def get_cid_url(self, doc):
"""infer URL for contribution detail page from MongoDB doc"""
from mpcontribs.config import mp_id_pattern
is_mp_id = mp_id_pattern.match(doc['mp_cat_id'])
collection = 'materials' if is_mp_id else 'compositions'
return '/'.join([
self.preamble.rsplit('/', 1)[0], 'explorer', collection, doc['_id']
])
def get_cid_url(self, doc):
"""infer URL for contribution detail page from MongoDB doc"""
from mpcontribs.config import mp_id_pattern
is_mp_id = mp_id_pattern.match(doc['identifier'])
collection = 'materials' if is_mp_id else 'compositions'
return '/'.join([
self.preamble.rsplit('/', 1)[0], 'explorer', collection , doc['_id']
])
def normalize_root_level(title):
"""convert root-level title into conventional identifier; non-identifiers
become part of shared (meta-)data. Returns: (is_general, title)"""
from pymatgen.core.composition import CompositionError
try:
composition = get_composition_from_string(title)
return False, composition
except (CompositionError, KeyError, TypeError, ValueError):
if mp_id_pattern.match(title.lower()):
return False, title.lower()
return True, title
def normalize_root_level(title):
"""convert root-level title into conventional identifier; non-identifiers
become part of shared (meta-)data. Returns: (is_general, title)"""
try:
composition = get_composition_from_string(title)
return False, composition
except:
if mp_id_pattern.match(title.lower()):
return False, title.lower()
else:
return True, title
def normalize_root_level(title):
"""convert root-level title into conventional identifier; non-identifiers
become part of shared (meta-)data. Returns: (is_general, title)"""
try:
composition = Composition(title).get_integer_formula_and_factor()[0]
return False, composition
except:
if mp_id_pattern.match(title.lower()):
return False, title.lower()
else:
return True, title
def normalize_root_level(title):
"""convert root-level title into conventional identifier; non-identifiers
become part of shared (meta-)data. Returns: (is_general, title)"""
try:
composition = Composition(title).get_integer_formula_and_factor()[0]
return False, composition
except:
if mp_id_pattern.match(title.lower()):
return False, title.lower()
else:
return True, title
def normalize_root_level(title):
"""convert root-level title into conventional identifier; non-identifiers
become part of shared (meta-)data. Returns: (is_general, title)"""
from pymatgen.core.composition import CompositionError
try:
composition = get_composition_from_string(title)
return False, composition
except (CompositionError, KeyError, TypeError, ValueError):
if mp_id_pattern.match(title.lower()):
return False, title.lower()
return True, title
def delete(self, project, cids):
for contrib in self.contributions.find({'_id': {'$in': cids}}):
mp_cat_id, cid = contrib['mp_cat_id'], contrib['_id']
is_mp_id = mp_id_pattern.match(mp_cat_id)
coll = self.materials if is_mp_id else self.compositions
key = '.'.join([project, str(cid)])
coll.update({}, {'$unset': {key: 1}}, multi=True)
# remove `project` field when no contributions remaining
for coll in [self.materials, self.compositions]:
for doc in coll.find({project: {'$exists': 1}}):
for d in doc.itervalues():
if not d:
coll.update({'_id': doc['_id']}, {'$unset': {project: 1}})
def run(mpfile, dup_check_test_site=True):
from pymatgen import MPRester
existing_identifiers = {}
#for b in [False, True]:
# with DlrVietenRester(test_site=b) as mpr:
# for doc in mpr.query_contributions():
# existing_identifiers[doc['mp_cat_id']] = doc['_id']
# if not dup_check_test_site:
# break
google_sheet = mpfile.document[mp_level01_titles[0]].pop('google_sheet')
google_sheet += '/export?format=xlsx'
df_dct = pd.read_excel(google_sheet, sheetname=None)
mpr = MPRester()
update = 0
for sheet in df_dct.keys():
print(sheet)
df = df_dct[sheet]
sheet_split = sheet.split()
composition = sheet_split[0]
identifier = get_composition_from_string(composition)
if len(sheet_split) > 1 and mp_id_pattern.match(sheet_split[1]):
identifier = sheet_split[1]
print('identifier = {}'.format(identifier))
if 'CIF' in sheet_split:
print('adding CIF ...')
df.columns = [df.columns[0]] + [''] * (df.shape[1] - 1)
cif = df.to_csv(na_rep='',
index=False,
sep='\t',
quoting=csv.QUOTE_NONE)
mpfile.add_structure(cif, identifier=identifier, fmt='cif')
else:
print('adding data ...')
mpfile.add_hierarchical_data({'composition': composition},
identifier=identifier)
mpfile.add_data_table(identifier, df, name='dH_dS')
if identifier in existing_identifiers:
cid = existing_identifiers[identifier]
mpfile.insert_id(identifier, cid)
update += 1
print len(mpfile.ids), 'contributions to submit.'
if update > 0:
print update, 'contributions to update.'
def to_backgrid_dict(self):
"""Backgrid-conform dict from DataFrame"""
# shorten global import times by importing django here
import numpy as np
from mpcontribs.io.core.utils import get_composition_from_string
from pandas import MultiIndex
import pymatgen.util as pmg_util
from pymatgen.core.composition import CompositionError
table = dict()
nrows_max = 260
nrows = self.shape[0]
df = Table(self.head(n=nrows_max)) if nrows > nrows_max else self
numeric_columns = df.select_dtypes(
include=[np.number]).columns.tolist()
if isinstance(df.index, MultiIndex):
df.reset_index(inplace=True)
table['columns'] = []
table['rows'] = super(Table, df).to_dict(orient='records')
for col_index, col in enumerate(list(df.columns)):
cell_type = 'number'
# avoid looping rows to minimize use of `df.iat` (time-consuming in 3d)
if not col.startswith('level_') and col not in numeric_columns:
is_url_column, prev_unit, old_col = True, None, col
for row_index in range(df.shape[0]):
cell = str(df.iat[row_index, col_index])
cell_split = cell.split(' ', 1)
if not cell or len(
cell_split) == 1: # empty cell or no space
is_url_column = bool(
is_url_column
and (not cell or mp_id_pattern.match(cell)))
if is_url_column:
if cell:
value = 'https://materialsproject.org/materials/{}'.format(
cell)
table['rows'][row_index][col] = value
elif cell:
try:
composition = get_composition_from_string(cell)
composition = pmg_util.string.unicodeify(
composition)
table['rows'][row_index][col] = composition
except (CompositionError, ValueError,
OverflowError):
try:
# https://stackoverflow.com/a/38020041
result = urlparse(cell)
if not all([
result.scheme, result.netloc,
result.path
]):
break
is_url_column = True
except:
break
else:
value, unit = cell_split # TODO convert cell_split[0] to float?
is_url_column = False
try:
float(value
) # unit is only a unit if value is number
except ValueError:
continue
table['rows'][row_index].pop(old_col)
if prev_unit is None:
prev_unit = unit
col = '{} [{}]'.format(col, unit)
table['rows'][row_index][
col] = cell if prev_unit != unit else value
cell_type = 'uri' if is_url_column else 'string'
col_split = col.split('##')
nesting = [col_split[0]] if len(col_split) > 1 else []
table['columns'].append({
'name': col,
'cell': cell_type,
'nesting': nesting,
'editable': 0
})
if len(col_split) > 1:
table['columns'][-1].update(
{'label': '##'.join(col_split[1:])})
if len(table['columns']) > 12:
table['columns'][-1]['renderable'] = 0
header = RecursiveDict()
for idx, col in enumerate(table['columns']):
if 'label' in col:
k, sk = col['name'].split('##')
sk_split = sk.split()
if len(sk_split) == 2:
d = {'name': sk_split[0], 'unit': sk_split[1], 'idx': idx}
if k not in header:
header[k] = [d]
else:
header[k].append(d)
elif k in header:
header.pop(k)
for k, skl in header.items():
units = [sk['unit'] for sk in skl]
if units.count(units[0]) == len(units):
for sk in skl:
table['columns'][sk['idx']]['label'] = sk['name']
table['columns'][sk['idx']]['nesting'][0] = '{} {}'.format(
k, sk['unit'])
return table
def get_card(request, cid, db_type=None, mdb=None):
"""
@api {post} /card/:cid?API_KEY=:api_key Contribution Card/Preview
@apiVersion 0.2.0
@apiName PostGetCard
@apiGroup Contribution
@apiDescription Either returns a string containing html for hierarchical
data, or if existent, a list of URLs for static versions of embedded graphs.
@apiParam {String} api_key User's unique API_KEY
@apiParam {json} provenance_keys List of provenance keys
@apiSuccess {String} created_at Response timestamp
@apiSuccess {Bool} valid_response Response is valid
@apiSuccess {String} response Response preview of h- or t-data/graphs ("card")
@apiSuccessExample Success-Response:
HTTP/1.1 200 OK
{
"created_at": "2017-08-09T19:59:59.936618",
"valid_response": true,
"response": ["<graph-url>"]
}
"""
from mpcontribs.io.core.components import Tree, Plots, render_plot
from mpcontribs.io.core.utils import nested_dict_iter
from mpcontribs.io.core.recdict import RecursiveDict, render_dict
from django.template import Template, Context
from django.core.urlresolvers import reverse
from mpcontribs.config import mp_id_pattern
prov_keys = loads(request.POST.get('provenance_keys', '["title"]'))
contrib = mdb.contrib_ad.query_contributions(
{'_id': ObjectId(cid)},
projection={'_id': 0, 'mp_cat_id': 1, 'content': 1, 'collaborators': 1}
)[0]
mpid = contrib['mp_cat_id']
hdata = Tree(contrib['content'])
plots = Plots(contrib['content'])
title = hdata.get('title', 'No title available.')
descriptions = hdata.get('description', 'No description available.').strip().split('.', 1)
description = '{}.'.format(descriptions[0])
if len(descriptions) > 1 and descriptions[1]:
description += '''<a href="#"
class="read_more">More »</a><span class="more_text"
hidden>{}</span>'''.format(descriptions[1])
authors = hdata.get('authors', 'No authors available.').split(',', 1)
provenance = '<h5>{}'.format(authors[0])
if len(authors) > 1:
provenance += '''<button class="btn-sm btn-link" type=button
data-toggle="tooltip" data-placement="bottom"
data-container="body" title="{}" style="padding: 0px 0px 0px 3px;"
>et al.</a>'''.format(authors[1].strip())
provenance += '</h5>'
dois = hdata.get('dois', hdata.get('urls', '')).split(' ')
doi_urls = []
for x in dois:
if x.startswith('http'):
doi_urls.append(x)
else:
doi_urls.append('https://doi.org/{}'.format(x))
provenance += ''.join(['''<a href={}
class="btn btn-link" role=button style="padding: 0"
target="_blank"><i class="fa fa-book fa-border fa-lg"></i></a>'''.format(x, y)
for x, y in zip(doi_urls, dois) if x
])
#if plots:
# card = []
# for name, plot in plots.items():
# filename = '{}_{}.png'.format(mpid, name)
# cwd = os.path.dirname(__file__)
# filepath = os.path.abspath(os.path.join(
# cwd, '..', '..', 'webtzite', 'static', 'img', filename
# ))
# if not os.path.exists(filepath):
# render_plot(plot, filename=filepath)
# index = request.build_absolute_uri(reverse('webtzite_index')[:-1])
# imgdir = '/'.join([index.rsplit('/', 1)[0], 'static', 'img'])
# fileurl = '/'.join([imgdir, filename])
# card.append(fileurl)
#else:
data = RecursiveDict()
for idx, (k,v) in enumerate(hdata.get('data', {}).items()):
data[k] = v
if idx >= 6:
break # humans can grasp 7 items quickly
data = render_dict(data, webapp=True)
is_mp_id = mp_id_pattern.match(mpid)
collection = 'materials' if is_mp_id else 'compositions'
more = reverse('mpcontribs_explorer_contribution', args=[collection, cid])
card = '''
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
{}
<a class="btn-sm btn-default pull-right" role="button"
style=" margin-top:-6px;"
href="{}" target="_blank">More Info</a>
</h4>
</div>
<div class="panel-body" style="padding-left: 0px">
<div class="col-md-8" style="padding-top: 0px">
<blockquote class="blockquote" style="font-size: 13px;">{}</blockquote>
</div>
<div class="col-md-4 well" style="padding: 0px 0px 5px 5px;">{}</div>
<div class="col-md-12" style="padding-right: 0px;">{}</div>
</div>
</div>
<script>
requirejs(['main'], function() {{
require(['jquery'], function() {{
$(function(){{
$("a.read_more").click(function(event){{
event.preventDefault();
$(this).parents(".blockquote").find(".more_text").show();
$(this).parents(".blockquote").find(".read_more").hide();
}});
}});
}});
}});
</script>
'''.format(
title, more, description, provenance, data
)
return {"valid_response": True, "response": card}
def to_backgrid_dict(self):
"""Backgrid-conform dict from DataFrame"""
# shorten global import times by importing django here
import numpy as np
from mpcontribs.io.core.utils import get_composition_from_string
from pandas import MultiIndex
import pymatgen.util as pmg_util
from pymatgen.core.composition import CompositionError
table = dict()
nrows_max = 260
nrows = self.shape[0]
df = Table(self.head(n=nrows_max)) if nrows > nrows_max else self
if isinstance(df.index, MultiIndex):
df.reset_index(inplace=True)
table['columns'] = []
table['rows'] = super(Table, df).to_dict(orient='records')
for col_index, col in enumerate(list(df.columns)):
cell_type = 'number'
# avoid looping rows to minimize use of `df.iat` (time-consuming in 3d)
if not col.startswith('level_') and col[-1] != ']':
is_url_column = True
for row_index in range(df.shape[0]):
cell = str(df.iat[row_index, col_index])
is_url_column = bool(
is_url_column
and (not cell or mp_id_pattern.match(cell)))
if is_url_column:
if cell:
value = 'https://materialsproject.org/materials/{}'.format(
cell)
table['rows'][row_index][col] = value
elif cell:
try:
composition = get_composition_from_string(cell)
composition = pmg_util.string.unicodeify(
composition)
table['rows'][row_index][col] = composition
except (CompositionError, ValueError, OverflowError):
try:
# https://stackoverflow.com/a/38020041
result = urlparse(cell)
if not all([
result.scheme, result.netloc,
result.path
]):
break
is_url_column = True
except:
break
cell_type = 'uri' if is_url_column else 'string'
col_split = col.split('.')
nesting = [col_split[0]] if len(col_split) > 1 else []
table['columns'].append({
'name': col,
'cell': cell_type,
'nesting': nesting,
'editable': 0
})
if len(col_split) > 1:
table['columns'][-1].update({'label': '.'.join(col_split[1:])})
if len(table['columns']) > 12:
table['columns'][-1]['renderable'] = 0
return table
def build(self, contributor_email, cid, api_key=None, endpoint=None):
"""update materials/compositions collections with contributed data"""
cid_short, cid_str = get_short_object_id(cid), str(cid)
contrib = self.find_contribution(cid)
if not contrib:
raise Exception('Contribution {} not found!'.format(cid))
if contributor_email not in contrib['collaborators']:
raise ValueError(
"Build stopped: building contribution {} not "
"allowed due to insufficient permissions of {}! Ask "
"someone of {} to make you a collaborator on {}.".format(
cid_short, contributor_email, contrib['collaborators'],
cid_short))
from pymatgen.util.provenance import Author
mpfile = MPFileCore.from_contribution(contrib)
mp_cat_id = mpfile.ids[0]
is_mp_id = mp_id_pattern.match(mp_cat_id)
self.curr_coll = self.materials if is_mp_id else self.compositions
author = Author.parse_author(contributor_email)
project = str(author.name).translate(None, '.') \
if 'project' not in contrib else contrib['project']
nb = nbf.new_notebook()
if isinstance(self.db, dict):
contrib.pop('_id')
if 'cid' in contrib['content']:
contrib['content'].pop('cid')
nb['cells'].append(
nbf.new_code_cell(
"from mpcontribs.io.core.mpfile import MPFileCore\n"
"from mpcontribs.io.core.recdict import RecursiveDict\n"
"mpfile = MPFileCore.from_contribution({})\n"
"identifier = '{}'".format(contrib, mp_cat_id)))
else:
nb['cells'].append(
nbf.new_code_cell(
"from mpcontribs.rest.rester import MPContribsRester"))
os.environ['PMG_MAPI_KEY'] = api_key
os.environ['PMG_MAPI_ENDPOINT'] = endpoint
nb['cells'].append(
nbf.new_code_cell(
"with MPContribsRester() as mpr:\n"
" mpfile = mpr.find_contribution('{}')\n"
" identifier = mpfile.ids[0]".format(cid)))
nb['cells'].append(
nbf.new_markdown_cell("## Contribution #{} for {}".format(
cid_short, mp_cat_id)))
nb['cells'].append(nbf.new_markdown_cell("### Hierarchical Data"))
nb['cells'].append(nbf.new_code_cell("mpfile.hdata[identifier]"))
if mpfile.tdata[mp_cat_id]:
nb['cells'].append(nbf.new_markdown_cell("### Tabular Data"))
for table_name, table in mpfile.tdata[mp_cat_id].iteritems():
nb['cells'].append(
nbf.new_markdown_cell("#### {}".format(table_name)))
nb['cells'].append(
nbf.new_code_cell(
"mpfile.tdata[identifier]['{}']".format(table_name)))
if mpfile.gdata[mp_cat_id]:
nb['cells'].append(nbf.new_markdown_cell("### Graphical Data"))
for plot_name, plot in mpfile.gdata[mp_cat_id].iteritems():
nb['cells'].append(
nbf.new_markdown_cell("#### {}".format(plot_name)))
nb['cells'].append(
nbf.new_code_cell(
"mpfile.gdata[identifier]['{}']".format(plot_name)))
if mpfile.sdata[mp_cat_id]:
nb['cells'].append(nbf.new_markdown_cell("### Structural Data"))
for structure_name, structure in mpfile.sdata[mp_cat_id].iteritems():
nb['cells'].append(
nbf.new_markdown_cell("#### {}".format(structure_name)))
nb['cells'].append(
nbf.new_code_cell(
"mpfile.sdata[identifier]['{}']".format(structure_name)))
self.ep.preprocess(nb, {'metadata': {'path': self.nbdir}})
if isinstance(self.db, dict):
return [mp_cat_id, project, cid_short, export_notebook(nb, cid)]
else:
build_doc = RecursiveDict()
build_doc['mp_cat_id'] = mp_cat_id
build_doc['project'] = project
build_doc['nb'] = nb
self.curr_coll.update({'_id': cid}, {'$set': build_doc},
upsert=True)
return '{}/{}'.format( # return URL for contribution page
('materials' if is_mp_id else 'compositions'), cid_str)
def get_backgrid_table(df):
"""Backgrid-conform dict from DataFrame"""
# shorten global import times by importing django here
import numpy as np
from django.core.validators import URLValidator
from django.core.exceptions import ValidationError
from pandas import MultiIndex
val = URLValidator()
table = dict()
nrows = df.shape[0]
nrows_max = 200
if nrows > nrows_max:
df = Table(df.head(n=nrows_max))
numeric_columns = df.select_dtypes(include=[np.number]).columns.tolist()
if isinstance(df.index, MultiIndex):
df.reset_index(inplace=True)
table['columns'] = []
table['rows'] = super(Table, df).to_dict(orient='records')
for col_index, col in enumerate(list(df.columns)):
cell_type = 'number'
# avoid looping rows to minimize use of `df.iat` (time-consuming in 3d)
if not col.startswith('level_') and col not in numeric_columns:
is_url_column, prev_unit, old_col = True, None, col
for row_index in xrange(nrows):
cell = unicode(df.iat[row_index, col_index])
cell_split = cell.split(' ', 1)
if not cell or len(cell_split) == 1: # empty cell or no space
if is_url_column:
is_url_column = bool(not cell
or mp_id_pattern.match(cell))
if is_url_column:
if cell:
value = 'https://materialsproject.org/materials/{}'.format(
cell)
table['rows'][row_index][col] = value
else:
try:
val(cell)
is_url_column = True
except ValidationError:
# is_url_column already set to False
break
else:
value, unit = cell_split # TODO convert cell_split[0] to float?
table['rows'][row_index].pop(old_col)
if prev_unit is None:
is_url_column = False
prev_unit = unit
col = '{} [{}]'.format(col, unit)
table['rows'][row_index][
col] = cell if prev_unit != unit else value
cell_type = 'uri' if is_url_column else 'string'
col_split = col.split('##')
nesting = [col_split[0]] if len(col_split) > 1 else []
table['columns'].append({
'name': col,
'cell': cell_type,
'nesting': nesting,
'editable': 0
})
if len(col_split) > 1:
table['columns'][-1].update({'label': '##'.join(col_split[1:])})
if len(table['columns']) > 9:
table['columns'][-1]['renderable'] = 0
return table