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inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | license | def license(self, key, value):
"""Populate the ``license`` key."""
def _get_license(value):
a_values = force_list(value.get('a'))
oa_licenses = [el for el in a_values if el == 'OA' or el == 'Open Access']
other_licenses = [el for el in a_values if el != 'OA' and el != 'Open Access']
if not other_licenses:
return force_single_element(oa_licenses)
return force_single_element(other_licenses)
def _get_material(value):
material = value.get('3', '').lower()
if material == 'article':
return 'publication'
return material
return {
'imposing': value.get('b'),
'license': _get_license(value),
'material': _get_material(value),
'url': value.get('u'),
} | python | def license(self, key, value):
"""Populate the ``license`` key."""
def _get_license(value):
a_values = force_list(value.get('a'))
oa_licenses = [el for el in a_values if el == 'OA' or el == 'Open Access']
other_licenses = [el for el in a_values if el != 'OA' and el != 'Open Access']
if not other_licenses:
return force_single_element(oa_licenses)
return force_single_element(other_licenses)
def _get_material(value):
material = value.get('3', '').lower()
if material == 'article':
return 'publication'
return material
return {
'imposing': value.get('b'),
'license': _get_license(value),
'material': _get_material(value),
'url': value.get('u'),
} | Populate the ``license`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L221-L244 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | license2marc | def license2marc(self, key, value):
"""Populate the ``540`` MARC field."""
return {
'a': value.get('license'),
'b': value.get('imposing'),
'u': value.get('url'),
'3': value.get('material'),
} | python | def license2marc(self, key, value):
"""Populate the ``540`` MARC field."""
return {
'a': value.get('license'),
'b': value.get('imposing'),
'u': value.get('url'),
'3': value.get('material'),
} | Populate the ``540`` MARC field. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L249-L256 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | copyright | def copyright(self, key, value):
"""Populate the ``copyright`` key."""
MATERIAL_MAP = {
'Article': 'publication',
'Published thesis as a book': 'publication',
}
material = value.get('e') or value.get('3')
return {
'holder': value.get('d'),
'material': MATERIAL_MAP.get(material),
'statement': value.get('f'),
'url': value.get('u'),
'year': maybe_int(value.get('g')),
} | python | def copyright(self, key, value):
"""Populate the ``copyright`` key."""
MATERIAL_MAP = {
'Article': 'publication',
'Published thesis as a book': 'publication',
}
material = value.get('e') or value.get('3')
return {
'holder': value.get('d'),
'material': MATERIAL_MAP.get(material),
'statement': value.get('f'),
'url': value.get('u'),
'year': maybe_int(value.get('g')),
} | Populate the ``copyright`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L261-L276 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | copyright2marc | def copyright2marc(self, key, value):
"""Populate the ``542`` MARC field."""
E_MAP = {
'publication': 'Article',
}
e_value = value.get('material')
return {
'd': value.get('holder'),
'e': E_MAP.get(e_value),
'f': value.get('statement'),
'g': value.get('year'),
'u': value.get('url'),
} | python | def copyright2marc(self, key, value):
"""Populate the ``542`` MARC field."""
E_MAP = {
'publication': 'Article',
}
e_value = value.get('material')
return {
'd': value.get('holder'),
'e': E_MAP.get(e_value),
'f': value.get('statement'),
'g': value.get('year'),
'u': value.get('url'),
} | Populate the ``542`` MARC field. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L281-L295 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | _private_notes | def _private_notes(self, key, value):
"""Populate the ``_private_notes`` key.
Also populates the ``_export_to`` key through side effects.
"""
def _is_for_cds(value):
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
return 'CDS' in normalized_c_values
def _is_for_hal(value):
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
return 'HAL' in normalized_c_values
def _is_not_for_hal(value):
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
return 'NOT HAL' in normalized_c_values
_private_notes = self.get('_private_notes', [])
_export_to = self.get('_export_to', {})
for value in force_list(value):
if _is_for_cds(value):
_export_to['CDS'] = True
if _is_for_hal(value):
_export_to['HAL'] = True
elif _is_not_for_hal(value):
_export_to['HAL'] = False
source = force_single_element(value.get('9'))
for _private_note in force_list(value.get('a')):
_private_notes.append({
'source': source,
'value': _private_note,
})
self['_export_to'] = _export_to
return _private_notes | python | def _private_notes(self, key, value):
"""Populate the ``_private_notes`` key.
Also populates the ``_export_to`` key through side effects.
"""
def _is_for_cds(value):
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
return 'CDS' in normalized_c_values
def _is_for_hal(value):
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
return 'HAL' in normalized_c_values
def _is_not_for_hal(value):
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
return 'NOT HAL' in normalized_c_values
_private_notes = self.get('_private_notes', [])
_export_to = self.get('_export_to', {})
for value in force_list(value):
if _is_for_cds(value):
_export_to['CDS'] = True
if _is_for_hal(value):
_export_to['HAL'] = True
elif _is_not_for_hal(value):
_export_to['HAL'] = False
source = force_single_element(value.get('9'))
for _private_note in force_list(value.get('a')):
_private_notes.append({
'source': source,
'value': _private_note,
})
self['_export_to'] = _export_to
return _private_notes | Populate the ``_private_notes`` key.
Also populates the ``_export_to`` key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L299-L336 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | _private_notes2marc | def _private_notes2marc(self, key, value):
"""Populate the ``595`` MARC key.
Also populates the `595_H` MARC key through side effects.
"""
def _is_from_hal(value):
return value.get('source') == 'HAL'
if not _is_from_hal(value):
return {
'9': value.get('source'),
'a': value.get('value'),
}
self.setdefault('595_H', []).append({'a': value.get('value')}) | python | def _private_notes2marc(self, key, value):
"""Populate the ``595`` MARC key.
Also populates the `595_H` MARC key through side effects.
"""
def _is_from_hal(value):
return value.get('source') == 'HAL'
if not _is_from_hal(value):
return {
'9': value.get('source'),
'a': value.get('value'),
}
self.setdefault('595_H', []).append({'a': value.get('value')}) | Populate the ``595`` MARC key.
Also populates the `595_H` MARC key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L341-L355 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | _export_to2marc | def _export_to2marc(self, key, value):
"""Populate the ``595`` MARC field."""
def _is_for_cds(value):
return 'CDS' in value
def _is_for_hal(value):
return 'HAL' in value and value['HAL']
def _is_not_for_hal(value):
return 'HAL' in value and not value['HAL']
result = []
if _is_for_cds(value):
result.append({'c': 'CDS'})
if _is_for_hal(value):
result.append({'c': 'HAL'})
elif _is_not_for_hal(value):
result.append({'c': 'not HAL'})
return result | python | def _export_to2marc(self, key, value):
"""Populate the ``595`` MARC field."""
def _is_for_cds(value):
return 'CDS' in value
def _is_for_hal(value):
return 'HAL' in value and value['HAL']
def _is_not_for_hal(value):
return 'HAL' in value and not value['HAL']
result = []
if _is_for_cds(value):
result.append({'c': 'CDS'})
if _is_for_hal(value):
result.append({'c': 'HAL'})
elif _is_not_for_hal(value):
result.append({'c': 'not HAL'})
return result | Populate the ``595`` MARC field. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L359-L380 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | _desy_bookkeeping | def _desy_bookkeeping(self, key, value):
"""Populate the ``_desy_bookkeeping`` key."""
return {
'date': normalize_date(value.get('d')),
'expert': force_single_element(value.get('a')),
'status': value.get('s'),
} | python | def _desy_bookkeeping(self, key, value):
"""Populate the ``_desy_bookkeeping`` key."""
return {
'date': normalize_date(value.get('d')),
'expert': force_single_element(value.get('a')),
'status': value.get('s'),
} | Populate the ``_desy_bookkeeping`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L385-L391 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd5xx.py | _desy_bookkeeping2marc | def _desy_bookkeeping2marc(self, key, value):
"""Populate the ``595_D`` MARC field.
Also populates the ``035`` MARC field through side effects.
"""
if 'identifier' not in value:
return {
'a': value.get('expert'),
'd': value.get('date'),
's': value.get('status'),
}
self.setdefault('035', []).append({
'9': 'DESY',
'z': value['identifier']
}) | python | def _desy_bookkeeping2marc(self, key, value):
"""Populate the ``595_D`` MARC field.
Also populates the ``035`` MARC field through side effects.
"""
if 'identifier' not in value:
return {
'a': value.get('expert'),
'd': value.get('date'),
's': value.get('status'),
}
self.setdefault('035', []).append({
'9': 'DESY',
'z': value['identifier']
}) | Populate the ``595_D`` MARC field.
Also populates the ``035`` MARC field through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd5xx.py#L396-L411 |
inspirehep/inspire-dojson | inspire_dojson/experiments/rules.py | _dates | def _dates(self, key, value):
"""Don't populate any key through the return value.
On the other hand, populates the ``date_proposed``, ``date_approved``,
``date_started``, ``date_cancelled``, and the ``date_completed`` keys
through side effects.
"""
if value.get('q'):
self['date_proposed'] = normalize_date(value['q'])
if value.get('r'):
self['date_approved'] = normalize_date(value['r'])
if value.get('s'):
self['date_started'] = normalize_date(value['s'])
if value.get('c'):
self['date_cancelled'] = normalize_date(value['c'])
if value.get('t'):
self['date_completed'] = normalize_date(value['t'])
raise IgnoreKey | python | def _dates(self, key, value):
"""Don't populate any key through the return value.
On the other hand, populates the ``date_proposed``, ``date_approved``,
``date_started``, ``date_cancelled``, and the ``date_completed`` keys
through side effects.
"""
if value.get('q'):
self['date_proposed'] = normalize_date(value['q'])
if value.get('r'):
self['date_approved'] = normalize_date(value['r'])
if value.get('s'):
self['date_started'] = normalize_date(value['s'])
if value.get('c'):
self['date_cancelled'] = normalize_date(value['c'])
if value.get('t'):
self['date_completed'] = normalize_date(value['t'])
raise IgnoreKey | Don't populate any key through the return value.
On the other hand, populates the ``date_proposed``, ``date_approved``,
``date_started``, ``date_cancelled``, and the ``date_completed`` keys
through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/experiments/rules.py#L42-L60 |
inspirehep/inspire-dojson | inspire_dojson/experiments/rules.py | experiment | def experiment(self, key, values):
"""Populate the ``experiment`` key.
Also populates the ``legacy_name``, the ``accelerator``, and the
``institutions`` keys through side effects.
"""
experiment = self.get('experiment', {})
legacy_name = self.get('legacy_name', '')
accelerator = self.get('accelerator', {})
institutions = self.get('institutions', [])
for value in force_list(values):
if value.get('c'):
experiment['value'] = value.get('c')
if value.get('d'):
experiment['short_name'] = value.get('d')
if value.get('a'):
legacy_name = value.get('a')
if value.get('b'):
accelerator['value'] = value.get('b')
institution = {}
if value.get('u'):
institution['value'] = value.get('u')
if value.get('z'):
record = get_record_ref(maybe_int(value.get('z')), 'institutions')
if record:
institution['curated_relation'] = True
institution['record'] = record
institutions.append(institution)
self['legacy_name'] = legacy_name
self['accelerator'] = accelerator
self['institutions'] = institutions
return experiment | python | def experiment(self, key, values):
"""Populate the ``experiment`` key.
Also populates the ``legacy_name``, the ``accelerator``, and the
``institutions`` keys through side effects.
"""
experiment = self.get('experiment', {})
legacy_name = self.get('legacy_name', '')
accelerator = self.get('accelerator', {})
institutions = self.get('institutions', [])
for value in force_list(values):
if value.get('c'):
experiment['value'] = value.get('c')
if value.get('d'):
experiment['short_name'] = value.get('d')
if value.get('a'):
legacy_name = value.get('a')
if value.get('b'):
accelerator['value'] = value.get('b')
institution = {}
if value.get('u'):
institution['value'] = value.get('u')
if value.get('z'):
record = get_record_ref(maybe_int(value.get('z')), 'institutions')
if record:
institution['curated_relation'] = True
institution['record'] = record
institutions.append(institution)
self['legacy_name'] = legacy_name
self['accelerator'] = accelerator
self['institutions'] = institutions
return experiment | Populate the ``experiment`` key.
Also populates the ``legacy_name``, the ``accelerator``, and the
``institutions`` keys through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/experiments/rules.py#L64-L100 |
inspirehep/inspire-dojson | inspire_dojson/experiments/rules.py | core | def core(self, key, value):
"""Populate the ``core`` key.
Also populates the ``deleted`` and ``project_type`` keys through side
effects.
"""
core = self.get('core')
deleted = self.get('deleted')
project_type = self.get('project_type', [])
if not core:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'CORE' in normalized_a_values:
core = True
if not deleted:
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
if 'DELETED' in normalized_c_values:
deleted = True
if not project_type:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'ACCELERATOR' in normalized_a_values:
project_type.append('accelerator')
self['project_type'] = project_type
self['deleted'] = deleted
return core | python | def core(self, key, value):
"""Populate the ``core`` key.
Also populates the ``deleted`` and ``project_type`` keys through side
effects.
"""
core = self.get('core')
deleted = self.get('deleted')
project_type = self.get('project_type', [])
if not core:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'CORE' in normalized_a_values:
core = True
if not deleted:
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
if 'DELETED' in normalized_c_values:
deleted = True
if not project_type:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'ACCELERATOR' in normalized_a_values:
project_type.append('accelerator')
self['project_type'] = project_type
self['deleted'] = deleted
return core | Populate the ``core`` key.
Also populates the ``deleted`` and ``project_type`` keys through side
effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/experiments/rules.py#L170-L197 |
inspirehep/inspire-dojson | inspire_dojson/common/rules.py | control_number | def control_number(endpoint):
"""Populate the ``control_number`` key.
Also populates the ``self`` key through side effects.
"""
def _control_number(self, key, value):
self['self'] = get_record_ref(int(value), endpoint)
return int(value)
return _control_number | python | def control_number(endpoint):
"""Populate the ``control_number`` key.
Also populates the ``self`` key through side effects.
"""
def _control_number(self, key, value):
self['self'] = get_record_ref(int(value), endpoint)
return int(value)
return _control_number | Populate the ``control_number`` key.
Also populates the ``self`` key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/common/rules.py#L586-L595 |
inspirehep/inspire-dojson | inspire_dojson/common/rules.py | acquisition_source | def acquisition_source(self, key, value):
"""Populate the ``acquisition_source`` key."""
def _get_datetime(value):
d_value = force_single_element(value.get('d', ''))
if d_value:
try:
date = PartialDate.loads(d_value)
except ValueError:
return d_value
else:
datetime_ = datetime(year=date.year, month=date.month, day=date.day)
return datetime_.isoformat()
internal_uid, orcid, source = None, None, None
a_values = force_list(value.get('a'))
for a_value in a_values:
if IS_INTERNAL_UID.match(a_value):
if a_value.startswith('inspire:uid:'):
internal_uid = int(a_value[12:])
else:
internal_uid = int(a_value)
elif IS_ORCID.match(a_value):
if a_value.startswith('orcid:'):
orcid = a_value[6:]
else:
orcid = a_value
else:
source = a_value
c_value = force_single_element(value.get('c', ''))
normalized_c_value = c_value.lower()
if normalized_c_value == 'batchupload':
method = 'batchuploader'
elif normalized_c_value == 'submission':
method = 'submitter'
else:
method = normalized_c_value
return {
'datetime': _get_datetime(value),
'email': value.get('b'),
'internal_uid': internal_uid,
'method': method,
'orcid': orcid,
'source': source,
'submission_number': value.get('e'),
} | python | def acquisition_source(self, key, value):
"""Populate the ``acquisition_source`` key."""
def _get_datetime(value):
d_value = force_single_element(value.get('d', ''))
if d_value:
try:
date = PartialDate.loads(d_value)
except ValueError:
return d_value
else:
datetime_ = datetime(year=date.year, month=date.month, day=date.day)
return datetime_.isoformat()
internal_uid, orcid, source = None, None, None
a_values = force_list(value.get('a'))
for a_value in a_values:
if IS_INTERNAL_UID.match(a_value):
if a_value.startswith('inspire:uid:'):
internal_uid = int(a_value[12:])
else:
internal_uid = int(a_value)
elif IS_ORCID.match(a_value):
if a_value.startswith('orcid:'):
orcid = a_value[6:]
else:
orcid = a_value
else:
source = a_value
c_value = force_single_element(value.get('c', ''))
normalized_c_value = c_value.lower()
if normalized_c_value == 'batchupload':
method = 'batchuploader'
elif normalized_c_value == 'submission':
method = 'submitter'
else:
method = normalized_c_value
return {
'datetime': _get_datetime(value),
'email': value.get('b'),
'internal_uid': internal_uid,
'method': method,
'orcid': orcid,
'source': source,
'submission_number': value.get('e'),
} | Populate the ``acquisition_source`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/common/rules.py#L634-L682 |
inspirehep/inspire-dojson | inspire_dojson/common/rules.py | public_notes_500 | def public_notes_500(self, key, value):
"""Populate the ``public_notes`` key."""
return [
{
'source': value.get('9'),
'value': public_note,
} for public_note in force_list(value.get('a'))
] | python | def public_notes_500(self, key, value):
"""Populate the ``public_notes`` key."""
return [
{
'source': value.get('9'),
'value': public_note,
} for public_note in force_list(value.get('a'))
] | Populate the ``public_notes`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/common/rules.py#L719-L726 |
inspirehep/inspire-dojson | inspire_dojson/common/rules.py | _private_notes_595 | def _private_notes_595(self, key, value):
"""Populate the ``_private_notes`` key."""
return [
{
'source': value.get('9'),
'value': _private_note,
} for _private_note in force_list(value.get('a'))
] | python | def _private_notes_595(self, key, value):
"""Populate the ``_private_notes`` key."""
return [
{
'source': value.get('9'),
'value': _private_note,
} for _private_note in force_list(value.get('a'))
] | Populate the ``_private_notes`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/common/rules.py#L747-L754 |
inspirehep/inspire-dojson | inspire_dojson/common/rules.py | external_system_identifiers | def external_system_identifiers(endpoint):
"""Populate the ``external_system_identifiers`` key.
Also populates the ``new_record`` key through side effects.
"""
@utils.flatten
@utils.for_each_value
def _external_system_identifiers(self, key, value):
new_recid = maybe_int(value.get('d'))
if new_recid:
self['new_record'] = get_record_ref(new_recid, endpoint)
return [
{
'schema': 'SPIRES',
'value': ext_sys_id,
} for ext_sys_id in force_list(value.get('a'))
]
return _external_system_identifiers | python | def external_system_identifiers(endpoint):
"""Populate the ``external_system_identifiers`` key.
Also populates the ``new_record`` key through side effects.
"""
@utils.flatten
@utils.for_each_value
def _external_system_identifiers(self, key, value):
new_recid = maybe_int(value.get('d'))
if new_recid:
self['new_record'] = get_record_ref(new_recid, endpoint)
return [
{
'schema': 'SPIRES',
'value': ext_sys_id,
} for ext_sys_id in force_list(value.get('a'))
]
return _external_system_identifiers | Populate the ``external_system_identifiers`` key.
Also populates the ``new_record`` key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/common/rules.py#L901-L920 |
inspirehep/inspire-dojson | inspire_dojson/common/rules.py | deleted_records | def deleted_records(endpoint):
"""Populate the ``deleted_records`` key."""
@utils.for_each_value
def _deleted_records(self, key, value):
deleted_recid = maybe_int(value.get('a'))
if deleted_recid:
return get_record_ref(deleted_recid, endpoint)
return _deleted_records | python | def deleted_records(endpoint):
"""Populate the ``deleted_records`` key."""
@utils.for_each_value
def _deleted_records(self, key, value):
deleted_recid = maybe_int(value.get('a'))
if deleted_recid:
return get_record_ref(deleted_recid, endpoint)
return _deleted_records | Populate the ``deleted_records`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/common/rules.py#L944-L952 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd6xx.py | accelerator_experiments | def accelerator_experiments(self, key, value):
"""Populate the ``accelerator_experiments`` key."""
result = []
a_value = force_single_element(value.get('a'))
e_values = [el for el in force_list(value.get('e')) if el != '-']
zero_values = force_list(value.get('0'))
if a_value and not e_values:
result.append({'accelerator': a_value})
# XXX: we zip only when they have the same length, otherwise
# we might match a value with the wrong recid.
if len(e_values) == len(zero_values):
for e_value, zero_value in zip(e_values, zero_values):
result.append({
'legacy_name': e_value,
'record': get_record_ref(zero_value, 'experiments'),
})
else:
for e_value in e_values:
result.append({'legacy_name': e_value})
return result | python | def accelerator_experiments(self, key, value):
"""Populate the ``accelerator_experiments`` key."""
result = []
a_value = force_single_element(value.get('a'))
e_values = [el for el in force_list(value.get('e')) if el != '-']
zero_values = force_list(value.get('0'))
if a_value and not e_values:
result.append({'accelerator': a_value})
# XXX: we zip only when they have the same length, otherwise
# we might match a value with the wrong recid.
if len(e_values) == len(zero_values):
for e_value, zero_value in zip(e_values, zero_values):
result.append({
'legacy_name': e_value,
'record': get_record_ref(zero_value, 'experiments'),
})
else:
for e_value in e_values:
result.append({'legacy_name': e_value})
return result | Populate the ``accelerator_experiments`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd6xx.py#L53-L76 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd6xx.py | keywords | def keywords(self, key, values):
"""Populate the ``keywords`` key.
Also populates the ``energy_ranges`` key through side effects.
"""
keywords = self.get('keywords', [])
energy_ranges = self.get('energy_ranges', [])
for value in force_list(values):
if value.get('a'):
schema = force_single_element(value.get('2', '')).upper()
sources = force_list(value.get('9'))
a_values = force_list(value.get('a'))
if 'conference' not in sources:
for a_value in a_values:
keywords.append({
'schema': schema,
'source': force_single_element(sources),
'value': a_value,
})
if value.get('e'):
energy_ranges.append(ENERGY_RANGES_MAP.get(value.get('e')))
self['energy_ranges'] = energy_ranges
return keywords | python | def keywords(self, key, values):
"""Populate the ``keywords`` key.
Also populates the ``energy_ranges`` key through side effects.
"""
keywords = self.get('keywords', [])
energy_ranges = self.get('energy_ranges', [])
for value in force_list(values):
if value.get('a'):
schema = force_single_element(value.get('2', '')).upper()
sources = force_list(value.get('9'))
a_values = force_list(value.get('a'))
if 'conference' not in sources:
for a_value in a_values:
keywords.append({
'schema': schema,
'source': force_single_element(sources),
'value': a_value,
})
if value.get('e'):
energy_ranges.append(ENERGY_RANGES_MAP.get(value.get('e')))
self['energy_ranges'] = energy_ranges
return keywords | Populate the ``keywords`` key.
Also populates the ``energy_ranges`` key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd6xx.py#L90-L117 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd6xx.py | keywords2marc | def keywords2marc(self, key, values):
"""Populate the ``695`` MARC field.
Also populates the ``084`` and ``6531`` MARC fields through side effects.
"""
result_695 = self.get('695', [])
result_084 = self.get('084', [])
result_6531 = self.get('6531', [])
for value in values:
schema = value.get('schema')
source = value.get('source')
keyword = value.get('value')
if schema == 'PACS' or schema == 'PDG':
result_084.append({
'2': schema,
'9': source,
'a': keyword,
})
elif schema == 'JACOW':
result_6531.append({
'2': 'JACoW',
'9': source,
'a': keyword,
})
elif schema == 'INSPIRE':
result_695.append({
'2': 'INSPIRE',
'9': source,
'a': keyword,
})
elif schema == 'INIS':
result_695.append({
'2': 'INIS',
'9': source,
'a': keyword,
})
elif source != 'magpie':
result_6531.append({
'9': source,
'a': keyword,
})
self['6531'] = result_6531
self['084'] = result_084
return result_695 | python | def keywords2marc(self, key, values):
"""Populate the ``695`` MARC field.
Also populates the ``084`` and ``6531`` MARC fields through side effects.
"""
result_695 = self.get('695', [])
result_084 = self.get('084', [])
result_6531 = self.get('6531', [])
for value in values:
schema = value.get('schema')
source = value.get('source')
keyword = value.get('value')
if schema == 'PACS' or schema == 'PDG':
result_084.append({
'2': schema,
'9': source,
'a': keyword,
})
elif schema == 'JACOW':
result_6531.append({
'2': 'JACoW',
'9': source,
'a': keyword,
})
elif schema == 'INSPIRE':
result_695.append({
'2': 'INSPIRE',
'9': source,
'a': keyword,
})
elif schema == 'INIS':
result_695.append({
'2': 'INIS',
'9': source,
'a': keyword,
})
elif source != 'magpie':
result_6531.append({
'9': source,
'a': keyword,
})
self['6531'] = result_6531
self['084'] = result_084
return result_695 | Populate the ``695`` MARC field.
Also populates the ``084`` and ``6531`` MARC fields through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd6xx.py#L132-L178 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd7xx.py | collaborations | def collaborations(self, key, value):
"""Populate the ``collaborations`` key."""
result = []
for g_value in force_list(value.get('g')):
collaborations = normalize_collaboration(g_value)
if len(collaborations) == 1:
result.append({
'record': get_record_ref(maybe_int(value.get('0')), 'experiments'),
'value': collaborations[0],
})
else:
result.extend({'value': collaboration} for collaboration in collaborations)
return result | python | def collaborations(self, key, value):
"""Populate the ``collaborations`` key."""
result = []
for g_value in force_list(value.get('g')):
collaborations = normalize_collaboration(g_value)
if len(collaborations) == 1:
result.append({
'record': get_record_ref(maybe_int(value.get('0')), 'experiments'),
'value': collaborations[0],
})
else:
result.extend({'value': collaboration} for collaboration in collaborations)
return result | Populate the ``collaborations`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd7xx.py#L49-L63 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd7xx.py | publication_info | def publication_info(self, key, value):
"""Populate the ``publication_info`` key."""
def _get_cnum(value):
w_value = force_single_element(value.get('w', ''))
normalized_w_value = w_value.replace('/', '-').upper()
return normalized_w_value
def _get_material(value):
schema = load_schema('elements/material')
valid_materials = schema['enum']
m_value = force_single_element(value.get('m', ''))
normalized_m_value = m_value.lower()
if normalized_m_value in valid_materials:
return normalized_m_value
def _get_parent_isbn(value):
z_value = force_single_element(value.get('z', ''))
if z_value:
return normalize_isbn(z_value)
def _get_pubinfo_freetext(value):
x_value = force_single_element(value.get('x', ''))
if not x_value.startswith('#DONE'):
return x_value
page_start, page_end, artid = split_page_artid(value.get('c'))
parent_recid = maybe_int(force_single_element(value.get('0')))
parent_record = get_record_ref(parent_recid, 'literature')
journal_recid = maybe_int(force_single_element(value.get('1')))
journal_record = get_record_ref(journal_recid, 'journals')
conference_recid = maybe_int(force_single_element(value.get('2')))
conference_record = get_record_ref(conference_recid, 'conferences')
return {
'artid': artid,
'cnum': _get_cnum(value),
'conf_acronym': force_single_element(value.get('q')),
'conference_record': conference_record,
'hidden': key.startswith('7731') or None,
'journal_issue': force_single_element(value.get('n')),
'journal_record': journal_record,
'journal_title': force_single_element(value.get('p')),
'journal_volume': force_single_element(value.get('v')),
'material': _get_material(value),
'page_end': page_end,
'page_start': page_start,
'parent_isbn': _get_parent_isbn(value),
'parent_record': parent_record,
'parent_report_number': force_single_element(value.get('r')),
'pubinfo_freetext': _get_pubinfo_freetext(value),
'year': maybe_int(force_single_element(value.get('y'))),
} | python | def publication_info(self, key, value):
"""Populate the ``publication_info`` key."""
def _get_cnum(value):
w_value = force_single_element(value.get('w', ''))
normalized_w_value = w_value.replace('/', '-').upper()
return normalized_w_value
def _get_material(value):
schema = load_schema('elements/material')
valid_materials = schema['enum']
m_value = force_single_element(value.get('m', ''))
normalized_m_value = m_value.lower()
if normalized_m_value in valid_materials:
return normalized_m_value
def _get_parent_isbn(value):
z_value = force_single_element(value.get('z', ''))
if z_value:
return normalize_isbn(z_value)
def _get_pubinfo_freetext(value):
x_value = force_single_element(value.get('x', ''))
if not x_value.startswith('#DONE'):
return x_value
page_start, page_end, artid = split_page_artid(value.get('c'))
parent_recid = maybe_int(force_single_element(value.get('0')))
parent_record = get_record_ref(parent_recid, 'literature')
journal_recid = maybe_int(force_single_element(value.get('1')))
journal_record = get_record_ref(journal_recid, 'journals')
conference_recid = maybe_int(force_single_element(value.get('2')))
conference_record = get_record_ref(conference_recid, 'conferences')
return {
'artid': artid,
'cnum': _get_cnum(value),
'conf_acronym': force_single_element(value.get('q')),
'conference_record': conference_record,
'hidden': key.startswith('7731') or None,
'journal_issue': force_single_element(value.get('n')),
'journal_record': journal_record,
'journal_title': force_single_element(value.get('p')),
'journal_volume': force_single_element(value.get('v')),
'material': _get_material(value),
'page_end': page_end,
'page_start': page_start,
'parent_isbn': _get_parent_isbn(value),
'parent_record': parent_record,
'parent_report_number': force_single_element(value.get('r')),
'pubinfo_freetext': _get_pubinfo_freetext(value),
'year': maybe_int(force_single_element(value.get('y'))),
} | Populate the ``publication_info`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd7xx.py#L75-L132 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd7xx.py | publication_info2marc | def publication_info2marc(self, key, values):
"""Populate the ``773`` MARC field.
Also populates the ``7731`` MARC field through side effects.
"""
result_773 = self.get('773', [])
result_7731 = self.get('7731', [])
for value in force_list(convert_new_publication_info_to_old(values)):
page_artid = []
if value.get('page_start') and value.get('page_end'):
page_artid.append(u'{page_start}-{page_end}'.format(**value))
elif value.get('page_start'):
page_artid.append(u'{page_start}'.format(**value))
elif value.get('artid'):
page_artid.append(u'{artid}'.format(**value))
result = {
'0': get_recid_from_ref(value.get('parent_record')),
'c': page_artid,
'm': value.get('material'),
'n': value.get('journal_issue'),
'p': value.get('journal_title'),
'q': value.get('conf_acronym'),
'r': value.get('parent_report_number'),
'v': value.get('journal_volume'),
'w': value.get('cnum'),
'x': value.get('pubinfo_freetext'),
'y': value.get('year'),
'z': value.get('parent_isbn'),
}
if value.get('hidden'):
result_7731.append(result)
else:
result_773.append(result)
self['7731'] = result_7731
return result_773 | python | def publication_info2marc(self, key, values):
"""Populate the ``773`` MARC field.
Also populates the ``7731`` MARC field through side effects.
"""
result_773 = self.get('773', [])
result_7731 = self.get('7731', [])
for value in force_list(convert_new_publication_info_to_old(values)):
page_artid = []
if value.get('page_start') and value.get('page_end'):
page_artid.append(u'{page_start}-{page_end}'.format(**value))
elif value.get('page_start'):
page_artid.append(u'{page_start}'.format(**value))
elif value.get('artid'):
page_artid.append(u'{artid}'.format(**value))
result = {
'0': get_recid_from_ref(value.get('parent_record')),
'c': page_artid,
'm': value.get('material'),
'n': value.get('journal_issue'),
'p': value.get('journal_title'),
'q': value.get('conf_acronym'),
'r': value.get('parent_report_number'),
'v': value.get('journal_volume'),
'w': value.get('cnum'),
'x': value.get('pubinfo_freetext'),
'y': value.get('year'),
'z': value.get('parent_isbn'),
}
if value.get('hidden'):
result_7731.append(result)
else:
result_773.append(result)
self['7731'] = result_7731
return result_773 | Populate the ``773`` MARC field.
Also populates the ``7731`` MARC field through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd7xx.py#L136-L174 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd7xx.py | related_records_78002 | def related_records_78002(self, key, value):
"""Populate the ``related_records`` key."""
record = get_record_ref(maybe_int(value.get('w')), 'literature')
if record:
return {
'curated_relation': record is not None,
'record': record,
'relation': 'predecessor',
} | python | def related_records_78002(self, key, value):
"""Populate the ``related_records`` key."""
record = get_record_ref(maybe_int(value.get('w')), 'literature')
if record:
return {
'curated_relation': record is not None,
'record': record,
'relation': 'predecessor',
} | Populate the ``related_records`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd7xx.py#L179-L187 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd7xx.py | related_records_78502 | def related_records_78502(self, key, value):
"""Populate the ``related_records`` key."""
record = get_record_ref(maybe_int(value.get('w')), 'literature')
if record:
return {
'curated_relation': record is not None,
'record': record,
'relation': 'successor',
} | python | def related_records_78502(self, key, value):
"""Populate the ``related_records`` key."""
record = get_record_ref(maybe_int(value.get('w')), 'literature')
if record:
return {
'curated_relation': record is not None,
'record': record,
'relation': 'successor',
} | Populate the ``related_records`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd7xx.py#L192-L200 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd7xx.py | related_records_78708 | def related_records_78708(self, key, value):
"""Populate the ``related_records`` key."""
record = get_record_ref(maybe_int(value.get('w')), 'literature')
if record:
return {
'curated_relation': record is not None,
'record': record,
'relation_freetext': value.get('i'),
} | python | def related_records_78708(self, key, value):
"""Populate the ``related_records`` key."""
record = get_record_ref(maybe_int(value.get('w')), 'literature')
if record:
return {
'curated_relation': record is not None,
'record': record,
'relation_freetext': value.get('i'),
} | Populate the ``related_records`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd7xx.py#L205-L213 |
inspirehep/inspire-dojson | inspire_dojson/hep/rules/bd7xx.py | related_records2marc | def related_records2marc(self, key, value):
"""Populate the ``78708`` MARC field
Also populates the ``78002``, ``78502`` MARC fields through side effects.
"""
if value.get('relation_freetext'):
return {
'i': value.get('relation_freetext'),
'w': get_recid_from_ref(value.get('record')),
}
elif value.get('relation') == 'successor':
self.setdefault('78502', []).append({
'i': 'superseded by',
'w': get_recid_from_ref(value.get('record')),
})
elif value.get('relation') == 'predecessor':
self.setdefault('78002', []).append({
'i': 'supersedes',
'w': get_recid_from_ref(value.get('record')),
})
else:
raise NotImplementedError(u"Unhandled relation in related_records: {}".format(value.get('relation'))) | python | def related_records2marc(self, key, value):
"""Populate the ``78708`` MARC field
Also populates the ``78002``, ``78502`` MARC fields through side effects.
"""
if value.get('relation_freetext'):
return {
'i': value.get('relation_freetext'),
'w': get_recid_from_ref(value.get('record')),
}
elif value.get('relation') == 'successor':
self.setdefault('78502', []).append({
'i': 'superseded by',
'w': get_recid_from_ref(value.get('record')),
})
elif value.get('relation') == 'predecessor':
self.setdefault('78002', []).append({
'i': 'supersedes',
'w': get_recid_from_ref(value.get('record')),
})
else:
raise NotImplementedError(u"Unhandled relation in related_records: {}".format(value.get('relation'))) | Populate the ``78708`` MARC field
Also populates the ``78002``, ``78502`` MARC fields through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/hep/rules/bd7xx.py#L218-L239 |
inspirehep/inspire-dojson | inspire_dojson/journals/rules.py | _private_notes | def _private_notes(self, key, value):
"""Populate the ``_private_notes`` key."""
return [
{
'source': value.get('9'),
'value': _private_note,
} for _private_note in force_list(value.get('x'))
] | python | def _private_notes(self, key, value):
"""Populate the ``_private_notes`` key."""
return [
{
'source': value.get('9'),
'value': _private_note,
} for _private_note in force_list(value.get('x'))
] | Populate the ``_private_notes`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/journals/rules.py#L149-L156 |
inspirehep/inspire-dojson | inspire_dojson/journals/rules.py | proceedings | def proceedings(self, key, value):
"""Populate the ``proceedings`` key.
Also populates the ``refereed`` key through side effects.
"""
proceedings = self.get('proceedings')
refereed = self.get('refereed')
if not proceedings:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'PROCEEDINGS' in normalized_a_values:
proceedings = True
if not refereed:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'PEER REVIEW' in normalized_a_values:
refereed = True
elif 'NON-PUBLISHED' in normalized_a_values:
refereed = False
self['refereed'] = refereed
return proceedings | python | def proceedings(self, key, value):
"""Populate the ``proceedings`` key.
Also populates the ``refereed`` key through side effects.
"""
proceedings = self.get('proceedings')
refereed = self.get('refereed')
if not proceedings:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'PROCEEDINGS' in normalized_a_values:
proceedings = True
if not refereed:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'PEER REVIEW' in normalized_a_values:
refereed = True
elif 'NON-PUBLISHED' in normalized_a_values:
refereed = False
self['refereed'] = refereed
return proceedings | Populate the ``proceedings`` key.
Also populates the ``refereed`` key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/journals/rules.py#L178-L199 |
inspirehep/inspire-dojson | inspire_dojson/journals/rules.py | short_title | def short_title(self, key, value):
"""Populate the ``short_title`` key.
Also populates the ``title_variants`` key through side effects.
"""
short_title = value.get('a')
title_variants = self.get('title_variants', [])
if value.get('u'):
short_title = value.get('u')
title_variants.append(value.get('a'))
self['title_variants'] = title_variants
return short_title | python | def short_title(self, key, value):
"""Populate the ``short_title`` key.
Also populates the ``title_variants`` key through side effects.
"""
short_title = value.get('a')
title_variants = self.get('title_variants', [])
if value.get('u'):
short_title = value.get('u')
title_variants.append(value.get('a'))
self['title_variants'] = title_variants
return short_title | Populate the ``short_title`` key.
Also populates the ``title_variants`` key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/journals/rules.py#L203-L216 |
inspirehep/inspire-dojson | inspire_dojson/journals/rules.py | deleted | def deleted(self, key, value):
"""Populate the ``deleted`` key.
Also populates the ``book_series`` key through side effects.
"""
deleted = self.get('deleted')
book_series = self.get('book_series')
if not deleted:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
if 'DELETED' in normalized_a_values or 'DELETED' in normalized_c_values:
deleted = True
if not book_series:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'BOOKSERIES' in normalized_a_values:
book_series = True
self['book_series'] = book_series
return deleted | python | def deleted(self, key, value):
"""Populate the ``deleted`` key.
Also populates the ``book_series`` key through side effects.
"""
deleted = self.get('deleted')
book_series = self.get('book_series')
if not deleted:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
normalized_c_values = [el.upper() for el in force_list(value.get('c'))]
if 'DELETED' in normalized_a_values or 'DELETED' in normalized_c_values:
deleted = True
if not book_series:
normalized_a_values = [el.upper() for el in force_list(value.get('a'))]
if 'BOOKSERIES' in normalized_a_values:
book_series = True
self['book_series'] = book_series
return deleted | Populate the ``deleted`` key.
Also populates the ``book_series`` key through side effects. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/journals/rules.py#L229-L249 |
inspirehep/inspire-dojson | inspire_dojson/jobs/rules.py | ranks | def ranks(self, key, value):
"""Populate the ``ranks`` key."""
return [normalize_rank(el) for el in force_list(value.get('a'))] | python | def ranks(self, key, value):
"""Populate the ``ranks`` key."""
return [normalize_rank(el) for el in force_list(value.get('a'))] | Populate the ``ranks`` key. | https://github.com/inspirehep/inspire-dojson/blob/17f3789cd3d5ae58efa1190dc0eea9efb9c8ca59/inspire_dojson/jobs/rules.py#L177-L179 |
walkr/oi | oi/core.py | BaseProgram.new_parser | def new_parser(self):
""" Create a command line argument parser
Add a few default flags, such as --version
for displaying the program version when invoked """
parser = argparse.ArgumentParser(description=self.description)
parser.add_argument(
'--version', help='show version and exit',
default=False, action='store_true')
parser.add_argument(
'--debug', help='enable debugging',
default=False, action='store_true')
return parser | python | def new_parser(self):
""" Create a command line argument parser
Add a few default flags, such as --version
for displaying the program version when invoked """
parser = argparse.ArgumentParser(description=self.description)
parser.add_argument(
'--version', help='show version and exit',
default=False, action='store_true')
parser.add_argument(
'--debug', help='enable debugging',
default=False, action='store_true')
return parser | Create a command line argument parser
Add a few default flags, such as --version
for displaying the program version when invoked | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L48-L61 |
walkr/oi | oi/core.py | BaseProgram.add_command | def add_command(self, command, function, description=None):
""" Register a new function with a the name `command` and
`description` (which will be shown then help is invoked). """
self.registered[command] = {
'function': function, 'description': description
} | python | def add_command(self, command, function, description=None):
""" Register a new function with a the name `command` and
`description` (which will be shown then help is invoked). """
self.registered[command] = {
'function': function, 'description': description
} | Register a new function with a the name `command` and
`description` (which will be shown then help is invoked). | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L63-L69 |
walkr/oi | oi/core.py | BaseProgram.run | def run(self, args=None):
""" Parse command line arguments if necessary then run program.
By default this method will just take of the --version flag.
The logic for other flags should be handled by your subclass """
args = args or self.parser.parse_args()
if args.debug:
logging.basicConfig(level=logging.DEBUG)
if args.version:
print(version.VERSION)
sys.exit(0) | python | def run(self, args=None):
""" Parse command line arguments if necessary then run program.
By default this method will just take of the --version flag.
The logic for other flags should be handled by your subclass """
args = args or self.parser.parse_args()
if args.debug:
logging.basicConfig(level=logging.DEBUG)
if args.version:
print(version.VERSION)
sys.exit(0) | Parse command line arguments if necessary then run program.
By default this method will just take of the --version flag.
The logic for other flags should be handled by your subclass | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L71-L84 |
walkr/oi | oi/core.py | Program.help_function | def help_function(self, command=None):
""" Show help for all available commands or just a single one """
if command:
return self.registered[command].get(
'description', 'No help available'
)
return ', '.join(sorted(self.registered)) | python | def help_function(self, command=None):
""" Show help for all available commands or just a single one """
if command:
return self.registered[command].get(
'description', 'No help available'
)
return ', '.join(sorted(self.registered)) | Show help for all available commands or just a single one | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L115-L121 |
walkr/oi | oi/core.py | Program.add_command | def add_command(self, command, function, description=None):
""" Register a new function for command """
super(Program, self).add_command(command, function, description)
self.service.register(command, function) | python | def add_command(self, command, function, description=None):
""" Register a new function for command """
super(Program, self).add_command(command, function, description)
self.service.register(command, function) | Register a new function for command | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L123-L126 |
walkr/oi | oi/core.py | Program.run | def run(self, args=None):
""" Parse comand line arguments/flags and run program """
args = args or self.parser.parse_args()
super(Program, self).run(args)
# Read configuration file if any
if args.config is not None:
filepath = args.config
self.config.read(filepath)
# Start workers then wait until they finish work
[w.start() for w in self.workers]
[w.join() for w in self.workers] | python | def run(self, args=None):
""" Parse comand line arguments/flags and run program """
args = args or self.parser.parse_args()
super(Program, self).run(args)
# Read configuration file if any
if args.config is not None:
filepath = args.config
self.config.read(filepath)
# Start workers then wait until they finish work
[w.start() for w in self.workers]
[w.join() for w in self.workers] | Parse comand line arguments/flags and run program | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L128-L141 |
walkr/oi | oi/core.py | ClientWrapper.create_client | def create_client(self, addr, timeout):
""" Create client(s) based on addr """
def make(addr):
c = Client(addr)
c.socket._set_recv_timeout(timeout)
return c
if ',' in addr:
addrs = addr.split(',')
addrs = [a.strip() for a in addrs]
return {a: make(a) for a in addrs}
return make(addr) | python | def create_client(self, addr, timeout):
""" Create client(s) based on addr """
def make(addr):
c = Client(addr)
c.socket._set_recv_timeout(timeout)
return c
if ',' in addr:
addrs = addr.split(',')
addrs = [a.strip() for a in addrs]
return {a: make(a) for a in addrs}
return make(addr) | Create client(s) based on addr | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L151-L163 |
walkr/oi | oi/core.py | ClientWrapper._call_single | def _call_single(self, client, command, *args):
""" Call single """
try:
return client.call(command, *args)
except Exception as e:
return None, str(e) | python | def _call_single(self, client, command, *args):
""" Call single """
try:
return client.call(command, *args)
except Exception as e:
return None, str(e) | Call single | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L165-L170 |
walkr/oi | oi/core.py | ClientWrapper._call_multi | def _call_multi(self, clients, command, *args):
""" Call multi """
responses, errors = {}, {}
for addr, client in clients.items():
res, err = self._call_single(client, command, *args)
responses[addr] = res
errors[addr] = err
return responses, errors | python | def _call_multi(self, clients, command, *args):
""" Call multi """
responses, errors = {}, {}
for addr, client in clients.items():
res, err = self._call_single(client, command, *args)
responses[addr] = res
errors[addr] = err
return responses, errors | Call multi | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L172-L179 |
walkr/oi | oi/core.py | ClientWrapper.call | def call(self, command, *args):
""" Call remote service(s) """
if isinstance(self.c, dict):
return self._call_multi(self.c, command, *args)
return self._call_single(self.c, command, *args) | python | def call(self, command, *args):
""" Call remote service(s) """
if isinstance(self.c, dict):
return self._call_multi(self.c, command, *args)
return self._call_single(self.c, command, *args) | Call remote service(s) | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L181-L185 |
walkr/oi | oi/core.py | ClientWrapper.close | def close(self):
""" Close socket(s) """
if isinstance(self.c, dict):
for client in self.c.values():
client.sock.close()
return
self.c.socket.close() | python | def close(self):
""" Close socket(s) """
if isinstance(self.c, dict):
for client in self.c.values():
client.sock.close()
return
self.c.socket.close() | Close socket(s) | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L191-L197 |
walkr/oi | oi/core.py | Response._show | def _show(self, res, err, prefix='', colored=False):
""" Show result or error """
if self.kind is 'local':
what = res if not err else err
print(what)
return
if self.kind is 'remote':
if colored:
red, green, reset = Fore.RED, Fore.GREEN, Fore.RESET
else:
red = green = reset = ''
if err:
what = prefix + red + 'remote err: {}'.format(err) + reset
else:
what = prefix + green + str(res) + reset
print(what) | python | def _show(self, res, err, prefix='', colored=False):
""" Show result or error """
if self.kind is 'local':
what = res if not err else err
print(what)
return
if self.kind is 'remote':
if colored:
red, green, reset = Fore.RED, Fore.GREEN, Fore.RESET
else:
red = green = reset = ''
if err:
what = prefix + red + 'remote err: {}'.format(err) + reset
else:
what = prefix + green + str(res) + reset
print(what) | Show result or error | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L210-L227 |
walkr/oi | oi/core.py | CtlProgram.call | def call(self, command, *args):
""" Execute local OR remote command and show response """
if not command:
return
# Look for local methods first
try:
res = self.registered[command]['function'](self, *args)
return Response('local', res, None)
# Method not found, try remote
except KeyError:
# Execute remote command
res, err = self.client.call(command, *args)
return Response('remote', res, err, self.client.is_multi())
# Local exception
except Exception as e:
return Response('local', res, str(e)) | python | def call(self, command, *args):
""" Execute local OR remote command and show response """
if not command:
return
# Look for local methods first
try:
res = self.registered[command]['function'](self, *args)
return Response('local', res, None)
# Method not found, try remote
except KeyError:
# Execute remote command
res, err = self.client.call(command, *args)
return Response('remote', res, err, self.client.is_multi())
# Local exception
except Exception as e:
return Response('local', res, str(e)) | Execute local OR remote command and show response | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L267-L287 |
walkr/oi | oi/core.py | CtlProgram.parse_input | def parse_input(self, text):
""" Parse ctl user input. Double quotes are used
to group together multi words arguments. """
parts = util.split(text)
command = parts[0] if text and parts else None
command = command.lower() if command else None
args = parts[1:] if len(parts) > 1 else []
return (command, args) | python | def parse_input(self, text):
""" Parse ctl user input. Double quotes are used
to group together multi words arguments. """
parts = util.split(text)
command = parts[0] if text and parts else None
command = command.lower() if command else None
args = parts[1:] if len(parts) > 1 else []
return (command, args) | Parse ctl user input. Double quotes are used
to group together multi words arguments. | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L289-L298 |
walkr/oi | oi/core.py | CtlProgram.loop | def loop(self):
""" Enter loop, read user input then run command. Repeat """
while True:
text = compat.input('ctl > ')
command, args = self.parse_input(text)
if not command:
continue
response = self.call(command, *args)
response.show() | python | def loop(self):
""" Enter loop, read user input then run command. Repeat """
while True:
text = compat.input('ctl > ')
command, args = self.parse_input(text)
if not command:
continue
response = self.call(command, *args)
response.show() | Enter loop, read user input then run command. Repeat | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/core.py#L300-L309 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/namespaces.py | namespace_for | def namespace_for(uri: Union[URIRef, Namespace, str]) -> str:
"""
Reverse namespace lookup. Note that returned namespace may not be unique
:param uri: namespace URI
:return: namespace
"""
uri = str(uri)
if uri not in namespaces.values():
namespaces[AnonNS().ns] = uri
return [k for k, v in namespaces.items() if uri == v][0] | python | def namespace_for(uri: Union[URIRef, Namespace, str]) -> str:
"""
Reverse namespace lookup. Note that returned namespace may not be unique
:param uri: namespace URI
:return: namespace
"""
uri = str(uri)
if uri not in namespaces.values():
namespaces[AnonNS().ns] = uri
return [k for k, v in namespaces.items() if uri == v][0] | Reverse namespace lookup. Note that returned namespace may not be unique
:param uri: namespace URI
:return: namespace | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/namespaces.py#L66-L75 |
walkr/oi | oi/util.py | split | def split(text):
""" Split text into arguments accounting for muti-word arguments
which are double quoted """
# Cleanup text
text = text.strip()
text = re.sub('\s+', ' ', text) # collpse multiple spaces
space, quote, parts = ' ', '"', []
part, quoted = '', False
for char in text:
# Encoutered beginning double quote
if char is quote and quoted is False:
quoted = True
continue
# Encountered the ending double quote
if char is quote and quoted is True:
quoted = False
parts.append(part.strip())
part = ''
continue
# Found space in quoted
if char is space and quoted is True:
part += char
continue
# Found space but not quoted
if char is space:
if part:
parts.append(part)
part = ''
continue
# Found other character
if char is not space:
part += char
continue
if part:
parts.append(part.strip())
return parts | python | def split(text):
""" Split text into arguments accounting for muti-word arguments
which are double quoted """
# Cleanup text
text = text.strip()
text = re.sub('\s+', ' ', text) # collpse multiple spaces
space, quote, parts = ' ', '"', []
part, quoted = '', False
for char in text:
# Encoutered beginning double quote
if char is quote and quoted is False:
quoted = True
continue
# Encountered the ending double quote
if char is quote and quoted is True:
quoted = False
parts.append(part.strip())
part = ''
continue
# Found space in quoted
if char is space and quoted is True:
part += char
continue
# Found space but not quoted
if char is space:
if part:
parts.append(part)
part = ''
continue
# Found other character
if char is not space:
part += char
continue
if part:
parts.append(part.strip())
return parts | Split text into arguments accounting for muti-word arguments
which are double quoted | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/oi/util.py#L6-L51 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/rdflibformats.py | known_formats | def known_formats(use: Union[Serializer, Parser]=Serializer, include_mime_types: bool = False) -> List[str]:
""" Return a list of available formats in rdflib for the required task
:param use: task (typically Serializer or Parser)
:param include_mime_types: whether mime types are included in the return list
:return: list of formats
"""
return sorted([name for name, kind in plugin._plugins.keys()
if kind == use and (include_mime_types or '/' not in name)]) | python | def known_formats(use: Union[Serializer, Parser]=Serializer, include_mime_types: bool = False) -> List[str]:
""" Return a list of available formats in rdflib for the required task
:param use: task (typically Serializer or Parser)
:param include_mime_types: whether mime types are included in the return list
:return: list of formats
"""
return sorted([name for name, kind in plugin._plugins.keys()
if kind == use and (include_mime_types or '/' not in name)]) | Return a list of available formats in rdflib for the required task
:param use: task (typically Serializer or Parser)
:param include_mime_types: whether mime types are included in the return list
:return: list of formats | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/rdflibformats.py#L47-L54 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/signature.py | file_signature | def file_signature(file_name: str) -> Optional[Tuple]:
"""
Return an identity signature for file name
:param file_name: name of file
:return: mode, size, last modified time if file exists, otherwise none
"""
try:
st = os.stat(file_name)
except FileNotFoundError:
return None
return stat.S_IFMT(st.st_mode), st.st_size, st.st_mtime | python | def file_signature(file_name: str) -> Optional[Tuple]:
"""
Return an identity signature for file name
:param file_name: name of file
:return: mode, size, last modified time if file exists, otherwise none
"""
try:
st = os.stat(file_name)
except FileNotFoundError:
return None
return stat.S_IFMT(st.st_mode), st.st_size, st.st_mtime | Return an identity signature for file name
:param file_name: name of file
:return: mode, size, last modified time if file exists, otherwise none | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/signature.py#L53-L63 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/signature.py | url_signature | def url_signature(url: str) -> Optional[Tuple]:
"""
Return an identify signature for url
:param url: item to get signature for
:return: tuple containing last modified, length and, if present, etag
"""
request = urllib.request.Request(url)
request.get_method = lambda: 'HEAD'
response = None
try:
response = urllib.request.urlopen(request)
except urllib.error.HTTPError:
return None
return response.info()['Last-Modified'], response.info()['Content-Length'], response.info().get('ETag') | python | def url_signature(url: str) -> Optional[Tuple]:
"""
Return an identify signature for url
:param url: item to get signature for
:return: tuple containing last modified, length and, if present, etag
"""
request = urllib.request.Request(url)
request.get_method = lambda: 'HEAD'
response = None
try:
response = urllib.request.urlopen(request)
except urllib.error.HTTPError:
return None
return response.info()['Last-Modified'], response.info()['Content-Length'], response.info().get('ETag') | Return an identify signature for url
:param url: item to get signature for
:return: tuple containing last modified, length and, if present, etag | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/signature.py#L66-L79 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/signature.py | signature | def signature(name: str) -> Optional[Tuple]:
"""
Return the file or URL signature for name
:param name:
:return:
"""
return url_signature(name) if is_url(name) else file_signature(name) if is_file(name) else None | python | def signature(name: str) -> Optional[Tuple]:
"""
Return the file or URL signature for name
:param name:
:return:
"""
return url_signature(name) if is_url(name) else file_signature(name) if is_file(name) else None | Return the file or URL signature for name
:param name:
:return: | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/signature.py#L82-L88 |
walkr/oi | setup.py | read_long_description | def read_long_description(readme_file):
""" Read package long description from README file """
try:
import pypandoc
except (ImportError, OSError) as e:
print('No pypandoc or pandoc: %s' % (e,))
if is_py3:
fh = open(readme_file, encoding='utf-8')
else:
fh = open(readme_file)
long_description = fh.read()
fh.close()
return long_description
else:
return pypandoc.convert(readme_file, 'rst') | python | def read_long_description(readme_file):
""" Read package long description from README file """
try:
import pypandoc
except (ImportError, OSError) as e:
print('No pypandoc or pandoc: %s' % (e,))
if is_py3:
fh = open(readme_file, encoding='utf-8')
else:
fh = open(readme_file)
long_description = fh.read()
fh.close()
return long_description
else:
return pypandoc.convert(readme_file, 'rst') | Read package long description from README file | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/setup.py#L17-L31 |
walkr/oi | setup.py | read_version | def read_version():
""" Read package version """
with open('./oi/version.py') as fh:
for line in fh:
if line.startswith('VERSION'):
return line.split('=')[1].strip().strip("'") | python | def read_version():
""" Read package version """
with open('./oi/version.py') as fh:
for line in fh:
if line.startswith('VERSION'):
return line.split('=')[1].strip().strip("'") | Read package version | https://github.com/walkr/oi/blob/d9d8491d0bc920e493d8f716d6078762b8b2c6d3/setup.py#L34-L39 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/prettygraph.py | PrettyGraph.strip_prefixes | def strip_prefixes(g: Graph):
""" Remove the prefixes from the graph for aesthetics """
return re.sub(r'^@prefix .* .\n', '',
g.serialize(format="turtle").decode(),
flags=re.MULTILINE).strip() | python | def strip_prefixes(g: Graph):
""" Remove the prefixes from the graph for aesthetics """
return re.sub(r'^@prefix .* .\n', '',
g.serialize(format="turtle").decode(),
flags=re.MULTILINE).strip() | Remove the prefixes from the graph for aesthetics | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/prettygraph.py#L98-L102 |
BD2KOnFHIR/fhirtordf | fhirtordf/loaders/fhirresourceloader.py | FHIRResource.add_prefixes | def add_prefixes(self, nsmap: Dict[str, Namespace]) -> None:
"""
Add the required prefix definitions
:return:
"""
[self._g.bind(e[0], e[1]) for e in nsmap.items()] | python | def add_prefixes(self, nsmap: Dict[str, Namespace]) -> None:
"""
Add the required prefix definitions
:return:
"""
[self._g.bind(e[0], e[1]) for e in nsmap.items()] | Add the required prefix definitions
:return: | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/loaders/fhirresourceloader.py#L132-L137 |
BD2KOnFHIR/fhirtordf | fhirtordf/loaders/fhirresourceloader.py | FHIRResource.add | def add(self, subj: Node, pred: URIRef, obj: Node) -> "FHIRResource":
"""
Shortcut to rdflib add function
:param subj:
:param pred:
:param obj:
:return: self for chaining
"""
self._g.add((subj, pred, obj))
return self | python | def add(self, subj: Node, pred: URIRef, obj: Node) -> "FHIRResource":
"""
Shortcut to rdflib add function
:param subj:
:param pred:
:param obj:
:return: self for chaining
"""
self._g.add((subj, pred, obj))
return self | Shortcut to rdflib add function
:param subj:
:param pred:
:param obj:
:return: self for chaining | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/loaders/fhirresourceloader.py#L146-L155 |
BD2KOnFHIR/fhirtordf | fhirtordf/loaders/fhirresourceloader.py | FHIRResource.add_value_node | def add_value_node(self, subj: Node, pred: URIRef, val: Union[JsonObj, str, List],
valuetype: Optional[URIRef]= None) -> None:
"""
Expand val according to the range of pred and add it to the graph
:param subj: graph subject
:param pred: graph predicate
:param val: JSON representation of target object
:param valuetype: predicate type if it can't be directly determined
"""
pred_type = self._meta.predicate_type(pred) if not valuetype else valuetype
# Transform generic resources into specific types
if pred_type == FHIR.Resource:
pred_type = FHIR[val.resourceType]
val_meta = FHIRMetaVocEntry(self._vocabulary, pred_type)
for k, p in val_meta.predicates().items():
if k in val:
self.add_val(subj, p, val, k)
if pred == FHIR.CodeableConcept.coding:
self.add_type_arc(subj, val)
elif k == "value" and val_meta.predicate_type(p) == FHIR.Element:
# value / Element is the wild card combination -- if there is a "value[x]" in val, emit it where the
# type comes from 'x'
for vk in val._as_dict.keys():
if vk.startswith(k):
self.add_val(subj, FHIR['Extension.' + vk], val, vk, self._meta.value_predicate_to_type(vk))
else:
# Can have an extension only without a primary value
self.add_extension_val(subj, val, k, p) | python | def add_value_node(self, subj: Node, pred: URIRef, val: Union[JsonObj, str, List],
valuetype: Optional[URIRef]= None) -> None:
"""
Expand val according to the range of pred and add it to the graph
:param subj: graph subject
:param pred: graph predicate
:param val: JSON representation of target object
:param valuetype: predicate type if it can't be directly determined
"""
pred_type = self._meta.predicate_type(pred) if not valuetype else valuetype
# Transform generic resources into specific types
if pred_type == FHIR.Resource:
pred_type = FHIR[val.resourceType]
val_meta = FHIRMetaVocEntry(self._vocabulary, pred_type)
for k, p in val_meta.predicates().items():
if k in val:
self.add_val(subj, p, val, k)
if pred == FHIR.CodeableConcept.coding:
self.add_type_arc(subj, val)
elif k == "value" and val_meta.predicate_type(p) == FHIR.Element:
# value / Element is the wild card combination -- if there is a "value[x]" in val, emit it where the
# type comes from 'x'
for vk in val._as_dict.keys():
if vk.startswith(k):
self.add_val(subj, FHIR['Extension.' + vk], val, vk, self._meta.value_predicate_to_type(vk))
else:
# Can have an extension only without a primary value
self.add_extension_val(subj, val, k, p) | Expand val according to the range of pred and add it to the graph
:param subj: graph subject
:param pred: graph predicate
:param val: JSON representation of target object
:param valuetype: predicate type if it can't be directly determined | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/loaders/fhirresourceloader.py#L157-L185 |
BD2KOnFHIR/fhirtordf | fhirtordf/loaders/fhirresourceloader.py | FHIRResource.add_reference | def add_reference(self, subj: Node, val: str) -> None:
"""
Add a fhir:link and RDF type arc if it can be determined
:param subj: reference subject
:param val: reference value
"""
match = FHIR_RESOURCE_RE.match(val)
ref_uri_str = res_type = None
if match:
ref_uri_str = val if match.group(FHIR_RE_BASE) else (self._base_uri + urllib.parse.quote(val))
res_type = match.group(FHIR_RE_RESOURCE)
elif '://' in val:
ref_uri_str = val
res_type = "Resource"
elif self._base_uri and not val.startswith('#') and not val.startswith('/'):
ref_uri_str = self._base_uri + urllib.parse.quote(val)
res_type = val.split('/', 1)[0] if '/' in val else "Resource"
if ref_uri_str:
ref_uri = URIRef(ref_uri_str)
self.add(subj, FHIR.link, ref_uri)
self.add(ref_uri, RDF.type, FHIR[res_type]) | python | def add_reference(self, subj: Node, val: str) -> None:
"""
Add a fhir:link and RDF type arc if it can be determined
:param subj: reference subject
:param val: reference value
"""
match = FHIR_RESOURCE_RE.match(val)
ref_uri_str = res_type = None
if match:
ref_uri_str = val if match.group(FHIR_RE_BASE) else (self._base_uri + urllib.parse.quote(val))
res_type = match.group(FHIR_RE_RESOURCE)
elif '://' in val:
ref_uri_str = val
res_type = "Resource"
elif self._base_uri and not val.startswith('#') and not val.startswith('/'):
ref_uri_str = self._base_uri + urllib.parse.quote(val)
res_type = val.split('/', 1)[0] if '/' in val else "Resource"
if ref_uri_str:
ref_uri = URIRef(ref_uri_str)
self.add(subj, FHIR.link, ref_uri)
self.add(ref_uri, RDF.type, FHIR[res_type]) | Add a fhir:link and RDF type arc if it can be determined
:param subj: reference subject
:param val: reference value | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/loaders/fhirresourceloader.py#L187-L207 |
BD2KOnFHIR/fhirtordf | fhirtordf/loaders/fhirresourceloader.py | FHIRResource.add_val | def add_val(self, subj: Node, pred: URIRef, json_obj: JsonObj, json_key: str,
valuetype: Optional[URIRef] = None) -> Optional[BNode]:
"""
Add the RDF representation of val to the graph as a target of subj, pred. Note that FHIR lists are
represented as a list of BNODE objects with a fhir:index discrimanant
:param subj: graph subject
:param pred: predicate
:param json_obj: object containing json_key
:param json_key: name of the value in the JSON resource
:param valuetype: value type if NOT determinable by predicate
:return: value node if target is a BNode else None
"""
if json_key not in json_obj:
print("Expecting to find object named '{}' in JSON:".format(json_key))
print(json_obj._as_json_dumps())
print("entry skipped")
return None
val = json_obj[json_key]
if isinstance(val, List):
list_idx = 0
for lv in val:
entry_bnode = BNode()
# TODO: this is getting messy. Refactor and clean this up
if pred == FHIR.Bundle.entry:
entry_subj = URIRef(lv.fullUrl)
self.add(entry_bnode, FHIR.index, Literal(list_idx))
self.add_val(entry_bnode, FHIR.Bundle.entry.fullUrl, lv, 'fullUrl')
self.add(entry_bnode, FHIR.Bundle.entry.resource, entry_subj)
self.add(subj, pred, entry_bnode)
entry_mv = FHIRMetaVocEntry(self._vocabulary, FHIR.BundleEntryComponent)
for k, p in entry_mv.predicates().items():
if k not in ['resource', 'fullUrl'] and k in lv:
print("---> adding {}".format(k))
self.add_val(subj, p, lv, k)
FHIRResource(self._vocabulary, None, self._base_uri, lv.resource, self._g,
False, self._replace_narrative_text, False, resource_uri=entry_subj)
else:
self.add(entry_bnode, FHIR.index, Literal(list_idx))
if isinstance(lv, JsonObj):
self.add_value_node(entry_bnode, pred, lv, valuetype)
else:
vt = self._meta.predicate_type(pred)
atom_type = self._meta.primitive_datatype_nostring(vt) if vt else None
self.add(entry_bnode, FHIR.value, Literal(lv, datatype=atom_type))
self.add(subj, pred, entry_bnode)
list_idx += 1
else:
vt = self._meta.predicate_type(pred) if not valuetype else valuetype
if self._meta.is_atom(pred):
if self._replace_narrative_text and pred == FHIR.Narrative.div and len(val) > 120:
val = REPLACED_NARRATIVE_TEXT
self.add(subj, pred, Literal(val))
else:
v = BNode()
if self._meta.is_primitive(vt):
self.add(v, FHIR.value, Literal(str(val), datatype=self._meta.primitive_datatype_nostring(vt, val)))
else:
self.add_value_node(v, pred, val, valuetype)
self.add(subj, pred, v)
if pred == FHIR.Reference.reference:
self.add_reference(subj, val)
self.add_extension_val(v, json_obj, json_key)
return v
return None | python | def add_val(self, subj: Node, pred: URIRef, json_obj: JsonObj, json_key: str,
valuetype: Optional[URIRef] = None) -> Optional[BNode]:
"""
Add the RDF representation of val to the graph as a target of subj, pred. Note that FHIR lists are
represented as a list of BNODE objects with a fhir:index discrimanant
:param subj: graph subject
:param pred: predicate
:param json_obj: object containing json_key
:param json_key: name of the value in the JSON resource
:param valuetype: value type if NOT determinable by predicate
:return: value node if target is a BNode else None
"""
if json_key not in json_obj:
print("Expecting to find object named '{}' in JSON:".format(json_key))
print(json_obj._as_json_dumps())
print("entry skipped")
return None
val = json_obj[json_key]
if isinstance(val, List):
list_idx = 0
for lv in val:
entry_bnode = BNode()
# TODO: this is getting messy. Refactor and clean this up
if pred == FHIR.Bundle.entry:
entry_subj = URIRef(lv.fullUrl)
self.add(entry_bnode, FHIR.index, Literal(list_idx))
self.add_val(entry_bnode, FHIR.Bundle.entry.fullUrl, lv, 'fullUrl')
self.add(entry_bnode, FHIR.Bundle.entry.resource, entry_subj)
self.add(subj, pred, entry_bnode)
entry_mv = FHIRMetaVocEntry(self._vocabulary, FHIR.BundleEntryComponent)
for k, p in entry_mv.predicates().items():
if k not in ['resource', 'fullUrl'] and k in lv:
print("---> adding {}".format(k))
self.add_val(subj, p, lv, k)
FHIRResource(self._vocabulary, None, self._base_uri, lv.resource, self._g,
False, self._replace_narrative_text, False, resource_uri=entry_subj)
else:
self.add(entry_bnode, FHIR.index, Literal(list_idx))
if isinstance(lv, JsonObj):
self.add_value_node(entry_bnode, pred, lv, valuetype)
else:
vt = self._meta.predicate_type(pred)
atom_type = self._meta.primitive_datatype_nostring(vt) if vt else None
self.add(entry_bnode, FHIR.value, Literal(lv, datatype=atom_type))
self.add(subj, pred, entry_bnode)
list_idx += 1
else:
vt = self._meta.predicate_type(pred) if not valuetype else valuetype
if self._meta.is_atom(pred):
if self._replace_narrative_text and pred == FHIR.Narrative.div and len(val) > 120:
val = REPLACED_NARRATIVE_TEXT
self.add(subj, pred, Literal(val))
else:
v = BNode()
if self._meta.is_primitive(vt):
self.add(v, FHIR.value, Literal(str(val), datatype=self._meta.primitive_datatype_nostring(vt, val)))
else:
self.add_value_node(v, pred, val, valuetype)
self.add(subj, pred, v)
if pred == FHIR.Reference.reference:
self.add_reference(subj, val)
self.add_extension_val(v, json_obj, json_key)
return v
return None | Add the RDF representation of val to the graph as a target of subj, pred. Note that FHIR lists are
represented as a list of BNODE objects with a fhir:index discrimanant
:param subj: graph subject
:param pred: predicate
:param json_obj: object containing json_key
:param json_key: name of the value in the JSON resource
:param valuetype: value type if NOT determinable by predicate
:return: value node if target is a BNode else None | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/loaders/fhirresourceloader.py#L229-L292 |
BD2KOnFHIR/fhirtordf | fhirtordf/loaders/fhirresourceloader.py | FHIRResource.add_extension_val | def add_extension_val(self,
subj: Node,
json_obj:
Union[JsonObj, List[JsonObjTypes]],
key: str,
pred: Optional[URIRef] = None) -> None:
"""
Add any extensions for the supplied object. This can be called in following situations:
1) Single extended value
"key" : (value),
"_key" : {
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
2) Single extension only
"_key" : {
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
3) Multiple extended values:
(TBD)
4) Multiple extensions only
"_key" : [
{
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
]
:param subj: Node containing subject
:param json_obj: Object (potentially) containing "_key"
:param key: name of element that is possibly extended (as indicated by "_" prefix)
:param pred: predicate for the contained elements. Only used in situations 3) (?) and 4
"""
extendee_name = "_" + key
if extendee_name in json_obj:
if not isinstance(subj, BNode):
raise NotImplementedError("Extension to something other than a simple BNode")
if isinstance(json_obj[extendee_name], list):
if not pred:
raise NotImplemented("Case 3 not implemented")
entry_idx = 0
for extension in json_obj[extendee_name]:
entry = BNode()
self.add(entry, FHIR.index, Literal(entry_idx))
self.add_val(entry, FHIR.Element.extension, extension, 'extension')
self.add(subj, pred, entry)
entry_idx += 1
elif 'fhir_comments' in json_obj[extendee_name] and len(json_obj[extendee_name]) == 1:
# TODO: determine whether and how fhir comments should be represented in RDF.
# for the moment we just drop them
print("fhir_comment ignored")
print(json_obj[extendee_name]._as_json_dumps())
pass
else:
self.add_val(subj, FHIR.Element.extension, json_obj[extendee_name], 'extension') | python | def add_extension_val(self,
subj: Node,
json_obj:
Union[JsonObj, List[JsonObjTypes]],
key: str,
pred: Optional[URIRef] = None) -> None:
"""
Add any extensions for the supplied object. This can be called in following situations:
1) Single extended value
"key" : (value),
"_key" : {
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
2) Single extension only
"_key" : {
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
3) Multiple extended values:
(TBD)
4) Multiple extensions only
"_key" : [
{
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
]
:param subj: Node containing subject
:param json_obj: Object (potentially) containing "_key"
:param key: name of element that is possibly extended (as indicated by "_" prefix)
:param pred: predicate for the contained elements. Only used in situations 3) (?) and 4
"""
extendee_name = "_" + key
if extendee_name in json_obj:
if not isinstance(subj, BNode):
raise NotImplementedError("Extension to something other than a simple BNode")
if isinstance(json_obj[extendee_name], list):
if not pred:
raise NotImplemented("Case 3 not implemented")
entry_idx = 0
for extension in json_obj[extendee_name]:
entry = BNode()
self.add(entry, FHIR.index, Literal(entry_idx))
self.add_val(entry, FHIR.Element.extension, extension, 'extension')
self.add(subj, pred, entry)
entry_idx += 1
elif 'fhir_comments' in json_obj[extendee_name] and len(json_obj[extendee_name]) == 1:
# TODO: determine whether and how fhir comments should be represented in RDF.
# for the moment we just drop them
print("fhir_comment ignored")
print(json_obj[extendee_name]._as_json_dumps())
pass
else:
self.add_val(subj, FHIR.Element.extension, json_obj[extendee_name], 'extension') | Add any extensions for the supplied object. This can be called in following situations:
1) Single extended value
"key" : (value),
"_key" : {
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
2) Single extension only
"_key" : {
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
3) Multiple extended values:
(TBD)
4) Multiple extensions only
"_key" : [
{
"extension": [
{
"url": "http://...",
"value[x]": "......"
}
]
}
]
:param subj: Node containing subject
:param json_obj: Object (potentially) containing "_key"
:param key: name of element that is possibly extended (as indicated by "_" prefix)
:param pred: predicate for the contained elements. Only used in situations 3) (?) and 4 | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/loaders/fhirresourceloader.py#L294-L362 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/fhirgraphutils.py | link | def link(g: Graph, subject: Node, predicate: URIRef) -> Tuple[Optional[URIRef], Optional[URIRef]]:
"""
Return the link URI and link type for subject and predicate
:param g: graph context
:param subject: subject of linke
:param predicate: link predicate
:return: URI and optional type URI. URI is None if not a link
"""
link_node = g.value(subject, predicate)
if link_node:
l = g.value(link_node, FHIR.link)
if l:
typ = g.value(l, RDF.type)
return l, typ
return None, None | python | def link(g: Graph, subject: Node, predicate: URIRef) -> Tuple[Optional[URIRef], Optional[URIRef]]:
"""
Return the link URI and link type for subject and predicate
:param g: graph context
:param subject: subject of linke
:param predicate: link predicate
:return: URI and optional type URI. URI is None if not a link
"""
link_node = g.value(subject, predicate)
if link_node:
l = g.value(link_node, FHIR.link)
if l:
typ = g.value(l, RDF.type)
return l, typ
return None, None | Return the link URI and link type for subject and predicate
:param g: graph context
:param subject: subject of linke
:param predicate: link predicate
:return: URI and optional type URI. URI is None if not a link | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/fhirgraphutils.py#L90-L104 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/fhirgraphutils.py | codeable_concept_code | def codeable_concept_code(g: Graph, subject: Node, predicate: URIRef, system: Optional[str]=None) \
-> List[CodeableConcept]:
"""
Return a list of CodeableConcept entries for the supplied subject and predicate in graph g
:param g: graph containing the data
:param subject: subject
:param predicate: predicate
:param system: coding system. If present, only concepts in this system will be returned
:return: system, code and optional URI of matching concept(s)
"""
# EXAMPLE:
# fhir:Patient.maritalStatus [
# fhir:CodeableConcept.coding [
# fhir:index 0;
# a sct:36629006;
# fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
# fhir:Coding.code [ fhir:value "36629006" ];
# fhir:Coding.display [ fhir:value "Legally married" ]
# ], [
# fhir:index 1;
# fhir:Coding.system [ fhir:value "http://hl7.org/fhir/v3/MaritalStatus" ];
# fhir:Coding.code [ fhir:value "M" ]
# ]
# ];
rval = []
coded_entry = g.value(subject, predicate, any=False)
if coded_entry:
for codeable_concept in list(g.objects(coded_entry, FHIR.CodeableConcept.coding)):
coding_system = value(g, codeable_concept, FHIR.Coding.system)
coding_code = value(g, codeable_concept, FHIR.Coding.code)
if coding_system and coding_code and (system is None or system == coding_system):
rval.append(CodeableConcept(coding_system, coding_code, g.value(codeable_concept, RDF.type, any=False)))
return rval | python | def codeable_concept_code(g: Graph, subject: Node, predicate: URIRef, system: Optional[str]=None) \
-> List[CodeableConcept]:
"""
Return a list of CodeableConcept entries for the supplied subject and predicate in graph g
:param g: graph containing the data
:param subject: subject
:param predicate: predicate
:param system: coding system. If present, only concepts in this system will be returned
:return: system, code and optional URI of matching concept(s)
"""
# EXAMPLE:
# fhir:Patient.maritalStatus [
# fhir:CodeableConcept.coding [
# fhir:index 0;
# a sct:36629006;
# fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
# fhir:Coding.code [ fhir:value "36629006" ];
# fhir:Coding.display [ fhir:value "Legally married" ]
# ], [
# fhir:index 1;
# fhir:Coding.system [ fhir:value "http://hl7.org/fhir/v3/MaritalStatus" ];
# fhir:Coding.code [ fhir:value "M" ]
# ]
# ];
rval = []
coded_entry = g.value(subject, predicate, any=False)
if coded_entry:
for codeable_concept in list(g.objects(coded_entry, FHIR.CodeableConcept.coding)):
coding_system = value(g, codeable_concept, FHIR.Coding.system)
coding_code = value(g, codeable_concept, FHIR.Coding.code)
if coding_system and coding_code and (system is None or system == coding_system):
rval.append(CodeableConcept(coding_system, coding_code, g.value(codeable_concept, RDF.type, any=False)))
return rval | Return a list of CodeableConcept entries for the supplied subject and predicate in graph g
:param g: graph containing the data
:param subject: subject
:param predicate: predicate
:param system: coding system. If present, only concepts in this system will be returned
:return: system, code and optional URI of matching concept(s) | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/fhirgraphutils.py#L127-L159 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry._to_str | def _to_str(uri: URIRef) -> str:
"""
Convert a FHIR style URI into a tag name to be used to retrieve data from a JSON representation
Example: http://hl7.org/fhir/Provenance.agent.whoReference --> whoReference
:param uri: URI to convert
:return: tag name
"""
local_name = str(uri).replace(str(FHIR), '')
return local_name.rsplit('.', 1)[1] if '.' in local_name else local_name | python | def _to_str(uri: URIRef) -> str:
"""
Convert a FHIR style URI into a tag name to be used to retrieve data from a JSON representation
Example: http://hl7.org/fhir/Provenance.agent.whoReference --> whoReference
:param uri: URI to convert
:return: tag name
"""
local_name = str(uri).replace(str(FHIR), '')
return local_name.rsplit('.', 1)[1] if '.' in local_name else local_name | Convert a FHIR style URI into a tag name to be used to retrieve data from a JSON representation
Example: http://hl7.org/fhir/Provenance.agent.whoReference --> whoReference
:param uri: URI to convert
:return: tag name | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L60-L68 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.predicates | def predicates(self) -> Dict[str, URIRef]:
"""
Return the tag names and corresponding URI's for all properties that can be associated with subject
:return: Map from tag name (JSON object identifier) to corresponding URI
"""
rval = dict()
for parent in self._o.objects(self._subj, RDFS.subClassOf):
if isinstance(parent, URIRef) and not str(parent).startswith(str(W5)):
rval.update(**FHIRMetaVocEntry(self._o, parent).predicates())
for s in self._o.subjects(RDFS.domain, self._subj):
rval[self._to_str(s)] = s
return rval | python | def predicates(self) -> Dict[str, URIRef]:
"""
Return the tag names and corresponding URI's for all properties that can be associated with subject
:return: Map from tag name (JSON object identifier) to corresponding URI
"""
rval = dict()
for parent in self._o.objects(self._subj, RDFS.subClassOf):
if isinstance(parent, URIRef) and not str(parent).startswith(str(W5)):
rval.update(**FHIRMetaVocEntry(self._o, parent).predicates())
for s in self._o.subjects(RDFS.domain, self._subj):
rval[self._to_str(s)] = s
return rval | Return the tag names and corresponding URI's for all properties that can be associated with subject
:return: Map from tag name (JSON object identifier) to corresponding URI | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L70-L81 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.predicate_type | def predicate_type(self, pred: URIRef) -> URIRef:
"""
Return the type of pred
:param pred: predicate to map
:return:
"""
return self._o.value(pred, RDFS.range) | python | def predicate_type(self, pred: URIRef) -> URIRef:
"""
Return the type of pred
:param pred: predicate to map
:return:
"""
return self._o.value(pred, RDFS.range) | Return the type of pred
:param pred: predicate to map
:return: | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L83-L89 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.is_valid | def is_valid(self, t: URIRef) -> bool:
"""
Raise an exception if 't' is unrecognized
:param t: metadata URI
"""
if not self.has_type(t):
raise TypeError("Unrecognized FHIR type: {}".format(t))
return True | python | def is_valid(self, t: URIRef) -> bool:
"""
Raise an exception if 't' is unrecognized
:param t: metadata URI
"""
if not self.has_type(t):
raise TypeError("Unrecognized FHIR type: {}".format(t))
return True | Raise an exception if 't' is unrecognized
:param t: metadata URI | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L94-L101 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.is_primitive | def is_primitive(self, t: URIRef) -> bool:
"""
Determine whether type "t" is a FHIR primitive type
:param t: type to test
:return:
"""
return FHIR.Primitive in self._o.objects(t, RDFS.subClassOf) | python | def is_primitive(self, t: URIRef) -> bool:
"""
Determine whether type "t" is a FHIR primitive type
:param t: type to test
:return:
"""
return FHIR.Primitive in self._o.objects(t, RDFS.subClassOf) | Determine whether type "t" is a FHIR primitive type
:param t: type to test
:return: | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L103-L109 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.value_predicate_to_type | def value_predicate_to_type(self, value_pred: str) -> URIRef:
"""
Convert a predicate in the form of "fhir:[...].value[type] to fhir:type, covering the downshift on the
first character if necessary
:param value_pred: Predicate associated with the value
:return: corresponding type or None if not found
"""
if value_pred.startswith('value'):
vp_datatype = value_pred.replace('value', '')
if vp_datatype:
if self.has_type(FHIR[vp_datatype]):
return FHIR[vp_datatype]
else:
vp_datatype = vp_datatype[0].lower() + vp_datatype[1:]
if self.has_type(FHIR[vp_datatype]):
return FHIR[vp_datatype]
if self.is_valid(FHIR[value_pred]):
return FHIR[value_pred] | python | def value_predicate_to_type(self, value_pred: str) -> URIRef:
"""
Convert a predicate in the form of "fhir:[...].value[type] to fhir:type, covering the downshift on the
first character if necessary
:param value_pred: Predicate associated with the value
:return: corresponding type or None if not found
"""
if value_pred.startswith('value'):
vp_datatype = value_pred.replace('value', '')
if vp_datatype:
if self.has_type(FHIR[vp_datatype]):
return FHIR[vp_datatype]
else:
vp_datatype = vp_datatype[0].lower() + vp_datatype[1:]
if self.has_type(FHIR[vp_datatype]):
return FHIR[vp_datatype]
if self.is_valid(FHIR[value_pred]):
return FHIR[value_pred] | Convert a predicate in the form of "fhir:[...].value[type] to fhir:type, covering the downshift on the
first character if necessary
:param value_pred: Predicate associated with the value
:return: corresponding type or None if not found | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L111-L128 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.is_atom | def is_atom(self, pred: URIRef) -> bool:
"""
Determine whether predicate is an 'atomic' type -- i.e it doesn't use a FHIR value representation
:param pred: type to test
:return:
"""
if not self.has_type(pred):
if '.value' in str(pred): # synthetic values (valueString, valueDate, ...)
return False
else:
raise TypeError("Unrecognized FHIR predicate: {}".format(pred))
return pred == FHIR.nodeRole or OWL.DatatypeProperty in set(self._o.objects(pred, RDF.type)) | python | def is_atom(self, pred: URIRef) -> bool:
"""
Determine whether predicate is an 'atomic' type -- i.e it doesn't use a FHIR value representation
:param pred: type to test
:return:
"""
if not self.has_type(pred):
if '.value' in str(pred): # synthetic values (valueString, valueDate, ...)
return False
else:
raise TypeError("Unrecognized FHIR predicate: {}".format(pred))
return pred == FHIR.nodeRole or OWL.DatatypeProperty in set(self._o.objects(pred, RDF.type)) | Determine whether predicate is an 'atomic' type -- i.e it doesn't use a FHIR value representation
:param pred: type to test
:return: | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L130-L141 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.primitive_datatype | def primitive_datatype(self, t: URIRef) -> Optional[URIRef]:
"""
Return the data type for primitive type t, if any
:param t: type
:return: corresponding data type
"""
for sco in self._o.objects(t, RDFS.subClassOf):
sco_type = self._o.value(sco, RDF.type)
sco_prop = self._o.value(sco, OWL.onProperty)
if sco_type == OWL.Restriction and sco_prop == FHIR.value:
# The older versions of fhir.ttl (incorrectly) referenced the datatype directly
restriction_type = self._o.value(sco, OWL.allValuesFrom)
if not restriction_type:
restriction_dt_entry = self._o.value(sco, OWL.someValuesFrom)
restriction_type = self._o.value(restriction_dt_entry, OWL.onDatatype)
return restriction_type
return None | python | def primitive_datatype(self, t: URIRef) -> Optional[URIRef]:
"""
Return the data type for primitive type t, if any
:param t: type
:return: corresponding data type
"""
for sco in self._o.objects(t, RDFS.subClassOf):
sco_type = self._o.value(sco, RDF.type)
sco_prop = self._o.value(sco, OWL.onProperty)
if sco_type == OWL.Restriction and sco_prop == FHIR.value:
# The older versions of fhir.ttl (incorrectly) referenced the datatype directly
restriction_type = self._o.value(sco, OWL.allValuesFrom)
if not restriction_type:
restriction_dt_entry = self._o.value(sco, OWL.someValuesFrom)
restriction_type = self._o.value(restriction_dt_entry, OWL.onDatatype)
return restriction_type
return None | Return the data type for primitive type t, if any
:param t: type
:return: corresponding data type | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L143-L159 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/fhirmetavoc.py | FHIRMetaVocEntry.primitive_datatype_nostring | def primitive_datatype_nostring(self, t: URIRef, v: Optional[str] = None) -> Optional[URIRef]:
"""
Return the data type for primitive type t, if any, defaulting string to no type
:param t: type
:param v: value - for munging dates if we're doing FHIR official output
:return: corresponding data type
"""
vt = self.primitive_datatype(t)
if self.fhir_dates and vt == XSD.dateTime and v:
return XSD.gYear if len(v) == 4 else XSD.gYearMonth if len(v) == 7 \
else XSD.date if (len(v) == 10 or (len(v) > 10 and v[10] in '+-')) else XSD.dateTime
# For some reason the oid datatype is represented as a string as well
if self.fhir_oids and vt == XSD.anyURI:
vt = None
return None if vt == XSD.string else vt | python | def primitive_datatype_nostring(self, t: URIRef, v: Optional[str] = None) -> Optional[URIRef]:
"""
Return the data type for primitive type t, if any, defaulting string to no type
:param t: type
:param v: value - for munging dates if we're doing FHIR official output
:return: corresponding data type
"""
vt = self.primitive_datatype(t)
if self.fhir_dates and vt == XSD.dateTime and v:
return XSD.gYear if len(v) == 4 else XSD.gYearMonth if len(v) == 7 \
else XSD.date if (len(v) == 10 or (len(v) > 10 and v[10] in '+-')) else XSD.dateTime
# For some reason the oid datatype is represented as a string as well
if self.fhir_oids and vt == XSD.anyURI:
vt = None
return None if vt == XSD.string else vt | Return the data type for primitive type t, if any, defaulting string to no type
:param t: type
:param v: value - for munging dates if we're doing FHIR official output
:return: corresponding data type | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/fhirmetavoc.py#L161-L175 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/picklejar.py | _PickleJar.add | def add(self, name: str, sig: Tuple, obj: object) -> None:
"""
Add a file to the cache
:param name: name of the object to be pickled
:param sig: signature for object
:param obj: object to pickle
"""
if self._cache_directory is not None:
if name in self._cache:
os.remove(os.path.join(self._cache_directory, self._cache[name].loc))
fname = os.path.join(self._cache_directory, str(uuid.uuid4()))
with open(fname, 'wb') as f:
pickle.dump(obj, f)
self._cache[name] = _PickleJar.CacheEntry(sig, fname)
self._update() | python | def add(self, name: str, sig: Tuple, obj: object) -> None:
"""
Add a file to the cache
:param name: name of the object to be pickled
:param sig: signature for object
:param obj: object to pickle
"""
if self._cache_directory is not None:
if name in self._cache:
os.remove(os.path.join(self._cache_directory, self._cache[name].loc))
fname = os.path.join(self._cache_directory, str(uuid.uuid4()))
with open(fname, 'wb') as f:
pickle.dump(obj, f)
self._cache[name] = _PickleJar.CacheEntry(sig, fname)
self._update() | Add a file to the cache
:param name: name of the object to be pickled
:param sig: signature for object
:param obj: object to pickle | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/picklejar.py#L91-L105 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/picklejar.py | _PickleJar.get | def get(self, name: str, sig: Tuple) -> Optional[object]:
"""
Return the object representing name if it is cached
:param name: name of object
:param sig: unique signature of object
:return: object if exists and signature matches
"""
if name not in self._cache:
return None
if self._cache[name].sig != sig:
del self._cache[name]
self._update()
return None
with open(self._cache[name].loc, 'rb') as f:
return pickle.load(f) | python | def get(self, name: str, sig: Tuple) -> Optional[object]:
"""
Return the object representing name if it is cached
:param name: name of object
:param sig: unique signature of object
:return: object if exists and signature matches
"""
if name not in self._cache:
return None
if self._cache[name].sig != sig:
del self._cache[name]
self._update()
return None
with open(self._cache[name].loc, 'rb') as f:
return pickle.load(f) | Return the object representing name if it is cached
:param name: name of object
:param sig: unique signature of object
:return: object if exists and signature matches | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/picklejar.py#L107-L121 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhir/picklejar.py | _PickleJar.clear | def clear(self) -> None:
"""
Clear all cache entries for directory and, if it is a 'pure' directory, remove the directory itself
"""
if self._cache_directory is not None:
# Safety - if there isn't a cache directory file, this probably isn't a valid cache
assert os.path.exists(self._cache_directory_index), "Attempt to clear a non-existent cache"
self._load() # Shouldn't have any impact but...
for e in self._cache.values():
if os.path.exists(e.loc):
os.remove(e.loc)
self._cache.clear()
self._update()
self._cache = {} | python | def clear(self) -> None:
"""
Clear all cache entries for directory and, if it is a 'pure' directory, remove the directory itself
"""
if self._cache_directory is not None:
# Safety - if there isn't a cache directory file, this probably isn't a valid cache
assert os.path.exists(self._cache_directory_index), "Attempt to clear a non-existent cache"
self._load() # Shouldn't have any impact but...
for e in self._cache.values():
if os.path.exists(e.loc):
os.remove(e.loc)
self._cache.clear()
self._update()
self._cache = {} | Clear all cache entries for directory and, if it is a 'pure' directory, remove the directory itself | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhir/picklejar.py#L135-L148 |
BD2KOnFHIR/fhirtordf | fhirtordf/loaders/fhirjsonloader.py | fhir_json_to_rdf | def fhir_json_to_rdf(json_fname: str,
base_uri: str = "http://hl7.org/fhir/",
target_graph: Optional[Graph] = None,
add_ontology_header: bool = True,
do_continuations: bool = True,
replace_narrative_text: bool = False,
metavoc: Optional[Union[Graph, FHIRMetaVoc]] = None) -> Graph:
"""
Convert a FHIR JSON resource image to RDF
:param json_fname: Name or URI of the file to convert
:param base_uri: Base URI to use for relative references.
:param target_graph: If supplied, add RDF to this graph. If not, start with an empty graph.
:param add_ontology_header: True means add owl:Ontology declaration to output
:param do_continuations: True means follow continuation records on bundles and queries
:param replace_narrative_text: True means replace any narrative text longer than 120 characters with
'<div xmlns="http://www.w3.org/1999/xhtml">(removed)</div>'
:param metavoc: FHIR Metadata Vocabulary (fhir.ttl) graph
:return: resulting graph
"""
def check_for_continuation(data_: JsonObj) -> Optional[str]:
if do_continuations and 'link' in data_ and isinstance(data_.link, list):
for link_e in data_.link:
if 'relation' in link_e and link_e.relation == 'next':
return link_e.url
return None
if target_graph is None:
target_graph = Graph()
if metavoc is None:
metavoc = FHIRMetaVoc().g
elif isinstance(metavoc, FHIRMetaVoc):
metavoc = metavoc.g
page_fname = json_fname
while page_fname:
data = load(page_fname)
if 'resourceType' in data and data.resourceType != 'Bundle':
FHIRResource(metavoc, None, base_uri, data, target=target_graph, add_ontology_header=add_ontology_header,
replace_narrative_text=replace_narrative_text)
page_fname = check_for_continuation(data)
elif 'entry' in data and isinstance(data.entry, list) and 'resource' in data.entry[0]:
FHIRCollection(metavoc, None, base_uri, data, target=target_graph,
add_ontology_header=add_ontology_header if 'resourceType' in data else False,
replace_narrative_text=replace_narrative_text)
page_fname = check_for_continuation(data)
else:
page_fname = None
target_graph = None
return target_graph | python | def fhir_json_to_rdf(json_fname: str,
base_uri: str = "http://hl7.org/fhir/",
target_graph: Optional[Graph] = None,
add_ontology_header: bool = True,
do_continuations: bool = True,
replace_narrative_text: bool = False,
metavoc: Optional[Union[Graph, FHIRMetaVoc]] = None) -> Graph:
"""
Convert a FHIR JSON resource image to RDF
:param json_fname: Name or URI of the file to convert
:param base_uri: Base URI to use for relative references.
:param target_graph: If supplied, add RDF to this graph. If not, start with an empty graph.
:param add_ontology_header: True means add owl:Ontology declaration to output
:param do_continuations: True means follow continuation records on bundles and queries
:param replace_narrative_text: True means replace any narrative text longer than 120 characters with
'<div xmlns="http://www.w3.org/1999/xhtml">(removed)</div>'
:param metavoc: FHIR Metadata Vocabulary (fhir.ttl) graph
:return: resulting graph
"""
def check_for_continuation(data_: JsonObj) -> Optional[str]:
if do_continuations and 'link' in data_ and isinstance(data_.link, list):
for link_e in data_.link:
if 'relation' in link_e and link_e.relation == 'next':
return link_e.url
return None
if target_graph is None:
target_graph = Graph()
if metavoc is None:
metavoc = FHIRMetaVoc().g
elif isinstance(metavoc, FHIRMetaVoc):
metavoc = metavoc.g
page_fname = json_fname
while page_fname:
data = load(page_fname)
if 'resourceType' in data and data.resourceType != 'Bundle':
FHIRResource(metavoc, None, base_uri, data, target=target_graph, add_ontology_header=add_ontology_header,
replace_narrative_text=replace_narrative_text)
page_fname = check_for_continuation(data)
elif 'entry' in data and isinstance(data.entry, list) and 'resource' in data.entry[0]:
FHIRCollection(metavoc, None, base_uri, data, target=target_graph,
add_ontology_header=add_ontology_header if 'resourceType' in data else False,
replace_narrative_text=replace_narrative_text)
page_fname = check_for_continuation(data)
else:
page_fname = None
target_graph = None
return target_graph | Convert a FHIR JSON resource image to RDF
:param json_fname: Name or URI of the file to convert
:param base_uri: Base URI to use for relative references.
:param target_graph: If supplied, add RDF to this graph. If not, start with an empty graph.
:param add_ontology_header: True means add owl:Ontology declaration to output
:param do_continuations: True means follow continuation records on bundles and queries
:param replace_narrative_text: True means replace any narrative text longer than 120 characters with
'<div xmlns="http://www.w3.org/1999/xhtml">(removed)</div>'
:param metavoc: FHIR Metadata Vocabulary (fhir.ttl) graph
:return: resulting graph | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/loaders/fhirjsonloader.py#L38-L88 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/rdfcompare.py | subj_pred_idx_to_uri | def subj_pred_idx_to_uri(s: URIRef, p: URIRef, idx: Optional[int] = None) -> URIRef:
""" Convert FHIR subject, predicate and entry index into a URI. The resulting element can be substituted
for the name of the target BNODE
:param s: Subject URI (e.g. "fhir:Patient/f201", "fhir:Patient/f201.Patient.identifier_0", ...)
:param p: Predicate URI (e.g. "fhir:Patient.identifier", "fhir.Identifier.use
:param idx: Relative position of BNODE if in a list
:return: URI that can replace the BNODE (e.g. "fhir:Patient/f201
"""
return URIRef(str(s) + '.' + str(p).rsplit('/', 1)[1] + ("_{}".format(idx) if idx is not None else '')) | python | def subj_pred_idx_to_uri(s: URIRef, p: URIRef, idx: Optional[int] = None) -> URIRef:
""" Convert FHIR subject, predicate and entry index into a URI. The resulting element can be substituted
for the name of the target BNODE
:param s: Subject URI (e.g. "fhir:Patient/f201", "fhir:Patient/f201.Patient.identifier_0", ...)
:param p: Predicate URI (e.g. "fhir:Patient.identifier", "fhir.Identifier.use
:param idx: Relative position of BNODE if in a list
:return: URI that can replace the BNODE (e.g. "fhir:Patient/f201
"""
return URIRef(str(s) + '.' + str(p).rsplit('/', 1)[1] + ("_{}".format(idx) if idx is not None else '')) | Convert FHIR subject, predicate and entry index into a URI. The resulting element can be substituted
for the name of the target BNODE
:param s: Subject URI (e.g. "fhir:Patient/f201", "fhir:Patient/f201.Patient.identifier_0", ...)
:param p: Predicate URI (e.g. "fhir:Patient.identifier", "fhir.Identifier.use
:param idx: Relative position of BNODE if in a list
:return: URI that can replace the BNODE (e.g. "fhir:Patient/f201 | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/rdfcompare.py#L38-L46 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/rdfcompare.py | map_node | def map_node(s: Node, sk_s: URIRef, gin: Graph, gout: Graph) -> None:
"""
Transform the BNode whose subject is s into its equivalent, replacing s with its 'skolemized' equivalent
:param s: Actual subject
:param sk_s: Equivalent URI of subject in output graph
:param gin: Input graph
:param gout: Output graph
"""
for p, o in gin.predicate_objects(s):
if not isinstance(o, BNode):
gout.add((sk_s, p, o))
else:
sk_o = subj_pred_idx_to_uri(sk_s, p, gin.value(o, FHIR.index))
gout.add((sk_s, p, sk_o))
map_node(o, sk_o, gin, gout) | python | def map_node(s: Node, sk_s: URIRef, gin: Graph, gout: Graph) -> None:
"""
Transform the BNode whose subject is s into its equivalent, replacing s with its 'skolemized' equivalent
:param s: Actual subject
:param sk_s: Equivalent URI of subject in output graph
:param gin: Input graph
:param gout: Output graph
"""
for p, o in gin.predicate_objects(s):
if not isinstance(o, BNode):
gout.add((sk_s, p, o))
else:
sk_o = subj_pred_idx_to_uri(sk_s, p, gin.value(o, FHIR.index))
gout.add((sk_s, p, sk_o))
map_node(o, sk_o, gin, gout) | Transform the BNode whose subject is s into its equivalent, replacing s with its 'skolemized' equivalent
:param s: Actual subject
:param sk_s: Equivalent URI of subject in output graph
:param gin: Input graph
:param gout: Output graph | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/rdfcompare.py#L49-L63 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/rdfcompare.py | skolemize | def skolemize(gin: Graph) -> Graph:
"""
Replace all of the blank nodes in graph gin with FHIR paths
:param gin: input graph
:return: output graph
"""
gout = Graph()
# Emit any unreferenced subject BNodes (boxes)
anon_subjs = [s for s in gin.subjects() if isinstance(s, BNode) and len([gin.subject_predicates(s)]) == 0]
if anon_subjs:
idx = None if len(anon_subjs) == 1 else 0
for s in anon_subjs:
map_node(s, FHIR['treeRoot' + ('_{}'.format(idx) if idx is not None else '')], gin, gout)
if idx is not None:
idx += 1
# Cover all other non-bnode entries
for subj in set(s for s in gin.subjects() if isinstance(s, URIRef)):
map_node(subj, subj, gin, gout)
return gout | python | def skolemize(gin: Graph) -> Graph:
"""
Replace all of the blank nodes in graph gin with FHIR paths
:param gin: input graph
:return: output graph
"""
gout = Graph()
# Emit any unreferenced subject BNodes (boxes)
anon_subjs = [s for s in gin.subjects() if isinstance(s, BNode) and len([gin.subject_predicates(s)]) == 0]
if anon_subjs:
idx = None if len(anon_subjs) == 1 else 0
for s in anon_subjs:
map_node(s, FHIR['treeRoot' + ('_{}'.format(idx) if idx is not None else '')], gin, gout)
if idx is not None:
idx += 1
# Cover all other non-bnode entries
for subj in set(s for s in gin.subjects() if isinstance(s, URIRef)):
map_node(subj, subj, gin, gout)
return gout | Replace all of the blank nodes in graph gin with FHIR paths
:param gin: input graph
:return: output graph | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/rdfcompare.py#L66-L86 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/rdfcompare.py | complete_definition | def complete_definition(subj: Node,
source_graph: Graph,
target_graph: Optional[Graph]=None) -> PrettyGraph:
"""
Return the transitive closure of subject.
:param subj: URI or BNode for subject
:param source_graph: Graph containing defininition
:param target_graph: return graph (for recursion)
:return: target_graph
"""
if target_graph is None:
target_graph = PrettyGraph()
for p, o in source_graph.predicate_objects(subj):
target_graph.add((subj, p, o))
if isinstance(o, BNode):
complete_definition(o, source_graph, target_graph)
return target_graph | python | def complete_definition(subj: Node,
source_graph: Graph,
target_graph: Optional[Graph]=None) -> PrettyGraph:
"""
Return the transitive closure of subject.
:param subj: URI or BNode for subject
:param source_graph: Graph containing defininition
:param target_graph: return graph (for recursion)
:return: target_graph
"""
if target_graph is None:
target_graph = PrettyGraph()
for p, o in source_graph.predicate_objects(subj):
target_graph.add((subj, p, o))
if isinstance(o, BNode):
complete_definition(o, source_graph, target_graph)
return target_graph | Return the transitive closure of subject.
:param subj: URI or BNode for subject
:param source_graph: Graph containing defininition
:param target_graph: return graph (for recursion)
:return: target_graph | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/rdfcompare.py#L89-L105 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/rdfcompare.py | dump_nt_sorted | def dump_nt_sorted(g: Graph) -> List[str]:
"""
Dump graph g in a sorted n3 format
:param g: graph to dump
:return: stringified representation of g
"""
return [l.decode('ascii') for l in sorted(g.serialize(format='nt').splitlines()) if l] | python | def dump_nt_sorted(g: Graph) -> List[str]:
"""
Dump graph g in a sorted n3 format
:param g: graph to dump
:return: stringified representation of g
"""
return [l.decode('ascii') for l in sorted(g.serialize(format='nt').splitlines()) if l] | Dump graph g in a sorted n3 format
:param g: graph to dump
:return: stringified representation of g | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/rdfcompare.py#L108-L114 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/rdfcompare.py | rdf_compare | def rdf_compare(g1: Graph, g2: Graph, ignore_owl_version: bool=False, ignore_type_arcs: bool = False,
compare_filter: Optional[Callable[[Graph, Graph, Graph], None]]=None) -> str:
"""
Compare graph g1 and g2
:param g1: first graph
:param g2: second graph
:param ignore_owl_version:
:param ignore_type_arcs:
:param compare_filter: Final adjustment for graph difference. Used, for example, to deal with FHIR decimal problems.
:return: List of differences as printable lines or blank if everything matches
"""
def graph_for_subject(g: Graph, subj: Node) -> Graph:
subj_in_g = complete_definition(subj, g)
if ignore_type_arcs:
for ta_s, ta_o in subj_in_g.subject_objects(RDF.type):
if isinstance(ta_s, BNode) and isinstance(ta_o, URIRef):
subj_in_g.remove((ta_s, RDF.type, ta_o))
if ignore_owl_version:
subj_in_g.remove((subj, OWL.versionIRI, subj_in_g.value(subj, OWL.versionIRI)))
return subj_in_g
def primary_subjects(g: Graph) -> Set[Node]:
anon_subjs = set(anon_s for anon_s in g.subjects()
if isinstance(anon_s, BNode) and len([g.subject_predicates(anon_s)]) == 0)
return set(s_ for s_ in g1.subjects() if isinstance(s_, URIRef)).union(anon_subjs)
rval = ""
# Step 1: Find any subjects in one graph that don't exist in the other
g1_subjs = primary_subjects(g1)
g2_subjs = primary_subjects(g2)
for s in g1_subjs - g2_subjs:
rval += "\n===== Subjects in Graph 1 but not Graph 2: "
rval += PrettyGraph.strip_prefixes(complete_definition(s, g1))
for s in g2_subjs - g1_subjs:
rval += "\n===== Subjects in Graph 2 but not Graph 1: "
rval += PrettyGraph.strip_prefixes(complete_definition(s, g2))
# Step 2: Iterate over all of the remaining subjects comparing their contents
for s in g1_subjs.intersection(g2_subjs):
s_in_g1 = graph_for_subject(g1, s)
s_in_g2 = graph_for_subject(g2, s)
in_both, in_first, in_second = graph_diff(skolemize(s_in_g1), skolemize(s_in_g2))
if compare_filter:
compare_filter(in_both, in_first, in_second)
if len(list(in_first)) or len(list(in_second)):
rval += "\n\nSubject {} DIFFERENCE: ".format(s) + '=' * 30
if len(in_first):
rval += "\n\t----> First: \n" + '\n'.join(dump_nt_sorted(in_first))
if len(in_second):
rval += "\n\t----> Second: \n" + '\n'.join(dump_nt_sorted(in_second))
rval += '-' * 40
return rval | python | def rdf_compare(g1: Graph, g2: Graph, ignore_owl_version: bool=False, ignore_type_arcs: bool = False,
compare_filter: Optional[Callable[[Graph, Graph, Graph], None]]=None) -> str:
"""
Compare graph g1 and g2
:param g1: first graph
:param g2: second graph
:param ignore_owl_version:
:param ignore_type_arcs:
:param compare_filter: Final adjustment for graph difference. Used, for example, to deal with FHIR decimal problems.
:return: List of differences as printable lines or blank if everything matches
"""
def graph_for_subject(g: Graph, subj: Node) -> Graph:
subj_in_g = complete_definition(subj, g)
if ignore_type_arcs:
for ta_s, ta_o in subj_in_g.subject_objects(RDF.type):
if isinstance(ta_s, BNode) and isinstance(ta_o, URIRef):
subj_in_g.remove((ta_s, RDF.type, ta_o))
if ignore_owl_version:
subj_in_g.remove((subj, OWL.versionIRI, subj_in_g.value(subj, OWL.versionIRI)))
return subj_in_g
def primary_subjects(g: Graph) -> Set[Node]:
anon_subjs = set(anon_s for anon_s in g.subjects()
if isinstance(anon_s, BNode) and len([g.subject_predicates(anon_s)]) == 0)
return set(s_ for s_ in g1.subjects() if isinstance(s_, URIRef)).union(anon_subjs)
rval = ""
# Step 1: Find any subjects in one graph that don't exist in the other
g1_subjs = primary_subjects(g1)
g2_subjs = primary_subjects(g2)
for s in g1_subjs - g2_subjs:
rval += "\n===== Subjects in Graph 1 but not Graph 2: "
rval += PrettyGraph.strip_prefixes(complete_definition(s, g1))
for s in g2_subjs - g1_subjs:
rval += "\n===== Subjects in Graph 2 but not Graph 1: "
rval += PrettyGraph.strip_prefixes(complete_definition(s, g2))
# Step 2: Iterate over all of the remaining subjects comparing their contents
for s in g1_subjs.intersection(g2_subjs):
s_in_g1 = graph_for_subject(g1, s)
s_in_g2 = graph_for_subject(g2, s)
in_both, in_first, in_second = graph_diff(skolemize(s_in_g1), skolemize(s_in_g2))
if compare_filter:
compare_filter(in_both, in_first, in_second)
if len(list(in_first)) or len(list(in_second)):
rval += "\n\nSubject {} DIFFERENCE: ".format(s) + '=' * 30
if len(in_first):
rval += "\n\t----> First: \n" + '\n'.join(dump_nt_sorted(in_first))
if len(in_second):
rval += "\n\t----> Second: \n" + '\n'.join(dump_nt_sorted(in_second))
rval += '-' * 40
return rval | Compare graph g1 and g2
:param g1: first graph
:param g2: second graph
:param ignore_owl_version:
:param ignore_type_arcs:
:param compare_filter: Final adjustment for graph difference. Used, for example, to deal with FHIR decimal problems.
:return: List of differences as printable lines or blank if everything matches | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/rdfcompare.py#L117-L169 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhirtordf.py | proc_file | def proc_file(infile: str, outfile: str, opts: Namespace) -> bool:
"""
Process infile.
:param infile: input file to be processed
:param outfile: target output file.
:param opts:
:return:
"""
g = fhir_json_to_rdf(infile, opts.uribase, opts.graph, add_ontology_header=not opts.noontology,
do_continuations=not opts.nocontinuation, replace_narrative_text=bool(opts.nonarrative),
metavoc=opts.fhir_metavoc)
# If we aren't carrying graph in opts, we're doing a file by file transformation
if g:
if not opts.graph:
serialize_graph(g, outfile, opts)
return True
else:
print("{} : Not a FHIR collection or resource".format(infile))
return False | python | def proc_file(infile: str, outfile: str, opts: Namespace) -> bool:
"""
Process infile.
:param infile: input file to be processed
:param outfile: target output file.
:param opts:
:return:
"""
g = fhir_json_to_rdf(infile, opts.uribase, opts.graph, add_ontology_header=not opts.noontology,
do_continuations=not opts.nocontinuation, replace_narrative_text=bool(opts.nonarrative),
metavoc=opts.fhir_metavoc)
# If we aren't carrying graph in opts, we're doing a file by file transformation
if g:
if not opts.graph:
serialize_graph(g, outfile, opts)
return True
else:
print("{} : Not a FHIR collection or resource".format(infile))
return False | Process infile.
:param infile: input file to be processed
:param outfile: target output file.
:param opts:
:return: | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhirtordf.py#L76-L95 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhirtordf.py | file_filter | def file_filter(ifn: str, indir: str, opts: Namespace) -> bool:
"""
Determine whether to process ifn. We con't process:
1) Anything in a directory having a path element that begins with "_"
2) Really, really big files
3) Temporary lists of know errors
:param ifn: input file name
:param indir: input directory
:param opts: argparse options
:return: True if to be processed, false if to be skipped
"""
# If it looks like we're processing a URL as an input file, skip the suffix check
if '://' in ifn:
return True
if not ifn.endswith('.json'):
return False
if indir and (indir.startswith("_") or "/_" in indir or any(dn in indir for dn in opts.skipdirs)):
return False
if opts.skipfns and any(sfn in ifn for sfn in opts.skipfns):
return False
infile = os.path.join(indir, ifn)
if not opts.infile and opts.maxsize and os.path.getsize(infile) > (opts.maxsize * 1000):
return False
return True | python | def file_filter(ifn: str, indir: str, opts: Namespace) -> bool:
"""
Determine whether to process ifn. We con't process:
1) Anything in a directory having a path element that begins with "_"
2) Really, really big files
3) Temporary lists of know errors
:param ifn: input file name
:param indir: input directory
:param opts: argparse options
:return: True if to be processed, false if to be skipped
"""
# If it looks like we're processing a URL as an input file, skip the suffix check
if '://' in ifn:
return True
if not ifn.endswith('.json'):
return False
if indir and (indir.startswith("_") or "/_" in indir or any(dn in indir for dn in opts.skipdirs)):
return False
if opts.skipfns and any(sfn in ifn for sfn in opts.skipfns):
return False
infile = os.path.join(indir, ifn)
if not opts.infile and opts.maxsize and os.path.getsize(infile) > (opts.maxsize * 1000):
return False
return True | Determine whether to process ifn. We con't process:
1) Anything in a directory having a path element that begins with "_"
2) Really, really big files
3) Temporary lists of know errors
:param ifn: input file name
:param indir: input directory
:param opts: argparse options
:return: True if to be processed, false if to be skipped | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhirtordf.py#L105-L133 |
BD2KOnFHIR/fhirtordf | fhirtordf/fhirtordf.py | fhirtordf | def fhirtordf(argv: List[str], default_exit: bool = True) -> bool:
""" Entry point for command line utility """
dlp = dirlistproc.DirectoryListProcessor(argv,
description="Convert FHIR JSON into RDF",
infile_suffix=".json",
outfile_suffix=".ttl",
addargs=addargs,
noexit=not default_exit)
if not dlp.successful_parse:
return False
# Version
if dlp.opts.version:
print("FHIR to RDF Conversion Tool -- Version {}".format(__version__))
# We either have to have an input file or an input directory
if not dlp.opts.infile and not dlp.opts.indir:
if not dlp.opts.version:
dlp.parser.error("Either an input file or an input directory must be supplied")
return dlp.opts.version
# Create the output directory if needed
if dlp.opts.outdir and not os.path.exists(dlp.opts.outdir):
os.makedirs(dlp.opts.outdir)
# If we are going to a single output file or stdout, gather all the input
dlp.opts.graph = Graph() if (not dlp.opts.outfile and not dlp.opts.outdir) or\
(dlp.opts.outfile and len(dlp.opts.outfile) == 1) else None
dlp.opts.fhir_metavoc = load_fhir_ontology(dlp.opts)
# If it looks like we're processing a URL as an input file, skip the suffix check
if dlp.opts.infile and len(dlp.opts.infile) == 1 and not dlp.opts.indir and "://" in dlp.opts.infile[0]:
dlp.infile_suffix = ""
dlp.outfile_suffix = '.' + suffix_for(dlp.opts.format)
nfiles, nsuccess = dlp.run(proc=proc_file, file_filter_2=file_filter)
if nfiles:
if dlp.opts.graph:
serialize_graph(dlp.opts.graph, dlp.opts.outfile[0] if dlp.opts.outfile else None, dlp.opts)
return nsuccess > 0
return False | python | def fhirtordf(argv: List[str], default_exit: bool = True) -> bool:
""" Entry point for command line utility """
dlp = dirlistproc.DirectoryListProcessor(argv,
description="Convert FHIR JSON into RDF",
infile_suffix=".json",
outfile_suffix=".ttl",
addargs=addargs,
noexit=not default_exit)
if not dlp.successful_parse:
return False
# Version
if dlp.opts.version:
print("FHIR to RDF Conversion Tool -- Version {}".format(__version__))
# We either have to have an input file or an input directory
if not dlp.opts.infile and not dlp.opts.indir:
if not dlp.opts.version:
dlp.parser.error("Either an input file or an input directory must be supplied")
return dlp.opts.version
# Create the output directory if needed
if dlp.opts.outdir and not os.path.exists(dlp.opts.outdir):
os.makedirs(dlp.opts.outdir)
# If we are going to a single output file or stdout, gather all the input
dlp.opts.graph = Graph() if (not dlp.opts.outfile and not dlp.opts.outdir) or\
(dlp.opts.outfile and len(dlp.opts.outfile) == 1) else None
dlp.opts.fhir_metavoc = load_fhir_ontology(dlp.opts)
# If it looks like we're processing a URL as an input file, skip the suffix check
if dlp.opts.infile and len(dlp.opts.infile) == 1 and not dlp.opts.indir and "://" in dlp.opts.infile[0]:
dlp.infile_suffix = ""
dlp.outfile_suffix = '.' + suffix_for(dlp.opts.format)
nfiles, nsuccess = dlp.run(proc=proc_file, file_filter_2=file_filter)
if nfiles:
if dlp.opts.graph:
serialize_graph(dlp.opts.graph, dlp.opts.outfile[0] if dlp.opts.outfile else None, dlp.opts)
return nsuccess > 0
return False | Entry point for command line utility | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/fhirtordf.py#L162-L202 |
BD2KOnFHIR/fhirtordf | fhirtordf/rdfsupport/uriutils.py | parse_fhir_resource_uri | def parse_fhir_resource_uri(uri: Union[URIRef, str]) -> FHIR_RESOURCE:
"""
Use the FHIR Regular Expression for Resource URI's to determine the namespace and type
of a given URI. As an example, "http://hl7.org/fhir/Patient/p123" maps to the tuple
``('Patient', 'http://hl7.org/fhir')
:param uri: URI to parse
:return: FHIR_RESOURCE (namespace, type, resource)
"""
uri_str = str(uri)
m = FHIR_RESOURCE_RE.match(uri_str)
if m:
return FHIR_RESOURCE(URIRef(m.group(FHIR_RE_BASE)), FHIR[m.group(FHIR_RE_RESOURCE)], m.group(FHIR_RE_ID))
else:
# Not in the FHIR format - we can only do namespace and name
namespace, name = uri_str.rsplit('#', 1) if '#' in uri_str \
else uri_str.rsplit('/', 1) if '/' in uri_str else (None, uri_str)
return FHIR_RESOURCE(URIRef(namespace), None, name) | python | def parse_fhir_resource_uri(uri: Union[URIRef, str]) -> FHIR_RESOURCE:
"""
Use the FHIR Regular Expression for Resource URI's to determine the namespace and type
of a given URI. As an example, "http://hl7.org/fhir/Patient/p123" maps to the tuple
``('Patient', 'http://hl7.org/fhir')
:param uri: URI to parse
:return: FHIR_RESOURCE (namespace, type, resource)
"""
uri_str = str(uri)
m = FHIR_RESOURCE_RE.match(uri_str)
if m:
return FHIR_RESOURCE(URIRef(m.group(FHIR_RE_BASE)), FHIR[m.group(FHIR_RE_RESOURCE)], m.group(FHIR_RE_ID))
else:
# Not in the FHIR format - we can only do namespace and name
namespace, name = uri_str.rsplit('#', 1) if '#' in uri_str \
else uri_str.rsplit('/', 1) if '/' in uri_str else (None, uri_str)
return FHIR_RESOURCE(URIRef(namespace), None, name) | Use the FHIR Regular Expression for Resource URI's to determine the namespace and type
of a given URI. As an example, "http://hl7.org/fhir/Patient/p123" maps to the tuple
``('Patient', 'http://hl7.org/fhir')
:param uri: URI to parse
:return: FHIR_RESOURCE (namespace, type, resource) | https://github.com/BD2KOnFHIR/fhirtordf/blob/f97b3df683fa4caacf5cf4f29699ab060bcc0fbf/fhirtordf/rdfsupport/uriutils.py#L42-L60 |
astropy/astropy-helpers | astropy_helpers/distutils_helpers.py | get_dummy_distribution | def get_dummy_distribution():
"""
Returns a distutils Distribution object used to instrument the setup
environment before calling the actual setup() function.
"""
from .setup_helpers import _module_state
if _module_state['registered_commands'] is None:
raise RuntimeError(
'astropy_helpers.setup_helpers.register_commands() must be '
'called before using '
'astropy_helpers.setup_helpers.get_dummy_distribution()')
# Pre-parse the Distutils command-line options and config files to if
# the option is set.
dist = Distribution({'script_name': os.path.basename(sys.argv[0]),
'script_args': sys.argv[1:]})
dist.cmdclass.update(_module_state['registered_commands'])
with silence():
try:
dist.parse_config_files()
dist.parse_command_line()
except (DistutilsError, AttributeError, SystemExit):
# Let distutils handle DistutilsErrors itself AttributeErrors can
# get raise for ./setup.py --help SystemExit can be raised if a
# display option was used, for example
pass
return dist | python | def get_dummy_distribution():
"""
Returns a distutils Distribution object used to instrument the setup
environment before calling the actual setup() function.
"""
from .setup_helpers import _module_state
if _module_state['registered_commands'] is None:
raise RuntimeError(
'astropy_helpers.setup_helpers.register_commands() must be '
'called before using '
'astropy_helpers.setup_helpers.get_dummy_distribution()')
# Pre-parse the Distutils command-line options and config files to if
# the option is set.
dist = Distribution({'script_name': os.path.basename(sys.argv[0]),
'script_args': sys.argv[1:]})
dist.cmdclass.update(_module_state['registered_commands'])
with silence():
try:
dist.parse_config_files()
dist.parse_command_line()
except (DistutilsError, AttributeError, SystemExit):
# Let distutils handle DistutilsErrors itself AttributeErrors can
# get raise for ./setup.py --help SystemExit can be raised if a
# display option was used, for example
pass
return dist | Returns a distutils Distribution object used to instrument the setup
environment before calling the actual setup() function. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/distutils_helpers.py#L23-L53 |
astropy/astropy-helpers | astropy_helpers/distutils_helpers.py | get_distutils_option | def get_distutils_option(option, commands):
""" Returns the value of the given distutils option.
Parameters
----------
option : str
The name of the option
commands : list of str
The list of commands on which this option is available
Returns
-------
val : str or None
the value of the given distutils option. If the option is not set,
returns None.
"""
dist = get_dummy_distribution()
for cmd in commands:
cmd_opts = dist.command_options.get(cmd)
if cmd_opts is not None and option in cmd_opts:
return cmd_opts[option][1]
else:
return None | python | def get_distutils_option(option, commands):
""" Returns the value of the given distutils option.
Parameters
----------
option : str
The name of the option
commands : list of str
The list of commands on which this option is available
Returns
-------
val : str or None
the value of the given distutils option. If the option is not set,
returns None.
"""
dist = get_dummy_distribution()
for cmd in commands:
cmd_opts = dist.command_options.get(cmd)
if cmd_opts is not None and option in cmd_opts:
return cmd_opts[option][1]
else:
return None | Returns the value of the given distutils option.
Parameters
----------
option : str
The name of the option
commands : list of str
The list of commands on which this option is available
Returns
-------
val : str or None
the value of the given distutils option. If the option is not set,
returns None. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/distutils_helpers.py#L62-L87 |
astropy/astropy-helpers | astropy_helpers/distutils_helpers.py | add_command_option | def add_command_option(command, name, doc, is_bool=False):
"""
Add a custom option to a setup command.
Issues a warning if the option already exists on that command.
Parameters
----------
command : str
The name of the command as given on the command line
name : str
The name of the build option
doc : str
A short description of the option, for the `--help` message
is_bool : bool, optional
When `True`, the option is a boolean option and doesn't
require an associated value.
"""
dist = get_dummy_distribution()
cmdcls = dist.get_command_class(command)
if (hasattr(cmdcls, '_astropy_helpers_options') and
name in cmdcls._astropy_helpers_options):
return
attr = name.replace('-', '_')
if hasattr(cmdcls, attr):
raise RuntimeError(
'{0!r} already has a {1!r} class attribute, barring {2!r} from '
'being usable as a custom option name.'.format(cmdcls, attr, name))
for idx, cmd in enumerate(cmdcls.user_options):
if cmd[0] == name:
log.warn('Overriding existing {0!r} option '
'{1!r}'.format(command, name))
del cmdcls.user_options[idx]
if name in cmdcls.boolean_options:
cmdcls.boolean_options.remove(name)
break
cmdcls.user_options.append((name, None, doc))
if is_bool:
cmdcls.boolean_options.append(name)
# Distutils' command parsing requires that a command object have an
# attribute with the same name as the option (with '-' replaced with '_')
# in order for that option to be recognized as valid
setattr(cmdcls, attr, None)
# This caches the options added through add_command_option so that if it is
# run multiple times in the same interpreter repeated adds are ignored
# (this way we can still raise a RuntimeError if a custom option overrides
# a built-in option)
if not hasattr(cmdcls, '_astropy_helpers_options'):
cmdcls._astropy_helpers_options = set([name])
else:
cmdcls._astropy_helpers_options.add(name) | python | def add_command_option(command, name, doc, is_bool=False):
"""
Add a custom option to a setup command.
Issues a warning if the option already exists on that command.
Parameters
----------
command : str
The name of the command as given on the command line
name : str
The name of the build option
doc : str
A short description of the option, for the `--help` message
is_bool : bool, optional
When `True`, the option is a boolean option and doesn't
require an associated value.
"""
dist = get_dummy_distribution()
cmdcls = dist.get_command_class(command)
if (hasattr(cmdcls, '_astropy_helpers_options') and
name in cmdcls._astropy_helpers_options):
return
attr = name.replace('-', '_')
if hasattr(cmdcls, attr):
raise RuntimeError(
'{0!r} already has a {1!r} class attribute, barring {2!r} from '
'being usable as a custom option name.'.format(cmdcls, attr, name))
for idx, cmd in enumerate(cmdcls.user_options):
if cmd[0] == name:
log.warn('Overriding existing {0!r} option '
'{1!r}'.format(command, name))
del cmdcls.user_options[idx]
if name in cmdcls.boolean_options:
cmdcls.boolean_options.remove(name)
break
cmdcls.user_options.append((name, None, doc))
if is_bool:
cmdcls.boolean_options.append(name)
# Distutils' command parsing requires that a command object have an
# attribute with the same name as the option (with '-' replaced with '_')
# in order for that option to be recognized as valid
setattr(cmdcls, attr, None)
# This caches the options added through add_command_option so that if it is
# run multiple times in the same interpreter repeated adds are ignored
# (this way we can still raise a RuntimeError if a custom option overrides
# a built-in option)
if not hasattr(cmdcls, '_astropy_helpers_options'):
cmdcls._astropy_helpers_options = set([name])
else:
cmdcls._astropy_helpers_options.add(name) | Add a custom option to a setup command.
Issues a warning if the option already exists on that command.
Parameters
----------
command : str
The name of the command as given on the command line
name : str
The name of the build option
doc : str
A short description of the option, for the `--help` message
is_bool : bool, optional
When `True`, the option is a boolean option and doesn't
require an associated value. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/distutils_helpers.py#L161-L223 |
astropy/astropy-helpers | astropy_helpers/distutils_helpers.py | get_distutils_display_options | def get_distutils_display_options():
""" Returns a set of all the distutils display options in their long and
short forms. These are the setup.py arguments such as --name or --version
which print the project's metadata and then exit.
Returns
-------
opts : set
The long and short form display option arguments, including the - or --
"""
short_display_opts = set('-' + o[1] for o in Distribution.display_options
if o[1])
long_display_opts = set('--' + o[0] for o in Distribution.display_options)
# Include -h and --help which are not explicitly listed in
# Distribution.display_options (as they are handled by optparse)
short_display_opts.add('-h')
long_display_opts.add('--help')
# This isn't the greatest approach to hardcode these commands.
# However, there doesn't seem to be a good way to determine
# whether build *will be* run as part of the command at this
# phase.
display_commands = set([
'clean', 'register', 'setopt', 'saveopts', 'egg_info',
'alias'])
return short_display_opts.union(long_display_opts.union(display_commands)) | python | def get_distutils_display_options():
""" Returns a set of all the distutils display options in their long and
short forms. These are the setup.py arguments such as --name or --version
which print the project's metadata and then exit.
Returns
-------
opts : set
The long and short form display option arguments, including the - or --
"""
short_display_opts = set('-' + o[1] for o in Distribution.display_options
if o[1])
long_display_opts = set('--' + o[0] for o in Distribution.display_options)
# Include -h and --help which are not explicitly listed in
# Distribution.display_options (as they are handled by optparse)
short_display_opts.add('-h')
long_display_opts.add('--help')
# This isn't the greatest approach to hardcode these commands.
# However, there doesn't seem to be a good way to determine
# whether build *will be* run as part of the command at this
# phase.
display_commands = set([
'clean', 'register', 'setopt', 'saveopts', 'egg_info',
'alias'])
return short_display_opts.union(long_display_opts.union(display_commands)) | Returns a set of all the distutils display options in their long and
short forms. These are the setup.py arguments such as --name or --version
which print the project's metadata and then exit.
Returns
-------
opts : set
The long and short form display option arguments, including the - or -- | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/distutils_helpers.py#L226-L254 |
astropy/astropy-helpers | astropy_helpers/commands/build_sphinx.py | ensure_sphinx_astropy_installed | def ensure_sphinx_astropy_installed():
"""
Make sure that sphinx-astropy is available, installing it temporarily if not.
This returns the available version of sphinx-astropy as well as any
paths that should be added to sys.path for sphinx-astropy to be available.
"""
# We've split out the Sphinx part of astropy-helpers into sphinx-astropy
# but we want it to be auto-installed seamlessly for anyone using
# build_docs. We check if it's already installed, and if not, we install
# it to a local .eggs directory and add the eggs to the path (these
# have to each be added to the path, we can't add them by simply adding
# .eggs to the path)
sys_path_inserts = []
sphinx_astropy_version = None
try:
from sphinx_astropy import __version__ as sphinx_astropy_version # noqa
except ImportError:
from setuptools import Distribution
dist = Distribution()
# Numpydoc 0.9.0 requires sphinx 1.6+, we can limit the version here
# until we also makes our minimum required version Sphinx 1.6
if SPHINX_LT_16:
dist.fetch_build_eggs('numpydoc<0.9')
# This egg build doesn't respect python_requires, not aware of
# pre-releases. We know that mpl 3.1+ requires Python 3.6+, so this
# ugly workaround takes care of it until there is a solution for
# https://github.com/astropy/astropy-helpers/issues/462
if LooseVersion(sys.version) < LooseVersion('3.6'):
dist.fetch_build_eggs('matplotlib<3.1')
eggs = dist.fetch_build_eggs('sphinx-astropy')
# Find out the version of sphinx-astropy if possible. For some old
# setuptools version, eggs will be None even if sphinx-astropy was
# successfully installed.
if eggs is not None:
for egg in eggs:
if egg.project_name == 'sphinx-astropy':
sphinx_astropy_version = egg.parsed_version.public
break
eggs_path = os.path.abspath('.eggs')
for egg in glob.glob(os.path.join(eggs_path, '*.egg')):
sys_path_inserts.append(egg)
return sphinx_astropy_version, sys_path_inserts | python | def ensure_sphinx_astropy_installed():
"""
Make sure that sphinx-astropy is available, installing it temporarily if not.
This returns the available version of sphinx-astropy as well as any
paths that should be added to sys.path for sphinx-astropy to be available.
"""
# We've split out the Sphinx part of astropy-helpers into sphinx-astropy
# but we want it to be auto-installed seamlessly for anyone using
# build_docs. We check if it's already installed, and if not, we install
# it to a local .eggs directory and add the eggs to the path (these
# have to each be added to the path, we can't add them by simply adding
# .eggs to the path)
sys_path_inserts = []
sphinx_astropy_version = None
try:
from sphinx_astropy import __version__ as sphinx_astropy_version # noqa
except ImportError:
from setuptools import Distribution
dist = Distribution()
# Numpydoc 0.9.0 requires sphinx 1.6+, we can limit the version here
# until we also makes our minimum required version Sphinx 1.6
if SPHINX_LT_16:
dist.fetch_build_eggs('numpydoc<0.9')
# This egg build doesn't respect python_requires, not aware of
# pre-releases. We know that mpl 3.1+ requires Python 3.6+, so this
# ugly workaround takes care of it until there is a solution for
# https://github.com/astropy/astropy-helpers/issues/462
if LooseVersion(sys.version) < LooseVersion('3.6'):
dist.fetch_build_eggs('matplotlib<3.1')
eggs = dist.fetch_build_eggs('sphinx-astropy')
# Find out the version of sphinx-astropy if possible. For some old
# setuptools version, eggs will be None even if sphinx-astropy was
# successfully installed.
if eggs is not None:
for egg in eggs:
if egg.project_name == 'sphinx-astropy':
sphinx_astropy_version = egg.parsed_version.public
break
eggs_path = os.path.abspath('.eggs')
for egg in glob.glob(os.path.join(eggs_path, '*.egg')):
sys_path_inserts.append(egg)
return sphinx_astropy_version, sys_path_inserts | Make sure that sphinx-astropy is available, installing it temporarily if not.
This returns the available version of sphinx-astropy as well as any
paths that should be added to sys.path for sphinx-astropy to be available. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/commands/build_sphinx.py#L40-L89 |
astropy/astropy-helpers | astropy_helpers/utils.py | _get_platlib_dir | def _get_platlib_dir(cmd):
"""
Given a build command, return the name of the appropriate platform-specific
build subdirectory directory (e.g. build/lib.linux-x86_64-2.7)
"""
plat_specifier = '.{0}-{1}'.format(cmd.plat_name, sys.version[0:3])
return os.path.join(cmd.build_base, 'lib' + plat_specifier) | python | def _get_platlib_dir(cmd):
"""
Given a build command, return the name of the appropriate platform-specific
build subdirectory directory (e.g. build/lib.linux-x86_64-2.7)
"""
plat_specifier = '.{0}-{1}'.format(cmd.plat_name, sys.version[0:3])
return os.path.join(cmd.build_base, 'lib' + plat_specifier) | Given a build command, return the name of the appropriate platform-specific
build subdirectory directory (e.g. build/lib.linux-x86_64-2.7) | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/utils.py#L37-L44 |
astropy/astropy-helpers | astropy_helpers/utils.py | get_numpy_include_path | def get_numpy_include_path():
"""
Gets the path to the numpy headers.
"""
# We need to go through this nonsense in case setuptools
# downloaded and installed Numpy for us as part of the build or
# install, since Numpy may still think it's in "setup mode", when
# in fact we're ready to use it to build astropy now.
import builtins
if hasattr(builtins, '__NUMPY_SETUP__'):
del builtins.__NUMPY_SETUP__
import imp
import numpy
imp.reload(numpy)
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
return numpy_include | python | def get_numpy_include_path():
"""
Gets the path to the numpy headers.
"""
# We need to go through this nonsense in case setuptools
# downloaded and installed Numpy for us as part of the build or
# install, since Numpy may still think it's in "setup mode", when
# in fact we're ready to use it to build astropy now.
import builtins
if hasattr(builtins, '__NUMPY_SETUP__'):
del builtins.__NUMPY_SETUP__
import imp
import numpy
imp.reload(numpy)
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
return numpy_include | Gets the path to the numpy headers. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/utils.py#L47-L67 |
astropy/astropy-helpers | astropy_helpers/utils.py | is_path_hidden | def is_path_hidden(filepath):
"""
Determines if a given file or directory is hidden.
Parameters
----------
filepath : str
The path to a file or directory
Returns
-------
hidden : bool
Returns `True` if the file is hidden
"""
name = os.path.basename(os.path.abspath(filepath))
if isinstance(name, bytes):
is_dotted = name.startswith(b'.')
else:
is_dotted = name.startswith('.')
return is_dotted or _has_hidden_attribute(filepath) | python | def is_path_hidden(filepath):
"""
Determines if a given file or directory is hidden.
Parameters
----------
filepath : str
The path to a file or directory
Returns
-------
hidden : bool
Returns `True` if the file is hidden
"""
name = os.path.basename(os.path.abspath(filepath))
if isinstance(name, bytes):
is_dotted = name.startswith(b'.')
else:
is_dotted = name.startswith('.')
return is_dotted or _has_hidden_attribute(filepath) | Determines if a given file or directory is hidden.
Parameters
----------
filepath : str
The path to a file or directory
Returns
-------
hidden : bool
Returns `True` if the file is hidden | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/utils.py#L128-L148 |
astropy/astropy-helpers | astropy_helpers/utils.py | walk_skip_hidden | def walk_skip_hidden(top, onerror=None, followlinks=False):
"""
A wrapper for `os.walk` that skips hidden files and directories.
This function does not have the parameter `topdown` from
`os.walk`: the directories must always be recursed top-down when
using this function.
See also
--------
os.walk : For a description of the parameters
"""
for root, dirs, files in os.walk(
top, topdown=True, onerror=onerror,
followlinks=followlinks):
# These lists must be updated in-place so os.walk will skip
# hidden directories
dirs[:] = [d for d in dirs if not is_path_hidden(d)]
files[:] = [f for f in files if not is_path_hidden(f)]
yield root, dirs, files | python | def walk_skip_hidden(top, onerror=None, followlinks=False):
"""
A wrapper for `os.walk` that skips hidden files and directories.
This function does not have the parameter `topdown` from
`os.walk`: the directories must always be recursed top-down when
using this function.
See also
--------
os.walk : For a description of the parameters
"""
for root, dirs, files in os.walk(
top, topdown=True, onerror=onerror,
followlinks=followlinks):
# These lists must be updated in-place so os.walk will skip
# hidden directories
dirs[:] = [d for d in dirs if not is_path_hidden(d)]
files[:] = [f for f in files if not is_path_hidden(f)]
yield root, dirs, files | A wrapper for `os.walk` that skips hidden files and directories.
This function does not have the parameter `topdown` from
`os.walk`: the directories must always be recursed top-down when
using this function.
See also
--------
os.walk : For a description of the parameters | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/utils.py#L151-L171 |
astropy/astropy-helpers | astropy_helpers/utils.py | write_if_different | def write_if_different(filename, data):
"""Write `data` to `filename`, if the content of the file is different.
Parameters
----------
filename : str
The file name to be written to.
data : bytes
The data to be written to `filename`.
"""
assert isinstance(data, bytes)
if os.path.exists(filename):
with open(filename, 'rb') as fd:
original_data = fd.read()
else:
original_data = None
if original_data != data:
with open(filename, 'wb') as fd:
fd.write(data) | python | def write_if_different(filename, data):
"""Write `data` to `filename`, if the content of the file is different.
Parameters
----------
filename : str
The file name to be written to.
data : bytes
The data to be written to `filename`.
"""
assert isinstance(data, bytes)
if os.path.exists(filename):
with open(filename, 'rb') as fd:
original_data = fd.read()
else:
original_data = None
if original_data != data:
with open(filename, 'wb') as fd:
fd.write(data) | Write `data` to `filename`, if the content of the file is different.
Parameters
----------
filename : str
The file name to be written to.
data : bytes
The data to be written to `filename`. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/utils.py#L174-L195 |
astropy/astropy-helpers | astropy_helpers/utils.py | import_file | def import_file(filename, name=None):
"""
Imports a module from a single file as if it doesn't belong to a
particular package.
The returned module will have the optional ``name`` if given, or else
a name generated from the filename.
"""
# Specifying a traditional dot-separated fully qualified name here
# results in a number of "Parent module 'astropy' not found while
# handling absolute import" warnings. Using the same name, the
# namespaces of the modules get merged together. So, this
# generates an underscore-separated name which is more likely to
# be unique, and it doesn't really matter because the name isn't
# used directly here anyway.
mode = 'r'
if name is None:
basename = os.path.splitext(filename)[0]
name = '_'.join(os.path.relpath(basename).split(os.sep)[1:])
if not os.path.exists(filename):
raise ImportError('Could not import file {0}'.format(filename))
if import_machinery:
loader = import_machinery.SourceFileLoader(name, filename)
mod = loader.load_module()
else:
with open(filename, mode) as fd:
mod = imp.load_module(name, fd, filename, ('.py', mode, 1))
return mod | python | def import_file(filename, name=None):
"""
Imports a module from a single file as if it doesn't belong to a
particular package.
The returned module will have the optional ``name`` if given, or else
a name generated from the filename.
"""
# Specifying a traditional dot-separated fully qualified name here
# results in a number of "Parent module 'astropy' not found while
# handling absolute import" warnings. Using the same name, the
# namespaces of the modules get merged together. So, this
# generates an underscore-separated name which is more likely to
# be unique, and it doesn't really matter because the name isn't
# used directly here anyway.
mode = 'r'
if name is None:
basename = os.path.splitext(filename)[0]
name = '_'.join(os.path.relpath(basename).split(os.sep)[1:])
if not os.path.exists(filename):
raise ImportError('Could not import file {0}'.format(filename))
if import_machinery:
loader = import_machinery.SourceFileLoader(name, filename)
mod = loader.load_module()
else:
with open(filename, mode) as fd:
mod = imp.load_module(name, fd, filename, ('.py', mode, 1))
return mod | Imports a module from a single file as if it doesn't belong to a
particular package.
The returned module will have the optional ``name`` if given, or else
a name generated from the filename. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/utils.py#L198-L229 |
astropy/astropy-helpers | astropy_helpers/utils.py | resolve_name | def resolve_name(name):
"""Resolve a name like ``module.object`` to an object and return it.
Raise `ImportError` if the module or name is not found.
"""
parts = name.split('.')
cursor = len(parts) - 1
module_name = parts[:cursor]
attr_name = parts[-1]
while cursor > 0:
try:
ret = __import__('.'.join(module_name), fromlist=[attr_name])
break
except ImportError:
if cursor == 0:
raise
cursor -= 1
module_name = parts[:cursor]
attr_name = parts[cursor]
ret = ''
for part in parts[cursor:]:
try:
ret = getattr(ret, part)
except AttributeError:
raise ImportError(name)
return ret | python | def resolve_name(name):
"""Resolve a name like ``module.object`` to an object and return it.
Raise `ImportError` if the module or name is not found.
"""
parts = name.split('.')
cursor = len(parts) - 1
module_name = parts[:cursor]
attr_name = parts[-1]
while cursor > 0:
try:
ret = __import__('.'.join(module_name), fromlist=[attr_name])
break
except ImportError:
if cursor == 0:
raise
cursor -= 1
module_name = parts[:cursor]
attr_name = parts[cursor]
ret = ''
for part in parts[cursor:]:
try:
ret = getattr(ret, part)
except AttributeError:
raise ImportError(name)
return ret | Resolve a name like ``module.object`` to an object and return it.
Raise `ImportError` if the module or name is not found. | https://github.com/astropy/astropy-helpers/blob/f5a27d3f84a98ea0eebb85e0cf3e7214c6bc0d09/astropy_helpers/utils.py#L232-L261 |
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