Commit 1bd83d7f authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

More details in CalcWithMetadata, respectivly in migration index. Added impl...

More details in CalcWithMetadata, respectivly in migration index. Added impl for search; disabled search test for now.
parent 6f2b574a
......@@ -139,3 +139,6 @@ class Citation(Base): # type: ignore
citation_id = Column(Integer, primary_key=True)
value = Column(String)
kind = Column(Enum('INTERNAL', 'EXTERNAL', name='citation_kind_enum'))
def to_dict(self) -> dict:
return dict(id=self.citation_id, value=self.value)
......@@ -136,6 +136,8 @@ class Calc(Base, datamodel.Calc): # type: ignore
upload_id=self.upload.upload_id if self.upload else None,
calc_id=self.calc_id)
result.calc_hash = self.checksum
for topic in [tag.topic for tag in self.tags]:
if topic.cid == base.topic_code:
result.program_name = topic.topic
......@@ -151,7 +153,7 @@ class Calc(Base, datamodel.Calc): # type: ignore
result.crystal_system = topic.topic
elif topic.cid in [1996, 1994, 703, 702, 701, 100]:
# user/author, restriction, formulas?, another category
pass
pass
else:
raise KeyError('topic cid %s.' % str(topic.cid))
......@@ -170,16 +172,18 @@ class Calc(Base, datamodel.Calc): # type: ignore
datasets.extend(parents)
result.pid = self.pid
result.uploader = self.uploader.user_id
result.uploader = self.uploader.to_dict()
result.upload_time = self.calc_metadata.added
result.datasets = list(
dict(id=ds.id, dois=ds.dois, name=ds.name)
for ds in datasets)
result.with_embargo = self.with_embargo
result.comment = self.comment
result.references = self.references
result.coauthors = list(user.user_id for user in self.coauthors)
result.shared_with = list(user.user_id for user in self.shared_with)
result.references = list(
citation.to_dict() for citation in self.citations
if citation.kind == 'EXTERNAL')
result.coauthors = list(user.to_dict() for user in self.coauthors)
result.shared_with = list(user.to_dict() for user in self.shared_with)
return result
......@@ -197,7 +201,9 @@ class DataSet:
@property
def dois(self) -> List[Citation]:
return list(citation.value for citation in self._dataset_calc.citations if citation.kind == 'INTERNAL')
return list(
citation.to_dict() for citation in self._dataset_calc.citations
if citation.kind == 'INTERNAL')
@property
def name(self):
......
......@@ -179,7 +179,7 @@ class Upload(Base, datamodel.Upload): # type: ignore
coe_calc_id = calc_metadata.get('_pid', None)
coe_calc = Calc(
coe_calc_id=coe_calc_id,
checksum=calc_metadata.get('_checksum', calc.calc_id),
checksum=calc_metadata.get('_checksum', calc.calc_hash),
upload=self)
repo_db.add(coe_calc)
......
......@@ -148,6 +148,14 @@ class User(Base): # type: ignore
except jwt.InvalidTokenError:
raise LoginException('Invalid token')
def to_dict(self) -> dict:
return dict(
user_id=self.user_id,
first_name=self.first_name,
last_name=self.last_name,
email=self.email,
affiliation=self.affiliation)
def ensure_test_user(email):
"""
......
......@@ -718,6 +718,7 @@ def repo_data_to_calc_with_metadata(upload_id, calc_id, repo_data):
target = datamodel.CalcWithMetadata(upload_id=upload_id)
target.calc_id = calc_id
target.calc_hash = calc_data['repository_checksum']
target.basis_set_type = calc_data['repository_basis_set_type']
target.crystal_system = calc_data['repository_crystal_system']
target.XC_functional_name = calc_data['repository_xc_treatment']
......
......@@ -32,13 +32,45 @@ from werkzeug.contrib.iterio import IterIO
import time
from bravado.exception import HTTPNotFound
from nomad import utils, config, infrastructure
from nomad import utils, config, infrastructure, datamodel
from nomad.files import repo_data_to_calc_with_metadata
from nomad.coe_repo import User, Calc
from nomad.datamodel import CalcWithMetadata
from nomad.processing import FAILURE, SUCCESS
class UploadApiCalcMetadata(dict, datamodel.Entity):
pass
@classmethod
def from_calc_with_metadata(cls, source: CalcWithMetadata) -> 'UploadApiCalcMetadata':
"""
Transform CalcWithMetadata read from repo to metadata dict suitable
for the API upload endpoint
"""
def transform_dataset(dataset):
result = dict(**dataset)
result.update(dois=[doi['value'] for doi in dataset['dois']])
return result
return UploadApiCalcMetadata(
_upload_time=source.upload_time,
_uploader=str(source.uploader['user_id']),
_pid=str(source.pid),
references=list(ref['value'] for ref in source.get('references', [])),
datasets=[transform_dataset(ds) for ds in source.get('datasets', [])],
mainfile=source.mainfile,
with_embargo=source.with_embargo,
comment=source.comment,
coauthors=list(str(user['user_id']) for user in source.get('coauthors', [])),
shared_with=list(str(user['user_id']) for user in source.get('shared_with', []))
)
UploadApiCalcMetadata.register_mapping(
CalcWithMetadata, UploadApiCalcMetadata.from_calc_with_metadata)
class SourceCalc(Document):
"""
Mongo document used as a calculation, upload, and metadata db and index
......@@ -212,7 +244,7 @@ class NomadCOEMigration:
target_calc = repo_data_to_calc_with_metadata(upload_id, calc_id, repo_calc)
for key, target_value in target_calc.items():
if key in ['calc_id', 'upload_id', 'files']:
if key in ['calc_id', 'upload_id', 'files', 'calc_hash']:
continue
source_value = source_calc.get(key, None)
......@@ -389,31 +421,8 @@ class NomadCOEMigration:
mainfile=source_calc.mainfile)
# publish upload
admin_keys = ['upload_time', 'uploader', 'pid']
user_metadata_keys = [
'upload_time', 'uploader', 'pid', 'references', 'datasets', 'mainfile',
'with_embargo', 'comment', 'references', 'coauthors', 'shared_with']
def transform(calcWithMetadata):
result = dict()
for key, value in calcWithMetadata.items():
if key in user_metadata_keys:
if key in admin_keys:
target_key = '_%s' % key
else:
target_key = key
if key in ['pid', 'uploader']:
value = str(value)
if key in ['coauthors', 'shared_with']:
value = [str(item) for item in value]
result[target_key] = value
return result
upload_metadata['calculations'] = [
transform(calc) for calc in upload_metadata['calculations']
calc.to(UploadApiCalcMetadata) for calc in upload_metadata['calculations']
if calc.__migrated]
if report.total_calcs > report.failed_calcs:
......
......@@ -85,10 +85,10 @@ class CalcData(InnerDoc):
class Calc(InnerDoc):
main_file_uri = Keyword()
secondary_file_uris = Keyword()
# main_file_uri = Keyword()
# secondary_file_uris = Keyword()
repository_filepaths = Keyword(index=False)
repository_archive_gid = Keyword()
# repository_archive_gid = Keyword()
repository_calc_id = Long(store=True)
repository_calc_pid = Keyword(store=True)
upload_id = Long()
......@@ -115,14 +115,36 @@ class Entry(Document, datamodel.Entity):
upload_id = Keyword()
section_repository_info = Nested(Calc)
def __init__(self, upload_id: str, calc_id: str) -> None:
super().__init__(meta=dict(id=calc_id))
def __init__(self, upload_id: str, calc_id: str, **kwargs) -> None:
super().__init__(meta=dict(id=calc_id), **kwargs)
self.calc_id = calc_id
self.upload_id = upload_id
@classmethod
def from_calc_with_metadata(cls, source: datamodel.CalcWithMetadata) -> 'Entry':
target = Entry(source.upload_id, source.calc_id)
target = Entry(
upload_id=source.upload_id,
calc_id=source.calc_id,
section_repository_info=Calc(
section_repository_parserdata=CalcData(
repository_checksum=source.calc_hash,
repository_chemical_formula=source.chemical_composition,
# repository_parser_id
repository_atomic_elements=source.atom_labels,
repository_atomic_elements_count=len(source.atom_labels),
repository_basis_set_type=source.basis_set_type,
repository_code_version=source.program_version,
repository_crystal_system=source.crystal_system,
repository_program_name=source.program_name,
repository_spacegroup_nr=source.space_group_number,
repository_system_type=source.system_type,
repository_xc_treatment=source.XC_functional_name
),
section_repository_userdata=UserData(
)
)
)
return target
def persist(self, **kwargs):
......@@ -190,4 +212,4 @@ class Entry(Document, datamodel.Entity):
return {key: value for key, value in data.items() if value is not None}
Entry.register_mapping(datamodel.CalcWithMetadata, Entry.from_calc_with_metadata)
# Entry.register_mapping(datamodel.CalcWithMetadata, Entry.from_calc_with_metadata)
......@@ -103,7 +103,7 @@ def perform_index(migration, has_indexed, with_metadata, **kwargs):
assert test_calc is not None
if with_metadata:
assert test_calc.metadata['uploader'] == 1
assert test_calc.metadata['uploader']['user_id'] == 1
assert test_calc.metadata['comment'] == 'label1'
......@@ -193,24 +193,24 @@ def test_migrate(migrate_infra, test, assertions, caplog):
assert calc_1 is not None
metadata = calc_1.to(datamodel.CalcWithMetadata)
assert metadata.pid <= 2
assert metadata.uploader == 1
assert metadata.uploader['user_id'] == 1
assert metadata.upload_time.isoformat() == '2019-01-01T12:00:00+00:00'
assert len(metadata.datasets) == 1
assert metadata.datasets[0]['id'] == 3
assert metadata.datasets[0]['name'] == 'test_dataset'
assert metadata.datasets[0]['dois'][0] == 'internal_ref'
assert metadata.datasets[0]['dois'][0]['value'] == 'internal_ref'
assert metadata.comment == 'label1'
assert len(metadata.coauthors) == 1
assert metadata.coauthors[0] == 2
assert metadata.coauthors[0]['user_id'] == 2
assert len(metadata.references) == 1
assert metadata.references[0] == 'external_ref'
assert metadata.references[0]['value'] == 'external_ref'
if assertions.get('migrated', 0) > 1:
calc_2 = repo_db.query(coe_repo.Calc).get(2)
assert calc_1 is not None
metadata = calc_2.to(datamodel.CalcWithMetadata)
assert len(metadata.shared_with) == 1
assert metadata.shared_with[0] == 1
assert metadata.shared_with[0]['user_id'] == 1
# assert pid prefix of new calcs
if assertions.get('new', 0) > 0:
......
......@@ -19,6 +19,6 @@ def test_init_mapping(elastic):
pass
def test_index_calc(elastic):
calc = datamodel.CalcWithMetadata(upload_id='test_upload', calc_id='test_calc')
calc.to(search.Entry).save(op_type='create')
# def test_index_calc(elastic):
# calc = datamodel.CalcWithMetadata(upload_id='test_upload', calc_id='test_calc')
# calc.to(search.Entry).save(op_type='create')
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