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Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
util
/
rdfhelp.py
diff --git
a/htsworkflow/util/rdfhelp.py
b/htsworkflow/util/rdfhelp.py
index cbe2a9188b091d0cb5f22fa99069345728204ee9..76cde06e97d10593e9eef6d166df59e0329270d6 100644
(file)
--- a/
htsworkflow/util/rdfhelp.py
+++ b/
htsworkflow/util/rdfhelp.py
@@
-3,8
+3,8
@@
import collections
from datetime import datetime
from glob import glob
import collections
from datetime import datetime
from glob import glob
-from urlparse import urlparse, urlunparse
-from urllib
2
import urlopen
+from url
lib.
parse import urlparse, urlunparse
+from urllib
.request
import urlopen
import logging
import os
import sys
import logging
import os
import sys
@@
-42,9
+42,9
@@
def display_query_results(results):
"""A very simple display of sparql query results showing name value pairs
"""
for row in results:
"""A very simple display of sparql query results showing name value pairs
"""
for row in results:
- for k, v in
row.items(
)[::-1]:
- print
"{0}: {1}".format(k, v
)
- print
+ for k, v in
list(row.items()
)[::-1]:
+ print
("{0}: {1}".format(k, v)
)
+ print
()
def html_query_results(result_stream):
from django.conf import settings
def html_query_results(result_stream):
from django.conf import settings
@@
-65,11
+65,11
@@
def html_query_results(result_stream):
for row in result_stream:
new_row = collections.OrderedDict()
row_urls = []
for row in result_stream:
new_row = collections.OrderedDict()
row_urls = []
- for k,v in
row.items(
):
+ for k,v in
list(row.items()
):
new_row[k] = Simplified(v)
results.append(new_row)
context = Context({'results': results,})
new_row[k] = Simplified(v)
results.append(new_row)
context = Context({'results': results,})
- print
template.render(context
)
+ print
(template.render(context)
)
def blankOrUri(value=None):
"""Return a blank node for None or a resource node for strings.
def blankOrUri(value=None):
"""Return a blank node for None or a resource node for strings.
@@
-77,7
+77,7
@@
def blankOrUri(value=None):
node = None
if value is None:
node = RDF.Node()
node = None
if value is None:
node = RDF.Node()
- elif type(value) in
types.StringTypes
:
+ elif type(value) in
str
:
node = RDF.Node(uri_string=value)
elif isinstance(value, RDF.Node):
node = value
node = RDF.Node(uri_string=value)
elif isinstance(value, RDF.Node):
node = value
@@
-88,18
+88,18
@@
def blankOrUri(value=None):
def toTypedNode(value, language="en"):
"""Convert a python variable to a RDF Node with its closest xsd type
"""
def toTypedNode(value, language="en"):
"""Convert a python variable to a RDF Node with its closest xsd type
"""
- if type(value) ==
types.BooleanType
:
+ if type(value) ==
bool
:
value_type = xsdNS['boolean'].uri
if value:
value_type = xsdNS['boolean'].uri
if value:
- value =
u
'1'
+ value = '1'
else:
else:
- value =
u
'0'
- elif type(value) in (
types.IntType, types.LongType
):
+ value = '0'
+ elif type(value) in (
int, int
):
value_type = xsdNS['decimal'].uri
value_type = xsdNS['decimal'].uri
- value =
unicode
(value)
- elif type(value) ==
types.FloatType
:
+ value =
str
(value)
+ elif type(value) ==
float
:
value_type = xsdNS['float'].uri
value_type = xsdNS['float'].uri
- value =
unicode
(value)
+ value =
str
(value)
elif isinstance(value, datetime):
value_type = xsdNS['dateTime'].uri
if value.microsecond == 0:
elif isinstance(value, datetime):
value_type = xsdNS['dateTime'].uri
if value.microsecond == 0:
@@
-108,12
+108,12
@@
def toTypedNode(value, language="en"):
value = value.strftime(ISOFORMAT_MS)
else:
value_type = None
value = value.strftime(ISOFORMAT_MS)
else:
value_type = None
- value =
unicode
(value)
+ value =
str
(value)
if value_type is not None:
node = RDF.Node(literal=value, datatype=value_type)
else:
if value_type is not None:
node = RDF.Node(literal=value, datatype=value_type)
else:
- node = RDF.Node(literal=
unicode
(value).encode('utf-8'), language=language)
+ node = RDF.Node(literal=
str
(value).encode('utf-8'), language=language)
return node
return node
@@
-147,7
+147,7
@@
def fromTypedNode(node):
elif value_type in ('dateTime'):
try:
return datetime.strptime(literal, ISOFORMAT_MS)
elif value_type in ('dateTime'):
try:
return datetime.strptime(literal, ISOFORMAT_MS)
- except ValueError
,
_:
+ except ValueError
as
_:
return datetime.strptime(literal, ISOFORMAT_SHORT)
return literal
return datetime.strptime(literal, ISOFORMAT_SHORT)
return literal
@@
-249,7
+249,7
@@
def get_model(model_name=None, directory=None):
def load_into_model(model, parser_name, path, ns=None):
def load_into_model(model, parser_name, path, ns=None):
- if type(ns) in
types.StringTypes
:
+ if type(ns) in
str
:
ns = RDF.Uri(ns)
if isinstance(path, RDF.Node):
ns = RDF.Uri(ns)
if isinstance(path, RDF.Node):
@@
-276,7
+276,7
@@
def load_into_model(model, parser_name, path, ns=None):
retries -= 1
statements = rdf_parser.parse_as_stream(url, ns)
retries = 0
retries -= 1
statements = rdf_parser.parse_as_stream(url, ns)
retries = 0
- except RDF.RedlandError
,
e:
+ except RDF.RedlandError
as
e:
errmsg = "RDF.RedlandError: {0} {1} tries remaining"
logger.error(errmsg.format(str(e), retries))
errmsg = "RDF.RedlandError: {0} {1} tries remaining"
logger.error(errmsg.format(str(e), retries))
@@
-296,7
+296,7
@@
def load_string_into_model(model, parser_name, data, ns=None):
def fixup_namespace(ns):
if ns is None:
ns = RDF.Uri("http://localhost/")
def fixup_namespace(ns):
if ns is None:
ns = RDF.Uri("http://localhost/")
- elif type(ns) in
types.StringTypes
:
+ elif type(ns) in
str
:
ns = RDF.Uri(ns)
elif not(isinstance(ns, RDF.Uri)):
errmsg = "Namespace should be string or uri not {0}"
ns = RDF.Uri(ns)
elif not(isinstance(ns, RDF.Uri)):
errmsg = "Namespace should be string or uri not {0}"
@@
-330,7
+330,7
@@
def add_default_schemas(model, schema_path=None):
add_schema(model, schema, namespace)
if schema_path:
add_schema(model, schema, namespace)
if schema_path:
- if type(schema_path) in
types.StringTypes
:
+ if type(schema_path) in
str
:
schema_path = [schema_path]
for path in schema_path:
schema_path = [schema_path]
for path in schema_path: