def get_global_hierarchical_data(self, keys):
projection = {'_id': 1, 'mp_cat_id': 1}
for key in keys:
projection['content.' + key] = 1
docs = self.query_contributions(projection=projection, limit=1)
if not docs:
raise Exception('No contributions found!')
from mpcontribs.io.core.mpfile import MPFileCore
mpfile = MPFileCore.from_contribution(docs[0])
identifier = mpfile.ids[0]
return mpfile.hdata[identifier]
if level_reduction:
del scope[level:]
# append scope
if value is None:
scope.append("".join([replacements.get(c, c)
for c in key]))
# correct scope to omit internal 'general' section
scope_corr = scope
if scope[0] == mp_level01_titles[0]:
scope_corr = scope[1:]
# insert scope line
if (value is None and scope_corr) or (value is not None
and level_reduction):
lines.append("\n{" + ".".join(scope_corr) + "}")
# insert key-value line
if value is not None:
val = str(value)
value_lines = ([val] if val.startswith("http") else
textwrap.wrap(val))
if len(value_lines) > 1:
value_lines = [""] + value_lines + [":end"]
lines.append(
make_pair(
"".join([replacements.get(c, c) for c in key]),
"\n".join(value_lines),
))
return "\n".join(lines) + "\n"
MPFileCore.register(MPFile)
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)