pymatgen.util.provenance — pymatgen 2020.7.3 documentation

# Source code for pymatgen.util.provenance

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    Classes and methods related to the Structure Notation Language (SNL)
    """

    import sys
    import re
    import datetime
    from collections import namedtuple
    import json
    from io import StringIO
    from monty.json import MontyDecoder, MontyEncoder
    from monty.string import remove_non_ascii

    from pymatgen.core.structure import Structure, Molecule
    from pybtex.database.input import bibtex
    from pybtex import errors

    __author__ = 'Anubhav Jain, Shyue Ping Ong'
    __credits__ = 'Dan Gunter'
    __copyright__ = 'Copyright 2013, The Materials Project'
    __version__ = '0.1'
    __maintainer__ = 'Anubhav Jain'
    __email__ = 'ajain@lbl.gov'
    __date__ = 'Feb 11, 2013'

    MAX_HNODE_SIZE = 64000  # maximum size (bytes) of SNL HistoryNode
    MAX_DATA_SIZE = 256000  # maximum size (bytes) of SNL data field
    MAX_HNODES = 100  # maximum number of HistoryNodes in SNL file
    MAX_BIBTEX_CHARS = 20000  # maximum number of characters for BibTeX reference

    def is_valid_bibtex(reference):
        """
        Use pybtex to validate that a reference is in proper BibTeX format

        Args:
            reference: A String reference in BibTeX format.

        Returns:
            Boolean indicating if reference is valid bibtex.
        """
        # str is necessary since pybtex seems to have an issue with unicode. The
        # filter expression removes all non-ASCII characters.
        sio = StringIO(remove_non_ascii(reference))
        parser = bibtex.Parser()
        errors.set_strict_mode(False)
        bib_data = parser.parse_stream(sio)
        return len(bib_data.entries) > 0

    class HistoryNode(namedtuple('HistoryNode', ['name', 'url', 'description'])):
        """
        A HistoryNode represents a step in the chain of events that lead to a
        Structure. HistoryNodes leave 'breadcrumbs' so that you can trace back how
        a Structure was created. For example, a HistoryNode might represent pulling
        a Structure from an external database such as the ICSD or CSD. Or, it might
        represent the application of a code (e.g. pymatgen) to the Structure, with
        a custom description of how that code was applied (e.g. a site removal
        Transformation was applied).

        A HistoryNode contains three fields:

        .. attribute:: name

            The name of a code or resource that this Structure encountered in
            its history (String)

        .. attribute:: url

            The URL of that code/resource (String)

        .. attribute:: description

            A free-form description of how the code/resource is related to the
            Structure (dict).
        """

        def as_dict(self):
            """
            Returns: Dict
            """
            return {"name": self.name, "url": self.url,
                    "description": self.description}

        @staticmethod
        def from_dict(h_node):
            """
            Args:
                d (dict): Dict representation

            Returns:
                HistoryNode
            """
            return HistoryNode(h_node['name'], h_node['url'],
                               h_node['description'])

        @staticmethod
        def parse_history_node(h_node):
            """
            Parses a History Node object from either a dict or a tuple.

            Args:
                h_node: A dict with name/url/description fields or a 3-element
                    tuple.

            Returns:
                History node.
            """
            if isinstance(h_node, dict):
                return HistoryNode.from_dict(h_node)

            else:
                if len(h_node) != 3:
                    raise ValueError("Invalid History node, "
                                     "should be dict or (name, version, "
                                     "description) tuple: {}".format(h_node))
                return HistoryNode(h_node[0], h_node[1], h_node[2])

    class Author(namedtuple('Author', ['name', 'email'])):
        """
        An Author contains two fields:

        .. attribute:: name

            Name of author (String)

        .. attribute:: email

            Email of author (String)
        """

        def __str__(self):
            """
            String representation of an Author
            """
            return '{} <{}>'.format(self.name, self.email)

        def as_dict(self):
            """
            Returns: MSONable dict.
            """
            return {"name": self.name, "email": self.email}

        @staticmethod
        def from_dict(d):
            """
            Args:
                d (dict): Dict representation

            Returns:
                Author
            """
            return Author(d['name'], d['email'])

        @staticmethod
        def parse_author(author):
            """
            Parses an Author object from either a String, dict, or tuple

            Args:
                author: A String formatted as "NAME <email@domain.com>",
                    (name, email) tuple, or a dict with name and email keys.

            Returns:
                An Author object.
            """
            if isinstance(author, str):
                # Regex looks for whitespace, (any name), whitespace, <, (email),
                # >, whitespace
                m = re.match(r'\s*(.*?)\s*<(.*?@.*?)>\s*', author)
                if not m or m.start() != 0 or m.end() != len(author):
                    raise ValueError("Invalid author format! {}".format(author))
                return Author(m.groups()[0], m.groups()[1])
            elif isinstance(author, dict):
                return Author.from_dict(author)
            else:
                if len(author) != 2:
                    raise ValueError("Invalid author, should be String or (name, "
                                     "email) tuple: {}".format(author))
                return Author(author[0], author[1])

    class StructureNL:
        """
        The Structure Notation Language (SNL, pronounced 'snail') is container
        for a pymatgen Structure/Molecule object with some additional fields for
        enhanced provenance. It is meant to be imported/exported in a JSON file
        format with the following structure:

        - about
            - created_at
            - authors
            - projects
            - references
            - remarks
            - data
            - history
        - lattice (optional)
        - sites
        """

        def __init__(self, struct_or_mol, authors, projects=None, references='',
                     remarks=None, data=None, history=None, created_at=None):
            """
            Args:
                struct_or_mol: A pymatgen.core.structure Structure/Molecule object
                authors: *List* of {"name":'', "email":''} dicts,
                    *list* of Strings as 'John Doe <johndoe@gmail.com>',
                    or a single String with commas separating authors
                projects: List of Strings ['Project A', 'Project B']
                references: A String in BibTeX format
                remarks: List of Strings ['Remark A', 'Remark B']
                data: A free form dict. Namespaced at the root level with an
                    underscore, e.g. {"_materialsproject": <custom data>}
                history: List of dicts - [{'name':'', 'url':'', 'description':{}}]
                created_at: A datetime object
            """
            # initialize root-level structure keys
            self.structure = struct_or_mol

            # turn authors into list of Author objects
            authors = authors.split(',')\
                if isinstance(authors, str) else authors
            self.authors = [Author.parse_author(a) for a in authors]

            # turn projects into list of Strings
            projects = projects if projects else []
            self.projects = [projects] if isinstance(projects, str) else projects

            # check that references are valid BibTeX
            if not isinstance(references, str):
                raise ValueError("Invalid format for SNL reference! Should be "
                                 "empty string or BibTeX string.")
            if references and not is_valid_bibtex(references):
                raise ValueError("Invalid format for SNL reference! Should be "
                                 "BibTeX string.")
            if len(references) > MAX_BIBTEX_CHARS:
                raise ValueError("The BibTeX string must be fewer than {} chars "
                                 ", you have {}"
                                 .format(MAX_BIBTEX_CHARS, len(references)))

            self.references = references

            # turn remarks into list of Strings
            remarks = remarks if remarks else []
            self.remarks = [remarks] if isinstance(remarks, str) else remarks

            # check remarks limit
            for r in self.remarks:
                if len(r) > 140:
                    raise ValueError("The remark exceeds the maximum size of"
                                     "140 characters: {}".format(r))

            # check data limit
            self.data = data if data else {}
            if not sys.getsizeof(self.data) < MAX_DATA_SIZE:
                raise ValueError("The data dict exceeds the maximum size limit of"
                                 " {} bytes (you have {})"
                                 .format(MAX_DATA_SIZE, sys.getsizeof(data)))

            for k, v in self.data.items():
                if not k.startswith("_"):
                    raise ValueError("data must contain properly namespaced data "
                                     "with keys starting with an underscore. The "
                                     "key {} does not start with an underscore.",
                                     format(k))

            # check for valid history nodes
            history = history if history else []  # initialize null fields
            if len(history) > MAX_HNODES:
                raise ValueError("A maximum of {} History nodes are supported, "
                                 "you have {}!".format(MAX_HNODES, len(history)))
            self.history = [HistoryNode.parse_history_node(h) for h in history]
            if not all([sys.getsizeof(h) < MAX_HNODE_SIZE for h in history]):
                raise ValueError("One or more history nodes exceeds the maximum "
                                 "size limit of {} bytes".format(MAX_HNODE_SIZE))

            self.created_at = created_at if created_at \
                else datetime.datetime.utcnow()

        def as_dict(self):
            """
            Returns: MSONable dict
            """
            d = self.structure.as_dict()
            d["@module"] = self.__class__.__module__
            d["@class"] = self.__class__.__name__
            d["about"] = {"authors": [a.as_dict() for a in self.authors],
                          "projects": self.projects,
                          "references": self.references,
                          "remarks": self.remarks,
                          "history": [h.as_dict() for h in self.history],
                          "created_at": json.loads(json.dumps(self.created_at,
                                                   cls=MontyEncoder))}
            d["about"].update(json.loads(json.dumps(self.data,
                                                    cls=MontyEncoder)))
            return d

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict representation

            Returns:
                Class
            """
            a = d["about"]
            dec = MontyDecoder()

            created_at = dec.process_decoded(a.get("created_at"))
            data = {k: v for k, v in d["about"].items()
                    if k.startswith("_")}
            data = dec.process_decoded(data)

            structure = Structure.from_dict(d) if "lattice" in d \
                else Molecule.from_dict(d)
            return cls(structure, a["authors"], projects=a.get("projects", None),
                       references=a.get("references", ""),
                       remarks=a.get("remarks", None), data=data,
                       history=a.get("history", None), created_at=created_at)

        @classmethod
        def from_structures(cls, structures, authors, projects=None,
                            references='', remarks=None, data=None,
                            histories=None, created_at=None):
            """
            A convenience method for getting a list of StructureNL objects by
            specifying structures and metadata separately. Some of the metadata
            is applied to all of the structures for ease of use.

            Args:
                structures: A list of Structure objects
                authors: *List* of {"name":'', "email":''} dicts,
                    *list* of Strings as 'John Doe <johndoe@gmail.com>',
                    or a single String with commas separating authors
                projects: List of Strings ['Project A', 'Project B']. This
                    applies to all structures.
                references: A String in BibTeX format. Again, this applies to all
                    structures.
                remarks: List of Strings ['Remark A', 'Remark B']
                data: A list of free form dict. Namespaced at the root level
                    with an underscore, e.g. {"_materialsproject":<custom data>}
                    . The length of data should be the same as the list of
                    structures if not None.
                histories: List of list of dicts - [[{'name':'', 'url':'',
                    'description':{}}], ...] The length of histories should be the
                    same as the list of structures if not None.
                created_at: A datetime object
            """
            data = [{}] * len(structures) if data is None else data
            histories = [[]] * len(structures) if histories is None else \
                histories

            snl_list = []
            for i, struct in enumerate(structures):
                snl = StructureNL(struct, authors, projects=projects,
                                  references=references,
                                  remarks=remarks, data=data[i],
                                  history=histories[i],
                                  created_at=created_at)
                snl_list.append(snl)

            return snl_list

        def __str__(self):
            return "\n".join(["{}\n{}".format(k, getattr(self, k))
                              for k in ("structure", "authors", "projects",
                                        "references", "remarks", "data", "history",
                                        "created_at")])

        def __eq__(self, other):
            return all(map(lambda n: getattr(self, n) == getattr(other, n),
                           ("structure", "authors", "projects", "references",
                            "remarks", "data", "history", "created_at")))

        def __ne__(self, other):
            return not self.__eq__(other)