def testCreated(self):
b = get_empty_nexson()
aa = validate_nexson(b)
annot = aa[0]
self.assertFalse(annot.has_error())
b = get_empty_nexson(include_cc0=True)
aa = validate_nexson(b)
annot = aa[0]
self.assertFalse(annot.has_error())
def testCreated(self):
b = get_empty_nexson()
aa = validate_nexson(b)
annot = aa[0]
self.assertFalse(annot.has_error())
b = get_empty_nexson(include_cc0=True)
aa = validate_nexson(b)
annot = aa[0]
self.assertFalse(annot.has_error())
def _new_nexson_with_crossref_metadata(doi, ref_string, include_cc0=False):
if doi:
# use the supplied DOI to fetch study metadata
search_term = doi
elif ref_string:
# use the supplied reference text to fetch study metadata
search_term = ref_string
# look for matching studies via CrossRef.org API
doi_lookup_response = fetch(
'http://search.crossref.org/dois?%s' %
urlencode({'q': search_term})
)
doi_lookup_response = unicode(doi_lookup_response, 'utf-8') # make sure it's Unicode!
matching_records = anyjson.loads(doi_lookup_response)
# if we got a match, grab the first (probably only) record
if len(matching_records) > 0:
match = matching_records[0];
# Convert HTML reference string to plain text
raw_publication_reference = match.get('fullCitation', '')
ref_element_tree = web2pyHTMLParser(raw_publication_reference).tree
# root of this tree is the complete mini-DOM
ref_root = ref_element_tree.elements()[0]
# reduce this root to plain text (strip any tags)
meta_publication_reference = ref_root.flatten().decode('utf-8')
meta_publication_url = match.get('doi', u'') # already in URL form
meta_year = match.get('year', u'')
else:
# Add a bogus reference string to signal the lack of results
if doi:
meta_publication_reference = u'No matching publication found for this DOI!'
else:
meta_publication_reference = u'No matching publication found for this reference string'
meta_publication_url = u''
meta_year = u''
# add any found values to a fresh NexSON template
nexson = get_empty_nexson(BY_ID_HONEY_BADGERFISH, include_cc0=include_cc0)
nexml_el = nexson['nexml']
nexml_el[u'^ot:studyPublicationReference'] = meta_publication_reference
if meta_publication_url:
nexml_el[u'^ot:studyPublication'] = {'@href': meta_publication_url}
if meta_year:
nexml_el[u'^ot:studyYear'] = meta_year
return nexson
def _main():
import argparse
_HELP_MESSAGE = '''Takes a filepath to Newick tree file with propinquity-style
leaf labels - unique numeric suffixes which identify the taxon.
Writes a NexSON representation of the tree to
'''
parser = argparse.ArgumentParser(description=_HELP_MESSAGE,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("-i", "--ids",
required=True,
help="comma separated list of tree IDs to be assigned to the trees in the newick file.")
parser.add_argument('newick', help='filepath of the newick tree')
args = parser.parse_args()
if not os.path.exists(args.newick):
sys.exit('The file "{}" does not exist'.format(args.newick))
tree_id_list = args.ids.split(',')
if not tree_id_list:
sys.exit('At least one tree ID must be provided')
tree_id_it = iter(tree_id_list)
out = codecs.getwriter('utf-8')(sys.stdout)
pyid2int = {}
curr_nd_counter = 1
with codecs.open(args.newick, 'r', encoding='utf8') as inp:
tree = parse_newick(stream=inp)
tree_id = tree_id_it.next()
nexson = get_empty_nexson()
body = nexson['nexml']
all_otus_groups = body['otusById'].values()
assert len(all_otus_groups) == 1
first_otus_group = all_otus_groups[0]
all_trees_groups = body['treesById'].values()
assert len(all_trees_groups) == 1
first_trees_group = all_trees_groups[0]
first_trees_group['^ot:treeElementOrder'].append(tree_id)
otus = first_otus_group['otuById']
all_trees_dict = first_trees_group['treeById']
ntree = all_trees_dict.setdefault(tree_id, {})
ebsi, nbi = {}, {}
ntree['edgeBySourceId'] = ebsi
ntree['nodeById'] = nbi
root_node_id = None
for node in tree._root.preorder_iter():
nid = id(node)
i = pyid2int.get(nid)
if i is None:
i = curr_nd_counter
curr_nd_counter += 1
pyid2int[nid] = i
node_id_s = 'node{}'.format(i)
otu_id_s = 'otu{}'.format(i)
n_obj = nbi.setdefault(node_id_s, {})
if node is tree._root:
n_obj['@root'] = True
root_node_id = node_id_s
else:
edge_id_s = 'edge{}'.format(i)
pid = id(node.parent)
pni = 'node{}'.format(pyid2int[pid])
ed = ebsi.setdefault(pni, {})
ed[edge_id_s] = {'@source': pni, '@target': node_id_s}
if not node.children:
n_obj['@otu'] = otu_id_s
orig = node._id
ott_id = ott_id_from_label(orig)
otus[otu_id_s] = {"^ot:originalLabel": orig, "^ot:ottId": ott_id, "^ot:ottTaxonName": orig}
assert root_node_id is not None
ntree['^ot:rootNodeId'] = root_node_id
write_as_json(nexson, out)
new_study_nexson = import_nexson_from_treebase(treebase_id, nexson_syntax_version=BY_ID_HONEY_BADGERFISH)
# elif importing_from_nexml_fetch:
# if not (nexml_fetch_url.startswith('http://') or nexml_fetch_url.startswith('https://')):
# raise HTTP(400, json.dumps({
# "error": 1,
# "description": 'Expecting: "nexml_fetch_url" to startwith http:// or https://',
# }))
# new_study_nexson = get_ot_study_info_from_treebase_nexml(src=nexml_fetch_url,
# nexson_syntax_version=BY_ID_HONEY_BADGERFISH)
# elif importing_from_nexml_string:
# new_study_nexson = get_ot_study_info_from_treebase_nexml(nexml_content=nexml_pasted_string,
# nexson_syntax_version=BY_ID_HONEY_BADGERFISH)
elif importing_from_crossref_API:
new_study_nexson = _new_nexson_with_crossref_metadata(doi=publication_doi_for_crossref, ref_string=publication_ref, include_cc0=cc0_agreement)
else: # assumes 'import-method-MANUAL_ENTRY', or insufficient args above
new_study_nexson = get_empty_nexson(BY_ID_HONEY_BADGERFISH, include_cc0=cc0_agreement)
if publication_doi:
# submitter entered an invalid DOI (or other URL); add it now
new_study_nexson['nexml'][u'^ot:studyPublication'] = {'@href': publication_doi}
nexml = new_study_nexson['nexml']
# If submitter requested the CC0 waiver or other waiver/license, make sure it's here
if importing_from_treebase_id or cc0_agreement:
nexml['^xhtml:license'] = {'@href': 'http://creativecommons.org/publicdomain/zero/1.0/'}
elif using_existing_license:
existing_license = kwargs.get('alternate_license', '')
if existing_license == 'CC-0':
nexml['^xhtml:license'] = {'@name': 'CC0', '@href': 'http://creativecommons.org/publicdomain/zero/1.0/'}
pass
elif existing_license == 'CC-BY-2.0':
