pynmrstar 3.3.5__pp310-pypy310_pp73-macosx_11_0_arm64.whl

pynmrstar/__init__.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+
+"""This module provides :py:class:`pynmrstar.Entry`, :py:class:`pynmrstar.Saveframe`,
+   :py:class:`pynmrstar.Loop`, and :py:class:`pynmrstar.Schema` objects.
+
+It also provides some utility functions in :py:obj:`pynmrstar.utils`
+
+Use python's built in help function for documentation."""
+
+import decimal as _decimal
+import logging
+import os
+
+try:
+    import cnmrstar
+except ImportError:
+    try:
+        import pynmrstar.cnmrstar as cnmrstar
+    except ImportError:
+        if os.environ.get('READTHEDOCS'):
+            cnmrstar = None
+        else:
+            raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')
+
+from pynmrstar import utils
+from pynmrstar._internal import __version__, min_cnmrstar_version
+from pynmrstar.entry import Entry
+from pynmrstar.loop import Loop
+from pynmrstar.parser import Parser as _Parser
+from pynmrstar.saveframe import Saveframe
+from pynmrstar.schema import Schema
+import pynmrstar.definitions as definitions
+
+if cnmrstar:
+    if "version" not in dir(cnmrstar):
+        raise ImportError(f"Could not determine the version of cnmrstar installed, and version {min_cnmrstar_version} or "
+                          "greater is required.")
+    if cnmrstar.version() < min_cnmrstar_version:
+        raise ImportError("The version of the cnmrstar module installed does not meet the requirements. As this should be "
+                          f"handled automatically, there may be an issue with your installation. Version installed: "
+                          f"{cnmrstar.version()}. Version required: {min_cnmrstar_version}")
+
+# Set up logging
+logger = logging.getLogger('pynmrstar')
+
+# This makes sure that when decimals are printed a lower case "e" is used
+_decimal.getcontext().capitals = 0
+
+del loop
+del entry
+del saveframe
+del schema
+del parser
+
+__all__ = ['Loop', 'Saveframe', 'Entry', 'Schema', 'definitions', 'utils', '__version__', 'exceptions', 'cnmrstar']

pynmrstar/_internal.py

@@ -0,0 +1,292 @@
+import decimal
+import json
+import logging
+import os
+import time
+import zlib
+from datetime import date
+from gzip import GzipFile
+from io import StringIO, BytesIO
+from typing import Dict, Union, IO, List, Tuple
+from urllib.error import HTTPError, URLError
+from urllib.request import urlopen, Request
+
+import pynmrstar
+
+__version__: str = "3.3.5"
+min_cnmrstar_version: str = "3.2.0"
+
+# If we have requests, open a session to reuse for the duration of the program run
+try:
+    from requests import session as _requests_session
+    # This replaces the urllib HTTPError if we have requests
+    from requests.exceptions import HTTPError, ConnectionError
+    _session = _requests_session()
+except ModuleNotFoundError:
+    _session = None
+
+logger = logging.getLogger('pynmrstar')
+
+
+# noinspection PyDefaultArgument
+def _get_comments(_comment_cache: Dict[str, Dict[str, str]] = {}) -> Dict[str, Dict[str, str]]:
+    """ Loads the comments that should be placed in written files.
+
+    The default argument is mutable on purpose, as it is used as a cache for memoization."""
+
+    # Comment dictionary already exists
+    if _comment_cache:
+        return _comment_cache
+
+    file_to_load = os.path.join(os.path.dirname(os.path.realpath(__file__)))
+    file_to_load = os.path.join(file_to_load, "reference_files/comments.str")
+
+    # The import needs to be here to avoid import errors due to circular imports
+    from pynmrstar.entry import Entry
+    try:
+        comment_entry = Entry.from_file(file_to_load)
+    except IOError:
+        # Load the comments from Github if we can't find them locally
+        try:
+            logger.warning('Could not load comments from disk. Loading from web...')
+            comment_entry = Entry.from_file(_interpret_file(pynmrstar.definitions.COMMENT_URL))
+        except Exception:
+            logger.exception('Could not load comments from web. No comments will be shown.')
+            # No comments will be printed
+            return {}
+
+    # Load the comments
+    comment_records = comment_entry[0][0].get_tag(["category", "comment", "every_flag"])
+    comment_map = {'N': False, 'Y': True}
+    for comment in comment_records:
+        if comment[1] != ".":
+            _comment_cache[comment[0]] = {'comment': comment[1].rstrip() + "\n\n",
+                                          'every_flag': comment_map[comment[2]]}
+
+    return _comment_cache
+
+
+def _json_serialize(obj: object) -> str:
+    """JSON serializer for objects not serializable by default json code"""
+
+    # Serialize datetime.date objects by calling str() on them
+    if isinstance(obj, (date, decimal.Decimal)):
+        return str(obj)
+    raise TypeError("Type not serializable: %s" % type(obj))
+
+
+def _get_url_reliably(url: str, wait_time: float = 10, raw: bool = False, timeout: int = 10, retries: int = 2):
+    """ Attempts to load data from a URL, retrying the specified number of times with an exponential
+    backoff if rate limited. Fails immediately on 4xx errors that are not 403."""
+
+    global _session
+
+    # If using Requests
+    if _session:
+        try:
+            response = _session.get(url, timeout=timeout,
+                                    headers={'Application': f'PyNMRSTAR {__version__}'})
+        except ConnectionError:
+            _session = _requests_session()
+            try:
+                response = _session.get(url, timeout=timeout,
+                                        headers={'Application': f'PyNMRSTAR {__version__}'})
+            except ConnectionError:
+                raise HTTPError("A ConnectionError was thrown during an attempt to load the entry.")
+
+        # We are rate limited - sleep and try again
+        if response.status_code == 403:
+            if retries > 0:
+                logger.warning(f'We were rate limited. Sleeping for {wait_time} seconds.')
+                time.sleep(wait_time)
+                return _get_url_reliably(url, wait_time=wait_time*2, raw=raw, timeout=timeout,
+                                         retries=retries - 1)
+            else:
+                raise HTTPError("Continued to receive 403 (forbidden, due to rate limit) after multiple wait times.") \
+                    from None
+        if response.status_code == 404:
+            raise KeyError(f"Server returned 404.") from None
+        response.raise_for_status()
+        if raw:
+            return response.content
+        else:
+            return response.text
+    else:
+        # Use the built in library
+        try:
+            req = Request(url)
+            req.add_header('Application', f'PyNMRSTAR {__version__}')
+            url_request = urlopen(req, timeout=timeout)
+            serialized_ent = url_request.read()
+            url_request.close()
+
+        except HTTPError as err:
+            if err.code == 404:
+                raise KeyError(f"Server returned 404.") from None
+            # We are rate limited - sleep and try again
+            elif err.code == 403:
+                if retries > 0:
+                    logger.warning(f'We were rate limited. Sleeping for {wait_time} seconds.')
+                    time.sleep(wait_time)
+                    return _get_url_reliably(url, wait_time=wait_time * 2, raw=raw, timeout=timeout,
+                                             retries=retries - 1)
+                else:
+                    raise HTTPError("Continued to receive 403 (forbidden, due to rate limit) after multiple wait "
+                                    "times.") from None
+            else:
+                raise err
+        if raw:
+            return serialized_ent
+        else:
+            return serialized_ent.decode()
+
+
+def _get_entry_from_database(entry_num: Union[str, int],
+                             convert_data_types: bool = False,
+                             schema: 'pynmrstar.Schema' = None) -> 'pynmrstar.Entry':
+    """ Fetches an entry from the API (or falls back to the FTP site) in
+    as reliable and robust a way as possible. Used by Entry.from_database(). """
+
+    entry_num = str(entry_num).lower()
+    if entry_num.startswith("bmr"):
+        entry_num = entry_num[3:]
+
+    # Try to load the entry using JSON
+
+    entry_url: str = (pynmrstar.definitions.API_URL + "/entry/%s?format=zlib") % entry_num
+
+    try:
+        serialized_ent = _get_url_reliably(entry_url, raw=True, retries=2)
+        json_data = json.loads(zlib.decompress(serialized_ent).decode())
+        if "error" in json_data:
+            raise RuntimeError('Something wrong with API response.')
+        ent = pynmrstar.Entry.from_json(json_data)
+    except (HTTPError, ConnectionError, RuntimeError):
+        # Can't fall back to FTP for chemcomps
+        if entry_num.startswith("chemcomp"):
+            raise IOError("Unable to load that chemcomp from the API.")
+
+        # We're going to try again from the FTP
+        logger.warning('Failed to download entry from the API, trying again from the FTP site.')
+        if "bmse" in entry_num or "bmst" in entry_num:
+            url = f"{pynmrstar.definitions.FTP_URL}/metabolomics/entry_directories/{entry_num}/{entry_num}.str"
+        else:
+            url = f"{pynmrstar.definitions.FTP_URL}/entry_directories/bmr{entry_num}/bmr{entry_num}_3.str"
+        try:
+            # Use a longer timeout for the timeout
+            entry_content = _get_url_reliably(url, raw=False, timeout=20, retries=1)
+            ent = pynmrstar.Entry.from_string(entry_content)
+        except HTTPError:
+            raise IOError(f"Entry {entry_num} does not exist in the public database.") from None
+        except URLError:
+            raise IOError("You don't appear to have an active internet connection. Cannot fetch entry.") from None
+
+    except KeyError:
+        raise IOError(f"Entry {entry_num} does not exist in the public database.") from None
+
+    # Update the entry source
+    ent.source = f"from_database({entry_num})"
+    for each_saveframe in ent:
+        each_saveframe.source = ent.source
+        for each_loop in each_saveframe:
+            each_loop.source = ent.source
+
+    if convert_data_types:
+        schema = pynmrstar.utils.get_schema(schema)
+        for each_saveframe in ent:
+            for tag in each_saveframe.tags:
+                cur_tag = each_saveframe.tag_prefix + "." + tag[0]
+                tag[1] = schema.convert_tag(cur_tag, tag[1])
+            for loop in each_saveframe:
+                for row in loop.data:
+                    for pos in range(0, len(row)):
+                        category = loop.category + "." + loop.tags[pos]
+                        row[pos] = schema.convert_tag(category, row[pos])
+
+    return ent
+
+
+def _interpret_file(the_file: Union[str, IO]) -> StringIO:
+    """Helper method returns some sort of object with a read() method.
+    the_file could be a URL, a file location, a file object, or a
+    gzipped version of any of the above."""
+
+    if hasattr(the_file, 'read'):
+        read_data: Union[bytes, str] = the_file.read()
+        if type(read_data) == bytes:
+            buffer: BytesIO = BytesIO(read_data)
+        elif type(read_data) == str:
+            buffer = BytesIO(read_data.encode())
+        else:
+            raise IOError("What did your file object return when .read() was called on it?")
+    elif isinstance(the_file, str):
+        if the_file.startswith("http://") or the_file.startswith("https://") or the_file.startswith("ftp://"):
+            buffer = BytesIO(_get_url_reliably(the_file, raw=True, retries=0))
+        else:
+            with open(the_file, 'rb') as read_file:
+                buffer = BytesIO(read_file.read())
+    else:
+        raise ValueError("Cannot figure out how to interpret the file you passed.")
+
+    # Decompress the buffer if we are looking at a gzipped file
+    try:
+        gzip_buffer = GzipFile(fileobj=buffer)
+        gzip_buffer.readline()
+        gzip_buffer.seek(0)
+        buffer = BytesIO(gzip_buffer.read())
+    # Apparently we are not looking at a gzipped file
+    except (IOError, AttributeError, UnicodeDecodeError):
+        pass
+
+    buffer.seek(0)
+    return StringIO(buffer.read().decode().replace("\r\n", "\n").replace("\r", "\n"))
+
+
+def get_clean_tag_list(item: Union[str, List[str], Tuple[str]]) -> List[Dict[str, str]]:
+    """ Converts the provided item to a list of dictionaries of
+    {
+     formatted -> just the lower case tag name (category stripped)
+     original -> whatever was provided, completely unmodified
+    }"""
+
+    if not isinstance(item, (str, list, tuple)):
+        raise ValueError('Invalid object provided. Only a tag name (str), or list of tags (list or tuple)'
+                         ' are valid inputs to this function.')
+
+    if isinstance(item, list):
+        tag_list: List[str] = item
+    elif isinstance(item, tuple):
+        tag_list = list(item)
+    elif isinstance(item, str):
+        tag_list = [item]
+    else:
+        raise ValueError(f'The value you provided was not a string, list, or tuple. Item: {repr(item)}')
+
+    try:
+        return [{"formatted": pynmrstar.utils.format_tag_lc(_), "original": _} for _ in tag_list]
+    except AttributeError:
+        raise ValueError('Your list or tuple may only contain tag names expressed as strings.')
+
+
+def write_to_file(nmrstar_object: Union['pynmrstar.Entry', 'pynmrstar.Saveframe'],
+                  file_name: str,
+                  format_: str = "nmrstar",
+                  show_comments: bool = True,
+                  skip_empty_loops: bool = False,
+                  skip_empty_tags: bool = False):
+    """ Writes the object to the specified file in NMR-STAR format. """
+
+    if format_ not in ["nmrstar", "json"]:
+        raise ValueError("Invalid output format.")
+
+    data_to_write = ''
+    if format_ == "nmrstar":
+        data_to_write = nmrstar_object.format(show_comments=show_comments,
+                                              skip_empty_loops=skip_empty_loops,
+                                              skip_empty_tags=skip_empty_tags)
+    elif format_ == "json":
+        data_to_write = nmrstar_object.get_json()
+
+    out_file = open(file_name, "w")
+    out_file.write(data_to_write)
+    out_file.close()

pynmrstar/definitions.py

@@ -0,0 +1,32 @@
+#!/usr/bin/python3
+
+""" NMR-STAR definitions and other module parameters live here. Technically
+you can edit them, but you should really know what you're doing.
+
+Adding key->value pairs to STR_CONVERSION_DICT will automatically convert tags
+whose value matches "key" to the string "value" when printing. This allows you
+to set the default conversion value for Booleans or other objects.
+
+WARNINGS:
+ * STR_CONVERSION_DICT cannot contain both booleans and arithmetic types.
+   Attempting to use both will cause an issue since boolean True == 1 in python
+   and False == 0.
+
+ * You must call utils.quote_value.clear_cache() after changing the
+   STR_CONVERSION_DICT or else your changes won't take effect due to caching!
+
+   The only exception is if you set STR_CONVERSION_DICT before performing any
+   actions which would call quote_value() - which include calling __str__ or
+   format() on Entry, Saveframe, and Loop objects.
+"""
+
+NULL_VALUES = ['', ".", "?", None]
+WHITESPACE: str = " \t\n\v"
+RESERVED_KEYWORDS = ["data_", "save_", "loop_", "stop_", "global_"]
+STR_CONVERSION_DICT: dict = {None: "."}
+
+API_URL: str = "https://api.bmrb.io/v2"
+SCHEMA_URL: str = 'https://raw.githubusercontent.com/uwbmrb/nmr-star-dictionary/master/xlschem_ann.csv'
+COMMENT_URL: str = "https://raw.githubusercontent.com/uwbmrb/PyNMRSTAR/v3/reference_files/comments.str"
+TYPES_URL: str = "https://raw.githubusercontent.com/uwbmrb/PyNMRSTAR/v3/pynmrstar/reference_files/data_types.csv"
+FTP_URL: str = "https://bmrb.io/ftp/pub/bmrb"