def connect(self, **kwargs):
super(Connector, self).connect(**kwargs)
self.contribs_db = self.default_db
db_type = kwargs.get('db_type')
if db_type is not None:
self.contribs_db = self.get_database(db_type)
from mpcontribs.rest.adapter import ContributionMongoAdapter
self.contrib_ad = ContributionMongoAdapter(self.contribs_db)
from mpcontribs.builder import MPContributionsBuilder
self.contrib_build_ad = MPContributionsBuilder(self.contribs_db)
import sys, json, os
from pympler import asizeof
if __name__ == '__main__':
if not os.path.exists('martin_lab.json'):
from mpcontribs.users.martin_lab.pre_submission import run
from mpcontribs.io.archieml.mpfile import MPFile
from mpcontribs.rest.adapter import ContributionMongoAdapter
from mpcontribs.builder import MPContributionsBuilder, export_notebook
mpfile = MPFile.from_file('MPContribs/mpcontribs/users/martin_lab/mpfile_init.txt')
run(mpfile)
cma = ContributionMongoAdapter()
for mpfile_single in mpfile.split():
contributor = 'Patrick Huck <*****@*****.**>'
doc = cma.submit_contribution(mpfile_single, contributor)
cid = doc['_id']
print doc.keys()
mcb = MPContributionsBuilder(doc)
build_doc = mcb.build(contributor, cid)
nb = build_doc[-1]
print nb.keys()
with open('martin_lab.json', 'w') as f:
json.dump(nb, f)
print 'DONE'
with open('martin_lab.json', 'r') as f:
nb = json.load(f)
for idx, cell in enumerate(nb['cells']):
if idx: # skip first cell
import sys, json, os
from pympler import asizeof
if not os.path.exists('martin_lab.json'):
from mpcontribs.users.martin_lab.pre_submission import run
from mpcontribs.io.archieml.mpfile import MPFile
from mpcontribs.rest.adapter import ContributionMongoAdapter
from mpcontribs.builder import MPContributionsBuilder, export_notebook
mpfile = MPFile.from_file('MPContribs/mpcontribs/users/martin_lab/mpfile_init.txt')
run(mpfile)
cma = ContributionMongoAdapter()
for mpfile_single in mpfile.split():
contributor = 'Patrick Huck <*****@*****.**>'
doc = cma.submit_contribution(mpfile_single, contributor)
cid = doc['_id']
print doc.keys()
mcb = MPContributionsBuilder(doc)
build_doc = mcb.build(contributor, cid)
nb = build_doc[-1]
print nb.keys()
with open('martin_lab.json', 'w') as f:
json.dump(nb, f)
print 'DONE'
with open('martin_lab.json', 'r') as f:
nb = json.load(f)
for idx, cell in enumerate(nb['cells']):
if idx: # skip first cell
obj_size = asizeof.asizeof(cell) / 1024. / 1024.
if obj_size > 1.:
def process_mpfile(path_or_mpfile, target=None, fmt='archieml'):
try:
if isinstance(path_or_mpfile, six.string_types) and \
not os.path.isfile(path_or_mpfile):
raise Exception('{} not found'.format(path_or_mpfile))
mod = import_module('mpcontribs.io.{}.mpfile'.format(fmt))
MPFile = getattr(mod, 'MPFile')
full_name = pwd.getpwuid(os.getuid())[4]
contributor = '{} <*****@*****.**>'.format(full_name) # fake
cma = ContributionMongoAdapter()
axes, ov_data = set(), dict()
# split input MPFile into contributions: treat every mp_cat_id as separate DB insert
mpfile, cid_shorts = MPFile.from_dict(), [] # output
for idx, mpfile_single in enumerate(
MPFile.from_file(path_or_mpfile).split()):
mp_cat_id = mpfile_single.document.keys()[0]
# TODO test update mode
cid = mpfile_single.document[mp_cat_id].get('cid', None)
update = bool(cid is not None)
if update:
cid_short = get_short_object_id(cid)
yield 'use contribution #{} to update ID #{} ... '.format(
idx, cid_short)
# always run local "submission" to catch failure before interacting with DB
yield 'locally process contribution #{} ... '.format(idx)
doc = cma.submit_contribution(
mpfile_single, contributor) # does not use get_string
cid = doc['_id']
yield 'check consistency ... '
mpfile_single_cmp = MPFile.from_string(mpfile_single.get_string())
if mpfile_single.document != mpfile_single_cmp.document:
json.encoder.FLOAT_REPR = lambda o: format(o, 'g')
# compare json strings to find first inconsistency
for a, b in zip(
json.dumps(mpfile_single.document,
indent=4).split('\n'),
json.dumps(mpfile_single_cmp.document,
indent=4).split('\n')):
if a != b:
raise Exception('{} <====> {}'.format(
a.strip(), b.strip()))
if target is not None:
yield 'submit to MP ... '
cid = target.submit_contribution(mpfile_single,
fmt) # uses get_string
cid_short = get_short_object_id(cid)
mpfile_single.insert_id(mp_cat_id, cid)
cid_shorts.append(cid_short)
yield 'build notebook ... '
if target is not None:
url = target.build_contribution(cid)
url = '/'.join(
[target.preamble.rsplit('/', 1)[0], 'explorer', url])
yield (
"OK. <a href='{}' class='btn btn-default btn-xs' " +
"role='button' target='_blank'>View</a></br>").format(url)
else:
mcb = MPContributionsBuilder(doc)
build_doc = mcb.build(contributor, cid)
yield build_doc
yield 'determine overview axes ... '
scope, local_axes = [], set()
mpfile_for_axes = MPFile.from_contribution(doc)
for k, v in mpfile_for_axes.hdata[mp_cat_id].iterate():
if v is None:
scope = scope[:k[0]]
scope.append(k[1])
else:
try:
if k[0] == len(scope): scope.append(k[1])
else: scope[-1] = k[1]
vf = float(v) # trigger exception
scope_str = '.'.join(scope)
if idx == 0:
axes.add(scope_str)
ov_data[scope_str] = {
cid_short: (vf, mp_cat_id)
}
else:
local_axes.add(scope_str)
ov_data[scope_str][cid_short] = (vf, mp_cat_id)
except:
pass
if idx > 0:
axes.intersection_update(local_axes)
yield 'OK.</br>'.format(idx, cid_short)
mpfile.concat(mpfile_single)
time.sleep(.01)
ncontribs = len(cid_shorts)
#if target is not None and \
# isinstance(path_or_mpfile, six.string_types) and \
# os.path.isfile(path_or_mpfile):
# yield 'embed #{} in MPFile ...'.format('/'.join(cid_shorts))
# mpfile.write_file(path_or_mpfile, with_comments=True)
if target is not None:
yield '<strong>{} contributions successfully submitted.</strong>'.format(
ncontribs)
else:
for k in ov_data:
if k not in axes:
ov_data.pop(k)
yield ov_data
yield '<strong>{} contributions successfully processed.</strong>'.format(
ncontribs)
except:
ex = sys.exc_info()[1]
yield 'FAILED.</br>'
yield str(ex).replace('"', "'")
return
def process_mpfile(path_or_mpfile, target=None, fmt='archieml', ids=None):
try:
if isinstance(path_or_mpfile, six.string_types) and \
not os.path.isfile(path_or_mpfile):
raise Exception('{} not found'.format(path_or_mpfile))
if ids is not None and not isinstance(ids, list) and not len(ids) == 2:
raise Exception('{} is not list of length 2!'.format(ids))
from pymatgen.analysis.structure_matcher import StructureMatcher
mod = import_module('mpcontribs.io.{}.mpfile'.format(fmt))
MPFile = getattr(mod, 'MPFile')
full_name = pwd.getpwuid(os.getuid())[4]
contributor = '{} <*****@*****.**>'.format(full_name) # fake
cma = ContributionMongoAdapter()
axes, ov_data = set(), dict()
mpfile_out, cid_shorts = MPFile(), [] # output
sm = StructureMatcher(primitive_cell=False, scale=False)
# split input MPFile into contributions: treat every mp_cat_id as separate DB insert
mpfile_in = path_or_mpfile
if isinstance(path_or_mpfile, six.string_types) or isinstance(
path_or_mpfile, StringIO):
mpfile_in = MPFile.from_file(path_or_mpfile)
for idx, mpfile_single in enumerate(mpfile_in.split()):
mp_cat_id = mpfile_single.document.keys()[0]
if ids is None or mp_cat_id == ids[0]:
cid = mpfile_single.document[mp_cat_id].get('cid', None)
update = bool(cid is not None)
if update:
cid_short = get_short_object_id(cid)
yield 'use #{} to update #{} ... '.format(idx, cid_short)
# always run local "submission" to catch failure before interacting with DB
yield 'process #{} ({}) ... '.format(idx, mp_cat_id)
doc = cma.submit_contribution(
mpfile_single, contributor) # does not use get_string
cid = doc['_id']
cid_short = get_short_object_id(cid)
if ids is None or cid_short == ids[1]:
yield 'check ... '
obj_size = asizeof.asizeof(mpfile_single) / 1024. / 1024.
if obj_size > 0.5:
yield 'skip ({:.3f}MB) ... '.format(obj_size)
else:
try:
mpfile_single_cmp_str = mpfile_single.get_string()
except Exception as ex:
yield 'get_string() FAILED!<br>'
continue
try:
mpfile_single_cmp = MPFile.from_string(
mpfile_single_cmp_str)
except Exception as ex:
yield 'from_string() FAILED!<br>'
continue
if mpfile_single.document != mpfile_single_cmp.document:
yield 'check again ... '
found_inconsistency = False
# check structural data
structures_ok = True
for name, s1 in mpfile_single.sdata[
mp_cat_id].iteritems():
s2 = mpfile_single_cmp.sdata[mp_cat_id][name]
if s1 != s2:
if len(s1) != len(s2):
yield 'different number of sites: {} -> {}!<br>'.format(
len(s1), len(s2))
structures_ok = False
break
if s1.lattice != s2.lattice:
yield 'lattices different!<br>'
structures_ok = False
break
for site in s1:
if site not in s2:
found_inconsistency = True
if not sm.fit(s1, s2):
yield 'structures do not match!<br>'
structures_ok = False
break
if not structures_ok:
break
if not structures_ok:
continue
# check hierarchical and tabular data
# compare json strings to find first inconsistency
json_compare(mpfile_single.hdata,
mpfile_single_cmp.hdata)
json_compare(mpfile_single.tdata,
mpfile_single_cmp.tdata)
if not found_inconsistency:
# documents are not equal, but all components checked, skip contribution
# should not happen
yield 'inconsistency found but not identified!<br>'
continue
if target is not None:
yield 'submit ... '
cid = target.submit_contribution(
mpfile_single, fmt) # uses get_string
mpfile_single.insert_id(mp_cat_id, cid)
cid_shorts.append(cid_short)
if target is not None:
if idx < 5:
yield 'build ... '
url = target.build_contribution(cid)
url = '/'.join([
target.preamble.rsplit('/', 1)[0], 'explorer',
url
])
yield (
"OK. <a href='{}' class='btn btn-default btn-xs' "
+ "role='button' target='_blank'>View</a></br>"
).format(url)
else:
target.set_build_flag(cid, True)
yield 'OK (queued).</br>'
else:
if (ids is None and idx < 5) or ids is not None:
yield 'build ... '
mcb = MPContributionsBuilder(doc)
build_doc = mcb.build(contributor, cid)
else:
yield 'skip ... '
from pymatgen.util.provenance import Author
author = Author.parse_author(contributor)
build_doc = [mp_cat_id, author.name, cid_short, '']
yield build_doc
yield 'overview axes ... '
scope, local_axes = [], set()
mpfile_for_axes = MPFile.from_contribution(doc)
for k, v in mpfile_for_axes.hdata[mp_cat_id].iterate():
if v is None:
scope = scope[:k[0]]
scope.append(k[1])
else:
try:
if k[0] == len(scope): scope.append(k[1])
else: scope[-1] = k[1]
vf = float(v) # trigger exception
scope_str = '.'.join(scope)
if idx == 0:
axes.add(scope_str)
ov_data[scope_str] = {
cid_short: (vf, mp_cat_id)
}
else:
local_axes.add(scope_str)
ov_data[scope_str][cid_short] = (
vf, mp_cat_id)
except:
pass
if idx > 0:
axes.intersection_update(local_axes)
yield 'OK.</br>'.format(idx, cid_short)
else:
yield 'wrong CID.</br>'
mpfile_out.concat(mpfile_single)
time.sleep(.01)
ncontribs = len(cid_shorts)
if target is not None:
yield '<strong>{} contributions successfully submitted.</strong>'.format(
ncontribs)
else:
for k in ov_data.keys():
if k not in axes:
ov_data.pop(k)
yield ov_data
yield '<strong>{} contributions successfully processed.</strong>'.format(
ncontribs)
except:
ex = sys.exc_info()[1]
yield 'FAILED.</br>'
yield str(ex).replace('"', "'")
return
def process_mpfile(path_or_mpfile, target=None, fmt='archieml'):
try:
if isinstance(path_or_mpfile, six.string_types) and \
not os.path.isfile(path_or_mpfile):
raise Exception('{} not found'.format(path_or_mpfile))
mod = import_module('mpcontribs.io.{}.mpfile'.format(fmt))
MPFile = getattr(mod, 'MPFile')
full_name = pwd.getpwuid(os.getuid())[4]
contributor = '{} <*****@*****.**>'.format(full_name) # fake
cma = ContributionMongoAdapter()
axes, ov_data = set(), dict()
# split input MPFile into contributions: treat every mp_cat_id as separate DB insert
mpfile, cid_shorts = MPFile.from_dict(), [] # output
for idx, mpfile_single in enumerate(MPFile.from_file(path_or_mpfile).split()):
mp_cat_id = mpfile_single.document.keys()[0]
# TODO test update mode
cid = mpfile_single.document[mp_cat_id].get('cid', None)
update = bool(cid is not None)
if update:
cid_short = get_short_object_id(cid)
yield 'use contribution #{} to update ID #{} ... '.format(idx, cid_short)
# always run local "submission" to catch failure before interacting with DB
yield 'locally process contribution #{} ... '.format(idx)
doc = cma.submit_contribution(mpfile_single, contributor) # does not use get_string
cid = doc['_id']
yield 'check consistency ... '
mpfile_single_cmp = MPFile.from_string(mpfile_single.get_string())
if mpfile_single.document != mpfile_single_cmp.document:
# compare json strings to find first inconsistency
for a, b in zip(
json.dumps(mpfile_single.document, indent=4).split('\n'),
json.dumps(mpfile_single_cmp.document, indent=4).split('\n')
):
if a != b:
raise Exception('{} <====> {}'.format(a.strip(), b.strip()))
if target is not None:
yield 'submit to MP ... '
cid = target.submit_contribution(mpfile_single, fmt) # uses get_string
cid_short = get_short_object_id(cid)
mpfile_single.insert_id(mp_cat_id, cid)
cid_shorts.append(cid_short)
yield 'build into {} ... '.format(mp_cat_id)
if target is not None:
url = target.build_contribution(cid)
url = '/'.join([target.preamble.rsplit('/', 1)[0], 'explorer', url])
yield ("OK. <a href='{}' class='btn btn-default btn-xs' " +
"role='button' target='_blank'>View</a></br>").format(url)
else:
mcb = MPContributionsBuilder(doc)
build_doc = mcb.build(contributor, cid)
yield build_doc
yield 'determine overview axes ... '
scope, local_axes = [], set()
for k,v in build_doc[3]['tree_data'].iterate():
if v is None:
scope = scope[:k[0]]
scope.append(k[1])
else:
try:
if k[0] == len(scope): scope.append(k[1])
else: scope[-1] = k[1]
vf = float(v) # trigger exception
scope_str = '.'.join(scope)
if idx == 0:
axes.add(scope_str)
ov_data[scope_str] = {cid_short: (vf, mp_cat_id)}
else:
local_axes.add(scope_str)
ov_data[scope_str][cid_short] = (vf, mp_cat_id)
except:
pass
if idx > 0:
axes.intersection_update(local_axes)
yield 'OK.</br>'.format(idx, cid_short)
mpfile.concat(mpfile_single)
time.sleep(.01)
ncontribs = len(cid_shorts)
#if target is not None and \
# isinstance(path_or_mpfile, six.string_types) and \
# os.path.isfile(path_or_mpfile):
# yield 'embed #{} in MPFile ...'.format('/'.join(cid_shorts))
# mpfile.write_file(path_or_mpfile, with_comments=True)
if target is not None:
yield '<strong>{} contributions successfully submitted.</strong>'.format(ncontribs)
else:
for k in ov_data:
if k not in axes:
ov_data.pop(k)
yield ov_data
yield '<strong>{} contributions successfully processed.</strong>'.format(ncontribs)
except:
ex = sys.exc_info()[1]
yield 'FAILED.</br>'
yield str(ex).replace('"',"'")
return