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data_package.py
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data_package.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Modifications from DataONE CLI data_package.py code to reuse for
# VisTrails
#
# Modifications by David Koop, NYU-Poly, 2013
# -- also fixed a few bugs (typos, mismatched arguments)
# This work was created by participants in the DataONE project, and is
# jointly copyrighted by participating institutions in DataONE. For
# more information on DataONE, see our web site at http://dataone.org.
#
# Copyright ${year}
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
'''
:mod:`data_package`
===================
:Synopsis: Wrapper around a data package
:Created: 2012-03-29
:Author: DataONE (Pippin)
'''
# Stdlib.
import os
import sys
import StringIO
from xml.dom.minidom import parse, parseString #@UnusedImport
# 3rd party
try:
from rdflib import Namespace, URIRef
import foresite
import foresite.utils
except ImportError as e:
sys.stderr.write('Import error: {0}\n'.format(str(e)))
sys.stderr.write(' available at: https://foresite-toolkit.googlecode.com/svn/foresite-python/trunk\n')
raise
# DataONE
# common
try:
import d1_common.util as util
from d1_common.types.exceptions import DataONEException
except ImportError as e:
sys.stderr.write('Import error: {0}\n'.format(str(e)))
sys.stderr.write('Please install d1_common.\n')
raise
# vistrails package
import utils
from config import configuration
ALLOWABLE_PACKAGE_SERIALIZATIONS = ('xml', 'pretty-xml', 'n3', 'rdfa', 'json',
'pretty-json', 'turtle', 'nt', 'trix')
RDFXML_FORMATID = 'http://www.openarchives.org/ore/terms'
RDF_NS = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
CITO_NS = 'http://purl.org/spar/cito/'
DCTERMS_NS = 'http://purl.org/dc/terms/'
#** DataPackage ***************************************************************
class DataPackage(object):
def __init__(self, pid=None):
''' Create a package
'''
self.pid = pid
#
# Objects in here a dicts with keywords pid, dirty, obj, meta; which are
# string, boolean, blob, and pyxb objects respectively.
self.original_pid = None
self.sysmeta = None
self.scimeta = None
self.scidata_dict = {}
self.resmap = None
#== Informational =========================================================
def is_dirty(self):
''' Check to see if anything needs to be saved.
'''
if self.pid != self.original_pid:
return True
if self.scimeta is not None:
if (self.scimeta.dirty) and self.scimeta.dirty:
return True
if self.scidata_dict is not None:
for item in self.scidata_dict.values():
if (item.dirty is not None) and item.dirty:
return True
return False
#== Manipulation ==========================================================
def name(self, pid):
''' Rename the package
'''
self.pid = pid
# if pid is None:
# if cli_util.confirm('Do you really want to clear the name of the package?'):
# self.pid = None
# else:
# raise Exception('Missing the new pid')
# else:
# if self.pid is not None:
# print_info('Package name is cleared.')
# self.pid = pid
def load(self):
''' Get the object referred to by pid and make sure it is a
package.
'''
if self.pid is None:
raise Exception('Missing pid')
sysmeta = utils.get_sysmeta_by_pid(self.pid)
if not sysmeta:
raise Exception('Couldn\'t find "%s" in DataONE.' % self.pid)
if sysmeta.formatId != RDFXML_FORMATID:
raise Exception('Package must be in RDF/XML format (not "%s").' % \
sysmeta.formatId)
rdf_xml_file = utils.get_object_by_pid(self.pid)
if not self._parse_rdf_xml(rdf_xml_file):
raise Exception('Unable to load package "%s".' % self.pid)
self.original_pid = self.pid
self.sysmeta = sysmeta
self.scimeta = self._download_object(self.scimeta)
loaded_scidata = {}
for pid, scidata in self.scidata_dict.iteritems():
loaded_scidata[pid] = self._download_object(scidata)
self.scidata_dict = loaded_scidata
return self
def _parse_rdf_xml(self, xml_file):
doc = parse(xml_file)
# print 'doc:\n', doc.toxml()
self.scimeta = None
self.scidata_dict = {}
for desc in doc.getElementsByTagNameNS(RDF_NS, 'Description'):
documentedBy = desc.getElementsByTagNameNS(CITO_NS, 'isDocumentedBy')
if documentedBy and len(documentedBy) > 0:
scidata = DataObject(dirty=False)
pid_element = desc.getElementsByTagNameNS(DCTERMS_NS, 'identifier')
if pid_element and pid_element.item(0) and pid_element.item(0).hasChildNodes():
scidata.pid = pid_element.item(0).firstChild.nodeValue
if len(documentedBy) > 1:
print 'Using the first Science Metadata Object for %s' % scidata.pid
about_url = documentedBy.item(0).getAttributeNS(RDF_NS, 'resource')
scidata.documented_by = about_url
self.scidata_dict[scidata.pid] = scidata
# scimeta?
elif desc.getElementsByTagNameNS(CITO_NS, 'documents'):
if self.scimeta:
print 'Already have a science metadata object (%s). Skipping...' % \
self.scimeta.pid
else:
self.scimeta = DataObject(dirty=False)
pid_element = desc.getElementsByTagNameNS(DCTERMS_NS, 'identifier')
if pid_element and pid_element.item(0) and pid_element.item(0).hasChildNodes():
self.scimeta.pid = pid_element.item(0).firstChild.nodeValue
return True
def save(self, mn_client=None, cn_client=None, **kwargs):
''' Save this object referred to by this pid.
'''
if self.pid is None:
raise Exception('Missing pid')
if mn_client is None:
mn_client = utils.get_d1_mn_client()
if cn_client is None:
cn_client = utils.get_d1_cn_client()
pkg_xml = self._serialize('xml', mn_client)
if not pkg_xml:
raise Exception("Couldn't serialize object.")
algorithm = configuration.checksum_alg
hash_fcn = util.get_checksum_calculator_by_dataone_designator(algorithm)
hash_fcn.update(pkg_xml)
checksum = hash_fcn.hexdigest()
sysmeta = utils.create_system_metadata(self.pid, len(pkg_xml),
checksum, algorithm, RDFXML_FORMATID,
**kwargs)
flo = StringIO.StringIO(pkg_xml)
# Save all the objects.
if self.scimeta and self.scimeta.dirty:
self._create_or_update(mn_client, cn_client, self.scimeta)
for scidata_pid in self.scidata_dict.keys():
scidata = self.scidata_dict.get(scidata_pid)
if scidata and scidata.dirty:
self._create_or_update(mn_client, cn_client, scidata)
response = mn_client.create(pid=self.pid, obj=flo, sysmeta=sysmeta)
if response is None:
return None
else:
self.original_pid = self.pid
if self.scimeta:
self.scimeta.dirty = False
if self.scidata_dict:
for scidata in self.scidata_dict.values():
scidata.dirty = False
return response.value()
def _create_or_update(self, mn_client, cn_client, data_object):
''' Either update the specified pid if it already exists or create a new one.
'''
if not data_object:
raise Exception('data object cannot be null')
if not data_object.pid:
raise Exception('data object must have a pid')
if not data_object.fname:
raise Exception('data object must have a file to write')
if not data_object.meta:
raise Exception('data object must have system metadata')
curr_sysmeta = utils.get_sysmeta_by_pid(data_object.pid, True,
cn_client, mn_client)
# Create
if not curr_sysmeta:
with open(utils.expand_path(data_object.fname), 'r') as f:
try:
return mn_client.create(data_object.pid, f, data_object.meta)
except DataONEException as e:
raise Exception('Unable to create Science Object on Member Node\n{0}'
.format(e.friendly_format()))
# Update
else:
data_object.meta.serialVersion = (curr_sysmeta.serialVersion + 1)
with open(utils.expand_path(data_object.fname), 'r') as f:
try:
return mn_client.update(data_object.pid, f, data_object.pid, data_object.meta)
except DataONEException as e:
raise Exception('Unable to update Science Object on Member Node\n{0}'
.format(e.friendly_format()))
# Nothing good happened.
return None
def scimeta_add(self, pid, file_name=None, format_id=None, **kwargs):
''' Add a scimeta object.
'''
if not pid:
raise Exception('Missing the pid')
# if (self.scimeta and not
# cli_util.confirm('Do you wish to delete the existing science metadata object?')):
# return
else:
self.scimeta = None
if not file_name:
new_meta = utils.get_sysmeta_by_pid(pid, True)
if not new_meta:
raise Exception('Couldn\'t find scimeta in DataONE, and there was no file specified.')
if not self._is_metadata_format(new_meta.formatId):
raise Exception('"%s" is not an allowable science metadata type.' % new_meta.formatId)
new_pid = new_meta.identifier.value()
if new_pid != pid:
pid = new_pid
self.scimeta = self._get_by_pid(pid, new_meta)
authMN = new_meta.authoritativeMemberNode
if authMN:
baseURL = utils.get_baseUrl(authMN.value())
if baseURL:
self.scimeta.url = utils.create_get_url_for_pid(baseURL, pid)
else:
complex_path = utils.create_complex_path(file_name)
if not os.path.exists(complex_path.path):
raise Exception('%s: file not found' % complex_path.path)
if not format_id:
format_id = complex_path.formatId
if not format_id and configuration.check("format"):
format_id = configuration.format
if not format_id:
raise Exception('The object format could not be determined and was not defined.')
if not self._is_metadata_format(format_id):
raise Exception('"%s" is not an allowable science metadata type.' % new_meta.formatId)
return
#
sysmeta = utils.create_sysmeta_from_path(pid, complex_path.path,
format_id=format_id, **kwargs)
self.scimeta = DataObject(pid, True, complex_path.path, None, sysmeta,
format_id)
scidata_list = self._find_scidata(self.scimeta)
if scidata_list:
for scidata in scidata_list:
self.scidata_add(scidata.pid, scidata.fname)
def scimeta_del(self):
''' Remove the science metadata object.
'''
# if cli_util.confirm('Are you sure you want to remove the science meta object?'):
# self.scimeta = None
self.scimeta = None
def scidata_add(self, pid, file_name=None, format_id=None, **kwargs):
''' Add a science data object to the list.
'''
if not pid:
raise Exception('Missing the pid')
if file_name:
# if utils.get_sysmeta_by_pid(pid):
# if not cli_util.confirm('That pid (%s) already exists in DataONE. Continue?' % pid):
# return
# raise Exception("The identifer (%s) already exists in DataONE." % pid)
complex_path = utils.create_complex_path(file_name)
if not format_id:
format_id = complex_path.formatId
if not format_id and configuration.check("format"):
format_id = configuration.format
if not format_id:
raise Exception('The object format could not be determined and was not defined.')
meta = utils.create_sysmeta_from_path(pid, complex_path.path,
format_id=format_id, **kwargs)
self.scidata_dict[pid] = DataObject(pid, True, complex_path.path,
None, meta, format_id)
else:
sysmeta = utils.get_sysmeta_by_pid(pid, True)
if not sysmeta:
raise Exception('The identifier (%s) was not found in DataONE.' % pid)
else:
pid = sysmeta.identifier.value()
# if pid in self.scidata_dict:
# if not cli_util.confirm('That science data object (%s) is already in the package. Replace?' % pid):
# return
# Get the scidata object.
scidata = self._get_by_pid(pid, sysmeta)
authMN = sysmeta.authoritativeMemberNode
if authMN:
baseURL = utils.get_baseUrl(authMN.value())
if baseURL:
scidata.url = utils.create_get_url_for_pid(baseURL, pid)
self.scidata_dict[pid] = scidata
def scidata_get(self, pid):
''' Get the specified scidata object.
'''
if pid and pid in self.scidata_dict:
return self.scidata_dict
else:
return None
def scidata_del(self, pid):
''' Remove a science data object.
'''
if pid is None:
raise Exception('Missing the pid')
if pid in self.scidata_dict:
# if cli_util.confirm('Are you sure you want to remove the science data object "%s"?' % pid):
del self.scidata_dict[pid]
def scidata_clear(self):
''' Remove all science data objects
'''
if self.scidata_dict is None:
self.scidata_dict = {}
elif ((len(self.scidata_dict) > 0)):
# and cli_util.confirm('Are you sure you want to remove all the science data objects?')):
self.scidata_dict.clear()
#== Helpers ===============================================================
def _get_by_pid(self, pid, sysmeta=None, mn_client=None, cn_client=None):
''' Return DataObject
'''
if pid is None:
raise Exception('Missing pid')
fname = utils.get_object_by_pid(pid, resolve=True, mn_client=mn_client,
cn_client=cn_client)
if fname:
meta = sysmeta
if not meta:
meta = utils.get_sysmeta_by_pid(pid, True)
url = utils.create_get_url_for_pid(mn_client.base_url, pid)
return DataObject(pid, False, fname, url, meta, meta.formatId, None)
else:
return None
def _is_metadata_format(self, formatId):
''' Check to see if this formatId specifies a resource map.
'''
if formatId is None:
return False
elif ((len(formatId) >= 4) and (formatId[:4] == "eml:")):
return True
elif ((len(formatId) >= 9) and (formatId[:9] == "FGDC-STD-")):
return True
else:
return False
def _generate_resmap(self, mn_client_base_url):
''' Create a package.
'''
# Create the aggregation
foresite.utils.namespaces['cito'] = Namespace("http://purl.org/spar/cito/")
aggr = foresite.Aggregation(self.pid)
aggr._dcterms.title = 'Simple aggregation of science metadata and data.'
# Create a reference to the science metadata
uri_scimeta = URIRef(self.scimeta.url)
res_scimeta = foresite.AggregatedResource(uri_scimeta)
res_scimeta._dcterms.identifier = self.scimeta.pid
res_scimeta._dcterms.description = 'Science metadata object.'
# Create references to the science data
resource_list = []
for scidata in self.scidata_dict.values():
uri_scidata = URIRef(scidata.url)
res_scidata = foresite.AggregatedResource(uri_scidata)
res_scidata._dcterms.identifier = scidata.pid
res_scidata._dcterms.description = 'Science data object'
res_scidata._cito.isDocumentedBy = uri_scimeta
res_scimeta._cito.documents = uri_scidata
resource_list.append(res_scidata)
# Add all the resources.
aggr.add_resource(res_scimeta)
for resource in resource_list:
aggr.add_resource(resource)
# Create the resource map
resmap_url = utils.create_get_url_for_pid(mn_client_base_url,
format(self.pid))
self.resmap = foresite.ResourceMap(resmap_url)
self.resmap._dcterms.identifier = self.pid
self.resmap.set_aggregation(aggr)
return self.resmap
def _serialize(self, fmt='xml', mn_client=None):
assert(fmt in ALLOWABLE_PACKAGE_SERIALIZATIONS)
if mn_client is None:
mn_client = utils.get_d1_mn_client()
if not self._prepare_urls(mn_client):
return
self._generate_resmap(mn_client.base_url)
if self.resmap.serializer is not None:
self.resmap.serializer = None
serializer = foresite.RdfLibSerializer(fmt)
self.resmap.register_serialization(serializer)
doc = self.resmap.get_serialization()
return doc.data
def _prepare_urls(self, mn_client=None):
''' Walk through the objects make sure that everything can be
serialized.
'''
if mn_client is None:
mn_client = utils.get_d1_mn_client()
if self.scimeta and not self.scimeta.url:
if not self._check_item(self.scimeta):
return False
elif not self.scimeta.url:
self.scimeta.url = utils.create_resolve_url_for_pid(mn_client.base_url,
self.scimeta.pid)
if self.scidata_dict:
for scidata in self.scidata_dict.values():
if not self._check_item(scidata):
return False
elif not scidata.url:
scidata.url = utils.create_resolve_url_for_pid(mn_client.base_url,
scidata.pid)
return True
def _check_item(self, item):
errors = []
if not self.scimeta.pid:
errors.append('missing pid')
if not self.scimeta.fname:
errors.append('missing fname')
if not self.scimeta.format_id:
errors.append('missing format-id')
if len(errors) == 0:
return True
else:
msg = 'Cannot serialize the science object: '
msg += ', '.join(errors)
raise Exception(msg)
def _create_object(self, item, mn_client=None, **kwargs):
''' Create an object in DataONE. '''
path = utils.expand_path(item.fname)
# cli_util.assert_file_exists(path)
assert(os.path.exists(path))
if 'format_id' in kwargs:
del kwargs['format_id']
sysmeta = utils.create_sysmeta_from_path(item.pid, path,
format_id=item.format_id,
**kwargs)
if mn_client is None:
mn_client = utils.get_d1_mn_client()
with open(path, 'r') as f:
try:
result = mn_client.create(item.pid, f, sysmeta)
print 'Created object "%s"' % item.pid
return result
except DataONEException as e:
raise Exception('Unable to create Science Object on Member Node\n{0}'
.format(e.friendly_format()))
def _download_object(self, data_object):
''' Download the object. '''
if not data_object.pid:
raise Exception('There is no pid specified')
return self._get_by_pid(data_object.pid, data_object.meta)
def _find_scidata(self, scimeta):
''' Search through an eml://ecoinformatics.org/eml-2.x.x document '''
''' looking for science data objects. '''
''' '''
''' THIS IS GOING TO BE DIFFICULT! '''
return ()
class DataObject(object):
def __init__(self, pid=None, dirty=None, fname=None, url=None, meta=None,
format_id=None, documented_by=None):
''' Create a data object
'''
self.pid = pid
self.dirty = dirty
self.fname = fname
self.url = url
self.meta = meta
self.format_id = format_id
self.documented_by = documented_by
def is_dirty(self):
return (self.dirty is not None) and self.dirty
def str(self): #@ReservedAssignment
m = 'None'
if self.meta is not None:
m = '<...>'
return 'DataObject[pid=%s,dirty=%s,fname=%s,meta=%s]' % \
(self.pid, str(self.dirty), self.fname, m)
def from_url(self, url):
self.url = url;
ndx = url.find('/resolve/') + 8
if ndx > 8:
self.pid = url[ndx:]
def summary(self, prefix, pretty, verbose):
p = prefix
if not prefix:
p = ' '
if (verbose is not None) and verbose:
pass
else:
flags = ''
pre = ' ('
post = ''
if (self.dirty is not None) and self.dirty:
flags += pre + 'needs saving'
pre = ', '
post = ')'
if self.fname is not None:
flags += pre + 'has an object file'
if verbose:
flags += ' (%s)' % self.fname
pre = ', '
post = ')'
if self.meta is not None:
flags += pre + 'has sysmeta'
pre = ', '
post = ')'
flags = flags + post
print '%s%s%s' % (p, self.pid, flags)
def run_pkg_test():
configuration.mn_url = "https://mn-demo-9.test.dataone.org/knb/d1/mn"
configuration.cn_url = "https://cn-stage-2.test.dataone.org/cn"
cn_client = utils.get_d1_cn_client()
mn_client = utils.get_d1_mn_client()
pid = "dakoop_test_pkg603"
meta_pid = "dakoop_cadwsap003"
meta_fname = \
"/vistrails/local_packages/dataone/package_data/cadwsap-s2910001-001.xml"
meta_format = "FGDC-STD-001-1998"
data_list = [("dakoop_cadwsap_main003", "/vistrails/local_packages/dataone/package_data/cadwsap-s2910001-001-main.csv", "text/csv"),
("dakoop_cadwsap_vuln003", "/vistrails/local_packages/dataone/package_data/cadwsap-s2910001-001-vuln.csv", "text/csv")]
pkg = DataPackage(pid)
sysmeta_kwargs = {"format_id": meta_format,
"submitter": "dakoop",
"owner": "dakoop",
"orig_mn": configuration.mn_url,
"auth_mn": configuration.mn_url}
pkg.scimeta_add(meta_pid, meta_fname, **sysmeta_kwargs)
for (data_pid, data_fname, data_format) in data_list:
sysmeta_kwargs["format_id"] = data_format
pkg.scidata_add(data_pid, data_fname, **sysmeta_kwargs)
del sysmeta_kwargs["format_id"]
pkg.save(mn_client, cn_client, **sysmeta_kwargs)
if __name__ == '__main__':
run_pkg_test()