sequence of filenames one at time producing file objects.
-    The file is closed immediately when proceeding to the next iteration.
-
-    :param generator filenames: Generator object that yields the path to each file, one at a time.
-    :return: Filehandle to be processed into a :class:`~nmrstarlib.nmrstarlib.StarFile` instance.
-    """
-    for fname in filenames:
-        if VERBOSE:
-            print("Processing file: {}".format(os.path.abspath(fname)))
-        path = GenericFilePath(fname)
-        for filehandle, source in path.open():
-            yield filehandle, source
-            filehandle.close()
-
-
-def read_files(*sources):
-    """Construct a generator that yields :class:`~nmrstarlib.nmrstarlib.StarFile` instances.
-
-    :param sources: One or more strings representing path to file(s).
-    :return: :class:`~nmrstarlib.nmrstarlib.StarFile` instance(s).
-    :rtype: :class:`~nmrstarlib.nmrstarlib.StarFile`
-    """
-    filenames = _generate_filenames(sources)
-    filehandles = _generate_handles(filenames)
-    for fh, source in filehandles:
-        starfile = StarFile(source)
-        starfile.read(fh)
-        yield starfile
-
-
-class GenericFilePath(object):
-    """`GenericFilePath` class knows how to open local files or files over URL."""
-
-    def __init__(self, path):
-        """Initialize path.
-
-        :param str path: String representing a path to local file(s) or valid URL address of file(s).
-        """
-        self.path = path
-
-    def open(self):
-        """Generator that opens and yields filehandles using appropriate facilities:
-        test if path represents a local file or file over URL, if file is compressed
-        or not.
-
-        :return: Filehandle to be processed into a :class:`~nmrstarlib.nmrstarlib.StarFile` instance.
-        """
-        is_url = self.is_url(self.path)
-        compressiontype = self.is_compressed(self.path)
-
-        if not compressiontype:
-            if is_url:
-                filehandle = urlopen(self.path)
-            else:
-                filehandle = open(self.path, "r")
-            source = self.path
-            yield filehandle, source
-            filehandle.close()
-
-        elif compressiontype:
-            if is_url:
-                response = urlopen(self.path)
-                path = response.read()
-                response.close()
-            else:
-                path = self.path
-
-            if compressiontype == "zip":
-                ziparchive = zipfile.ZipFile(io.BytesIO(path), "r") if is_url else zipfile.ZipFile(path)
-                for name in ziparchive.infolist():
-                    if not name.filename.endswith("/"):
-                        filehandle = ziparchive.open(name)
-                        source = self.path + "/" + name.filename
-                        yield filehandle, source
-                        filehandle.close()
-
-            elif compressiontype in ("tar", "tar.bz2", "tar.gz"):
-                tararchive = tarfile.open(fileobj=io.BytesIO(path)) if is_url else tarfile.open(path)
-                for name in tararchive:
-                    if name.isfile():
-                        filehandle = tararchive.extractfile(name)
-                        source = self.path + "/" + name.name
-                        yield filehandle, source
-                        filehandle.close()
-
-            elif compressiontype == "bz2":
-                filehandle = bz2.BZ2File(io.BytesIO(path)) if is_url else bz2.BZ2File(path)
-                source = self.path
-                yield filehandle, source
-                filehandle.close()
-
-            elif compressiontype == "gz":
-                filehandle = gzip.open(io.BytesIO(path)) if is_url else gzip.open(path)
-                source = self.path
-                yield filehandle, source
-                filehandle.close()
-
-    @staticmethod
-    def is_compressed(path):
-        """Test if path represents compressed file(s).
-
-        :param str path: Path to file(s).
-        :return: String specifying compression type if compressed, "" otherwise.
-        :rtype: :py:class:`str`
-        """
-        if path.endswith(".zip"):
-            return "zip"
-        elif path.endswith(".tar.gz"):
-            return "tar.gz"
-        elif path.endswith(".tar.bz2"):
-            return "tar.bz2"
-        elif path.endswith(".gz"):
-            return "gz"
-        elif path.endswith(".bz2"):
-            return "bz2"
-        elif path.endswith(".tar"):
-            return "tar"
-        return ""
-
-    @staticmethod
-    def is_url(path):
-        """Test if path represents a valid URL.
-
-        :param str path: Path to file.
-        :return: True if path is valid url string, False otherwise.
-        :rtype: :py:obj:`True` or :py:obj:`False`
-        """
-        try:
-            parse_result = urlparse(path)
-            return all((parse_result.scheme, parse_result.netloc, parse_result.path))
-        except ValueError:
-            return False
-
-
 class InvalidToken(Exception):
     def __init__(self, value):
         self.parameter = value

nmrstarlib/translator.py

@@ -14,6 +14,7 @@
 import itertools
 
 from . import nmrstarlib
+from . import fileio
 from . import plsimulator
 
 
@@ -32,8 +33,8 @@ def __init__(self, from_path, to_path, from_format=None, to_format=None):
         self.to_path = to_path
         self.from_format = from_format
         self.to_format = to_format
-        self.from_path_compression = nmrstarlib.GenericFilePath.is_compressed(from_path)
-        self.to_path_compression = nmrstarlib.GenericFilePath.is_compressed(to_path)
+        self.from_path_compression = fileio.GenericFilePath.is_compressed(from_path)
+        self.to_path_compression = fileio.GenericFilePath.is_compressed(to_path)
 
     def __iter__(self):
         """Abstract iterator must be implemented in a subclass."""
@@ -62,7 +63,7 @@ def __iter__(self):
         :return: instance of :class:`~nmrstarlib.nmrstarlib.StarFile` object instance.
         :rtype: :class:`~nmrstarlib.nmrstarlib.StarFile`
         """
-        for starfile in nmrstarlib.read_files(self.from_path):
+        for starfile in fileio.read_files(self.from_path):
             yield starfile
 
 
@@ -248,7 +249,7 @@ def __iter__(self):
         :return: instance of :class:`~nmrstarlib.plsimulator.PeakList` object instance.
         :rtype: :class:`~nmrstarlib.plsimulator.PeakList`
         """
-        for starfile in nmrstarlib.read_files(self.from_path):
+        for starfile in fileio.read_files(self.from_path):
             chains = starfile.chem_shifts_by_residue(amino_acids_and_atoms=self.spectrum.amino_acids_and_atoms,
                                                      nmrstar_version=self.nmrstar_version)