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# coding: utf-8 

# Copyright (c) Pymatgen Development Team. 

# Distributed under the terms of the MIT License. 

 

from __future__ import unicode_literals 

 

""" 

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

""" 

 

__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' 

 

import sys 

import re 

import datetime 

from collections import namedtuple 

import json 

 

from six.moves import map, cStringIO 

from six import string_types 

 

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 

 

 

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 = cStringIO(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): 

return {"name": self.name, "url": self.url, 

"description": self.description} 

 

@staticmethod 

def from_dict(h_node): 

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): 

return {"name": self.name, "email": self.email} 

 

@staticmethod 

def from_dict(d): 

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, string_types): 

# Regex looks for whitespace, (any name), whitespace, <, (email), 

# >, whitespace 

m = re.match('\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(object): 

""" 

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 

 

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 

""" 

 

def __init__(self, struct_or_mol, authors, projects=None, references='', 

remarks=None, data=None, history=None, created_at=None): 

# initialize root-level structure keys 

self.structure = struct_or_mol 

 

# turn authors into list of Author objects 

authors = authors.split(',')\ 

if isinstance(authors, string_types) 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, string_types) else projects 

 

# check that references are valid BibTeX 

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, string_types) \ 

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): 

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): 

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)