Merge pull request #2167 from eerovaher/rm-parse-pedantic

Replace the `pedantic` option for VOTable parsing

Author: bsipocz

astroquery/casda/core.py

@@ -262,7 +262,7 @@ def _parse_datalink_for_service_and_id(self, response, service_name):
         """
         data = BytesIO(response.content)
 
-        votable = parse(data, pedantic=False)
+        votable = parse(data, verify='warn')
         results = next(resource for resource in votable.resources if
                        resource.type == "results")
         if results is None:

astroquery/casda/tests/test_casda.py

@@ -221,7 +221,7 @@ def test_query_region_async_box(patch_get):
 
 
 def test_filter_out_unreleased():
-    all_records = parse(data_path('partial_unreleased.xml'), pedantic=False).get_first_table().to_table()
+    all_records = parse(data_path('partial_unreleased.xml'), verify='warn').get_first_table().to_table()
     assert all_records[0]['obs_release_date'] == '2017-08-02T03:51:19.728Z'
     assert all_records[1]['obs_release_date'] == '2218-01-02T16:51:00.728Z'
     assert all_records[2]['obs_release_date'] == ''

astroquery/ipac/irsa/core.py

@@ -336,7 +336,7 @@ def _parse_result(self, response, verbose=False):
         # Read it in using the astropy VO table reader
         try:
             first_table = votable.parse(BytesIO(response.content),
-                                        pedantic=False).get_first_table()
+                                        verify='warn').get_first_table()
         except Exception as ex:
             self.response = response
             self.table_parse_error = ex

astroquery/ipac/ned/core.py

@@ -681,7 +681,7 @@ def _parse_result(self, response, verbose=False):
             commons.suppress_vo_warnings()
         try:
             tf = BytesIO(response.content)
-            first_table = votable.parse(tf, pedantic=False).get_first_table()
+            first_table = votable.parse(tf, verify='warn').get_first_table()
             table = first_table.to_table(use_names_over_ids=True)
             return table
         except Exception as ex:

astroquery/nrao/core.py

@@ -437,7 +437,7 @@ def _parse_votable_result(self, response, verbose=False):
         try:
             tf = BytesIO(new_content.encode())
             first_table = votable.parse(
-                tf, pedantic=False,
+                tf, verify='warn',
                 datatype_mapping=datatype_mapping).get_first_table()
             try:
                 table = first_table.to_table(use_names_over_ids=True)

astroquery/simbad/core.py

@@ -189,7 +189,7 @@ def __init__(self, txt, verbose=False, pedantic=False):
     def table(self):
         if self.__table is None:
             self.bytes = BytesIO(self.data.encode('utf8'))
-            tbl = votable.parse_single_table(self.bytes, pedantic=False)
+            tbl = votable.parse_single_table(self.bytes, verify='warn')
             self.__table = tbl.to_table()
             self.__table.convert_bytestring_to_unicode()
         return self.__table

astroquery/utils/commons.py

@@ -457,5 +457,5 @@ def parse_votable(content):
     """
     Parse a votable in string format
     """
-    tables = votable.parse(BytesIO(content), pedantic=False)
+    tables = votable.parse(BytesIO(content), verify='warn')
     return tables

astroquery/vizier/core.py

@@ -761,15 +761,15 @@ def parse_vizier_votable(data, verbose=False, invalid='warn',
     tf = BytesIO(data)
 
     if invalid == 'mask':
-        vo_tree = votable.parse(tf, pedantic=False, invalid='mask')
+        vo_tree = votable.parse(tf, verify='warn', invalid='mask')
     elif invalid == 'warn':
         try:
-            vo_tree = votable.parse(tf, pedantic=False, invalid='exception')
+            vo_tree = votable.parse(tf, verify='warn', invalid='exception')
         except Exception as ex:
             warnings.warn("VOTABLE parsing raised exception: {0}".format(ex))
-            vo_tree = votable.parse(tf, pedantic=False, invalid='mask')
+            vo_tree = votable.parse(tf, verify='warn', invalid='mask')
     elif invalid == 'exception':
-        vo_tree = votable.parse(tf, pedantic=False, invalid='exception')
+        vo_tree = votable.parse(tf, verify='warn', invalid='exception')
     else:
         raise ValueError("Invalid keyword for 'invalid'. "
                          "Must be exception, mask, or warn")

astroquery/vo_conesearch/core.py

@@ -180,8 +180,9 @@ def _parse_result(self, response, url, pars={}, verbose=False):
         parsed_url = url + '&'.join(query)
 
         # Parse the result
+        pedantic = 'exception' if conf.pedantic else 'warn'
         tab = table.parse(BytesIO(response.content), filename=parsed_url,
-                          pedantic=conf.pedantic)
+                          verify=pedantic)
         try:
             result = vo_tab_parse(tab, url, pars)
         except VOSError as exc:

astroquery/vo_conesearch/validator/validate.py

@@ -301,7 +301,7 @@ def _do_validation(args):
         with warnings.catch_warnings(record=True) as warning_lines:
             try:
                 vo_tab_parse(votable.table.parse(
-                    r.get_vo_xml_path(), pedantic=False), r.url, {})
+                    r.get_vo_xml_path(), verify='warn'), r.url, {})
             except (E19, IndexError, VOSError) as e:  # pragma: no cover
                 lines.append(str(e))
                 nexceptions += 1