def get(self, study_id, content=None, schema=None, **kwargs):
"""Syntactic sugar around to make it easier to get fine-grained access
to the parts of a file without composing a PhyloSchema object.
Possible invocations include:
w.get('pg_10')
w.get('pg_10', 'trees')
w.get('pg_10', 'trees', format='nexus')
w.get('pg_10', tree_id='tree3')
see:
"""
if isinstance(study_id, TreeRef):
return self.get(study_id=study_id.study_id,
tree_id=study_id.tree_id,
content=content,
schema=schema,
**kwargs)
if schema is None:
schema = create_content_spec(content=content,
repo_nexml2json=self.repo_nexml2json,
**kwargs)
r = self.get_study(study_id, schema)
if schema.content == 'study' and schema.format_str == 'nexson':
return r
if isinstance(r, dict) and ('data' in r):
return r['data']
return r
def get(self, study_id, content=None, schema=None, **kwargs):
"""Syntactic sugar around to make it easier to get fine-grained access
to the parts of a file without composing a PhyloSchema object.
Possible invocations include:
w.get('pg_10')
w.get('pg_10', 'trees')
w.get('pg_10', 'trees', format='nexus')
w.get('pg_10', tree_id='tree3')
see:
"""
if isinstance(study_id, TreeRef):
return self.get(study_id=study_id.study_id,
tree_id=study_id.tree_id,
content=content,
schema=schema,
**kwargs)
if schema is None:
schema = create_content_spec(content=content,
repo_nexml2json=self.repo_nexml2json,
**kwargs)
r = self.get_study(study_id, schema)
if schema.content == 'study' and schema.format_str == 'nexson':
return r
if isinstance(r, dict) and ('data' in r):
return r['data']
return r
def fetch_nexsons(self, tree_list, download=False):
nc = self.nexson_cache
pa = self.phyleystem_api
if download:
pa.phylesystem_obj.pull()
schema = create_content_spec(nexson_version='0.0.0')
for id_obj in tree_list:
study_id = id_obj['study_id']
nexson = pa.get_study(study_id, schema=schema)
path = os.path.join(nc, study_id)
write_as_json(nexson, path)
def get_study(self, study_id, schema=None):
if self._src_code == _GET_EXTERNAL:
url = self.get_external_url(study_id)
nexson = self.json_http_get(url)
r = {'data': nexson}
elif self._src_code == _GET_LOCAL:
nexson, sha = self.phylesystem_obj.return_study(study_id) # pylint: disable=W0632
r = {'data': nexson,
'sha': sha}
else:
assert self._src_code == _GET_API
if self._trans_code == _TRANS_SERVER:
if schema is None:
schema = create_content_spec(nexson_version=self.repo_nexml2json)
r = self._remote_get_study(study_id, schema)
if (isinstance(r, dict) and 'data' in r) and (self._trans_code == _TRANS_CLIENT) and (schema is not None):
r['data'] = schema.convert(r['data'])
return r
def get_study(self, study_id, schema=None):
if self._src_code == _GET_EXTERNAL:
url = self.get_external_url(study_id)
nexson = self.json_http_get(url)
r = {'data': nexson}
elif self._src_code == _GET_LOCAL:
nexson, sha = self.phylesystem_obj.return_study(study_id) #pylint: disable=W0632
r = {'data': nexson,
'sha': sha}
else:
assert self._src_code == _GET_API
if self._trans_code == _TRANS_SERVER:
if schema is None:
schema = create_content_spec(nexson_version=self.repo_nexml2json)
r = self._remote_get_study(study_id, schema)
if (isinstance(r, dict) and 'data' in r) and (self._trans_code == _TRANS_CLIENT) and (schema is not None):
r['data'] = schema.convert(r['data'])
return r
#!/usr/bin/env python
from peyotl.utility.str_util import UNICODE, is_str_type
from peyotl.api.wrapper import _WSWrapper, APIWrapper
from peyotl.nexson_syntax import create_content_spec
from peyotl.utility import doi2url, get_config_object, get_logger
import anyjson
_LOG = get_logger(__name__)
_OTI_NEXSON_SCHEMA = create_content_spec(format='nexson', nexson_version='0.0.0')
class _OTIWrapper(_WSWrapper):
'''Wrapper around OTI which is a text-searching index that wraps the findAllStudies
stored in the phylesystem. You can search for studies, trees, or nodes.
The primary attributes of interest are:
node_search_term_set,
study_search_term_set, and
tree_search_term_set
The primary methods of interest are:
find_all_studies,
find_nodes,
find_studies, and
find_trees
The find_nodes, find_trees, and find_studies queries will do one of the following:
* raise an HTTPError (from requests),
* raise a RuntimeError (if the server returns an error statement), or
* return the matched_studies list for the query
search terms can be sent in as keys+values in a dict or using a keyword arguments
The key in the keyword arg will have "ot:" prepended to it, if it is not
an already valid search term.
#!/usr/bin/env python
from peyotl.utility.str_util import UNICODE, is_str_type, underscored2camel_case
from peyotl.api.wrapper import _WSWrapper, APIWrapper
from peyotl.api.study_ref import TreeRefList
from peyotl.nexson_syntax import create_content_spec
from peyotl.utility import doi2url, get_config_object, get_logger
import anyjson
_LOG = get_logger(__name__)
_OTI_NEXSON_SCHEMA = create_content_spec(format='nexson',
nexson_version='0.0.0')
class _OTIWrapper(_WSWrapper):
'''Wrapper around OTI which is a text-searching index that wraps the findAllStudies
stored in the phylesystem. You can search for studies, trees, or nodes.
The primary attributes of interest are:
node_search_term_set,
study_search_term_set, and
tree_search_term_set
The primary methods of interest are:
find_all_studies,
find_nodes,
find_studies, and
find_trees
The find_nodes, find_trees, and find_studies queries will do one of the following:
* raise an HTTPError (from requests),
* raise a RuntimeError (if the server returns an error statement), or
* return the matched_studies list for the query
search terms can be sent in as keys+values in a dict or using a keyword arguments
def _main():
import sys, codecs, json
import argparse
_HELP_MESSAGE = '''NexSON (or NeXML) to newick converter'''
_EPILOG = '''UTF-8 encoding is used (for input and output).
Environmental variables used:
NEXSON_LOGGING_LEVEL logging setting: NotSet, Debug, Warn, Info, Error
NEXSON_LOGGING_FORMAT format string for logging messages.
'''
tip_label_list = PhyloSchema._otu_label_list
for tl in tip_label_list:
assert(tl.startswith('ot:'))
tip_labels_choices = [i[3:] for i in tip_label_list]
parser = argparse.ArgumentParser(description=_HELP_MESSAGE,
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=_EPILOG)
parser.add_argument("input", help="filepath to input")
parser.add_argument("-i", "--id",
metavar="TREE-ID",
required=False,
help="The ID tree to emit")
parser.add_argument("-o", "--output",
metavar="FILE",
required=False,
help="output filepath. Standard output is used if omitted.")
parser.add_argument("-l", "--list",
action="store_true",
default=False,
help="Just list the tree IDs in the nexSON.")
parser.add_argument("-x", "--xml",
action="store_true",
default=False,
help="Parse input as NeXML rather than NexSON.")
tl_help = 'The field to use to label tips. Should be one of: "{}"'
tl_help = tl_help.format('", "'.join(tip_labels_choices))
parser.add_argument("-t", "--tip-label",
metavar="STRING",
required=False,
default='originallabel',
help=tl_help)
args = parser.parse_args()
otu_label = args.tip_label.lower()
if not otu_label.startswith('ot:'):
otu_label = 'ot:' + otu_label
if otu_label not in tip_label_list:
sys.exit('Illegal tip label choice "{}"\n'.format(args.tip_label))
inpfn = args.input
outfn = args.output
try:
inp = codecs.open(inpfn, mode='rU', encoding='utf-8')
except:
sys.exit('nexson_newick: Could not open file "{fn}"\n'.format(fn=inpfn))
if outfn is not None:
try:
out = codecs.open(outfn, mode='w', encoding='utf-8')
except:
sys.exit('nexson_newick: Could not open output filepath "{fn}"\n'.format(fn=outfn))
else:
out = codecs.getwriter('utf-8')(sys.stdout)
if args.xml:
src_schema = PhyloSchema('nexml')
blob = get_ot_study_info_from_nexml(inp)
else:
src_schema = None
blob = json.load(inp)
if args.list:
schema = PhyloSchema(content='treelist', output_nexml2json='1.2.1')
tl = schema.convert(src=blob, src_schema=src_schema)
out.write('{t}\n'.format(t='\n'.join(tl)))
else:
schema = create_content_spec(content='tree', content_id=args.id, format='newick', otu_label=otu_label)
try:
schema.convert(src=blob, serialize=True, output_dest=out, src_schema=src_schema)
except KeyError:
if 'nexml' not in blob and 'nex:nexml' not in blob:
blob = blob['data']
schema.convert(src=blob, serialize=True, output_dest=out, src_schema=src_schema)
else:
raise