Upgrade syntax to Python 3.7

config/plugins/webhooks/demo/tour_generator/__init__.py

@@ -163,7 +163,7 @@ def _generate_tour(self):
                 if name in test_inputs:
                     hid = self._hids[name]
                     dataset = self._test.inputs[name][0]
-                    step["content"] = "Select dataset: <b>{}: {}</b>".format(hid, dataset)
+                    step["content"] = f"Select dataset: <b>{hid}: {dataset}</b>"
                 else:
                     step["content"] = "Select a dataset"
 
@@ -192,7 +192,7 @@ def _generate_tour(self):
                             if case_id in self._data_inputs.keys():
                                 hid = self._hids[case_id]
                                 dataset = self._test.inputs[tour_id][0]
-                                step_msg = "Select dataset: <b>%s: %s</b>" % (hid, dataset)
+                                step_msg = f"Select dataset: <b>{hid}: {dataset}</b>"
                             else:
                                 case_params = ", ".join(self._test.inputs[tour_id])
                                 step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params

lib/galaxy/containers/docker_swarm.py

@@ -374,7 +374,7 @@ def node_ps(self, node_id):
     def node_update(self, node_id, **kwopts):
         return self._run_docker(
             subcommand="node update",
-            args="{kwopts} {node_id}".format(kwopts=self._stringify_kwopts(kwopts), node_id=node_id),
+            args=f"{self._stringify_kwopts(kwopts)} {node_id}",
         )
 
     @docker_json

lib/galaxy/datatypes/blast.py

@@ -102,7 +102,7 @@ def merge(split_files, output_file):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("Given no BLAST XML files, %r, to merge into %s" % (split_files, output_file))
+            raise ValueError(f"Given no BLAST XML files, {split_files!r}, to merge into {output_file}")
         with open(output_file, "w") as out:
             h = None
             old_header = None

lib/galaxy/datatypes/goldenpath.py

@@ -151,7 +151,7 @@ def _read_file(self):
 
         line_number = 0
         in_body = False
-        with open(self.fname, "r") as f:
+        with open(self.fname) as f:
             for line in f:
                 line_number += 1
                 line = line.rstrip("\n")
@@ -217,14 +217,12 @@ def num_lines(self):
 
     def iterate_objs(self):
         """Iterate over the objects of the AGP file."""
-        for obj in self._objects:
-            yield obj
+        yield from self._objects
 
     def iterate_lines(self):
         """Iterate over the non-comment lines of AGP file."""
         for obj in self.iterate_objs():
-            for j in obj.iterate_lines():
-                yield j
+            yield from obj.iterate_lines()
 
 
 class AGPObject:
@@ -302,11 +300,10 @@ def add_line(self, agp_line):
         self._agp_lines.append(agp_line)
 
     def iterate_lines(self):
-        for i in self._agp_lines:
-            yield i
+        yield from self._agp_lines
 
 
-class AGPLine(object, metaclass=abc.ABCMeta):
+class AGPLine(metaclass=abc.ABCMeta):
     """
     An abstract base class representing a single AGP file line. Inheriting subclasses should
     override or implement new methods to check the validity of a single AFP line. Validity
@@ -388,7 +385,7 @@ def __init__(
         self.orientation = orientation
 
         # Set the object attributes and perform superclass-defined validations
-        super(AGPSeqLine, self).__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
+        super().__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
 
         self.is_gap = False
         self.seqdict = dict(
@@ -509,7 +506,7 @@ def __init__(
         self.linkage_evidence = linkage_evidence
 
         # Set the object attributes and perform superclass-defined validations
-        super(AGPGapLine, self).__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
+        super().__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
 
         self.is_gap = True
         self.gapdict = dict(

lib/galaxy/datatypes/interval.py

@@ -315,9 +315,7 @@ def ucsc_links(self, dataset, type, app, base_url):
                 "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
                 % (base_url, app.url_for(controller="root"), dataset.id, type)
             )
-            redirect_url = quote_plus(
-                "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop)
-            )
+            redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
             link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
             ret_val.append((site_name, link))
         return ret_val
@@ -884,7 +882,7 @@ def get_estimated_display_viewport(self, dataset):
                                     stop = int(elems[1].split("..")[1])
                                     break  # use location declared in file
                                 else:
-                                    log.debug(f"line ({str(line)}) uses an unsupported ##sequence-region definition.")
+                                    log.debug(f"line ({line}) uses an unsupported ##sequence-region definition.")
                                     # break #no break, if bad definition, we try another line
                             elif line.startswith("browser position"):
                                 # Allow UCSC style browser and track info in the GFF file
@@ -933,7 +931,7 @@ def ucsc_links(self, dataset, type, app, base_url):
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
                     redirect_url = quote_plus(
-                        "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, seqid, start, stop)
+                        f"{site_url}db={dataset.dbkey}&position={seqid}:{start}-{stop}&hgt.customText=%s"
                     )
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))

lib/galaxy/datatypes/molecules.py

@@ -360,7 +360,7 @@ def merge(split_files, output_file):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("No fps files given, %r, to merge into %s" % (split_files, output_file))
+            raise ValueError(f"No fps files given, {split_files!r}, to merge into {output_file}")
         with open(output_file, "w") as out:
             first = True
             for filename in split_files:
@@ -682,7 +682,7 @@ def set_peek(self, dataset):
             hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
             chain_ids = ",".join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else "None"
             dataset.peek = get_file_peek(dataset.file_name)
-            dataset.blurb = f"{atom_numbers} atoms and {hetatm_numbers} HET-atoms\nchain_ids: {str(chain_ids)}"
+            dataset.blurb = f"{atom_numbers} atoms and {hetatm_numbers} HET-atoms\nchain_ids: {chain_ids}"
         else:
             dataset.peek = "file does not exist"
             dataset.blurb = "file purged from disk"
@@ -940,7 +940,7 @@ def merge(split_files, output_file):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("Given no CML files, %r, to merge into %s" % (split_files, output_file))
+            raise ValueError(f"Given no CML files, {split_files!r}, to merge into {output_file}")
         with open(output_file, "w") as out:
             for filename in split_files:
                 with open(filename) as handle:

lib/galaxy/datatypes/neo4j.py

@@ -34,7 +34,7 @@ def generate_primary_file(self, dataset=None):
             opt_text = ""
             if composite_file.optional:
                 opt_text = " (optional)"
-            rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
+            rval.append(f'<li><a href="{composite_name}">{composite_name}</a>{opt_text}')
         rval.append("</ul></html>")
         return "\n".join(rval)
 

lib/galaxy/datatypes/spaln.py

@@ -64,7 +64,7 @@ def generate_primary_file(self, dataset=None):
                     % (fn, fn, composite_file.get("description"), opt_text)
                 )
             else:
-                rval.append('<li><a href="%s" type="application/binary">%s</a>%s</li>' % (fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="application/binary">{fn}</a>{opt_text}</li>')
         rval.append("</ul></div></html>")
         return "\n".join(rval)
 
@@ -141,7 +141,7 @@ def display_data(self, trans, data, preview=False, filename=None, to_ext=None, s
             msg = title
         # Galaxy assumes HTML for the display of composite datatypes,
         return (
-            smart_str("<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg)),
+            smart_str(f"<html><head><title>{title}</title></head><body><pre>{msg}</pre></body></html>"),
             headers,
         )
 

lib/galaxy/datatypes/util/gff_util.py

@@ -121,7 +121,7 @@ def __init__(
         for interval in self.intervals:
             # Error checking. NOTE: intervals need not share the same strand.
             if interval.chrom != self.chrom:
-                raise ValueError("interval chrom does not match self chrom: %s != %s" % (interval.chrom, self.chrom))
+                raise ValueError(f"interval chrom does not match self chrom: {interval.chrom} != {self.chrom}")
             # Set start, end of interval.
             if interval.start < self.start:
                 self.start = interval.start

lib/galaxy/managers/base.py

@@ -173,12 +173,10 @@ def get_object(trans, id, class_name, check_ownership=False, check_accessible=Fa
         security_check(trans, item, check_ownership, check_accessible)
     if deleted is True and not item.deleted:
         raise exceptions.ItemDeletionException(
-            '%s "%s" is not deleted' % (class_name, getattr(item, "name", id)), type="warning"
+            f'{class_name} "{getattr(item, "name", id)}" is not deleted', type="warning"
         )
     elif deleted is False and item.deleted:
-        raise exceptions.ItemDeletionException(
-            '%s "%s" is deleted' % (class_name, getattr(item, "name", id)), type="warning"
-        )
+        raise exceptions.ItemDeletionException(f'{class_name} "{getattr(item, "name", id)}" is deleted', type="warning")
     return item
 
 
@@ -799,7 +797,7 @@ def matches_type(key: str, val: Any, types: Union[type, Tuple[Union[type, Tuple[
         :raises exceptions.RequestParameterInvalidException: if not an instance.
         """
         if not isinstance(val, types):
-            msg = f"must be a type: {str(types)}"
+            msg = f"must be a type: {types}"
             raise exceptions.RequestParameterInvalidException(msg, key=key, val=val)
         return val
 
@@ -1258,7 +1256,7 @@ def parse_bool(bool_string: Union[str, bool]) -> bool:
         return True
     if bool_string in ("False", False):
         return False
-    raise ValueError(f"invalid boolean: {str(bool_string)}")
+    raise ValueError(f"invalid boolean: {bool_string}")
 
 
 def raise_filter_err(attr, op, val, msg):

lib/galaxy/objectstore/cloud.py

@@ -614,7 +614,7 @@ def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}")
 
     def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
@@ -711,7 +711,7 @@ def _get_filename(self, obj, **kwargs):
         # even if it does not exist.
         # if dir_only:
         #     return cache_path
-        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}")
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -736,9 +736,7 @@ def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
             # Update the file on cloud
             self._push_to_os(rel_path, source_file)
         else:
-            raise ObjectNotFound(
-                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
-            )
+            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, kwargs: {kwargs}")
 
     def _get_object_url(self, obj, **kwargs):
         if self._exists(obj, **kwargs):

lib/galaxy/objectstore/irods.py

@@ -314,8 +314,8 @@ def _get_size_in_irods(self, rel_path):
         data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
-        collection_path = f"{self.home}/{str(subcollection_name)}"
-        data_object_path = f"{collection_path}/{str(data_object_name)}"
+        collection_path = f"{self.home}/{subcollection_name}"
+        data_object_path = f"{collection_path}/{data_object_name}"
         options = {kw.DEST_RESC_NAME_KW: self.resource}
 
         try:
@@ -334,8 +334,8 @@ def _data_object_exists(self, rel_path):
         data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
-        collection_path = f"{self.home}/{str(subcollection_name)}"
-        data_object_path = f"{collection_path}/{str(data_object_name)}"
+        collection_path = f"{self.home}/{subcollection_name}"
+        data_object_path = f"{collection_path}/{data_object_name}"
         options = {kw.DEST_RESC_NAME_KW: self.resource}
 
         try:
@@ -372,8 +372,8 @@ def _download(self, rel_path):
         data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
-        collection_path = f"{self.home}/{str(subcollection_name)}"
-        data_object_path = f"{collection_path}/{str(data_object_name)}"
+        collection_path = f"{self.home}/{subcollection_name}"
+        data_object_path = f"{collection_path}/{data_object_name}"
         options = {kw.DEST_RESC_NAME_KW: self.resource}
 
         try:
@@ -411,8 +411,8 @@ def _push_to_irods(self, rel_path, source_file=None, from_string=None):
             return False
 
         # Check if the data object exists in iRODS
-        collection_path = f"{self.home}/{str(subcollection_name)}"
-        data_object_path = f"{collection_path}/{str(data_object_name)}"
+        collection_path = f"{self.home}/{subcollection_name}"
+        data_object_path = f"{collection_path}/{data_object_name}"
         exists = False
 
         try:
@@ -542,7 +542,7 @@ def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}")
 
     def _size(self, obj, **kwargs):
         ipt_timer = ExecutionTimer()
@@ -584,7 +584,7 @@ def _delete(self, obj, entire_dir=False, **kwargs):
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path), ignore_errors=True)
 
-                col_path = f"{self.home}/{str(rel_path)}"
+                col_path = f"{self.home}/{rel_path}"
                 col = None
                 try:
                     col = self.session.collections.get(col_path)
@@ -612,8 +612,8 @@ def _delete(self, obj, entire_dir=False, **kwargs):
                 data_object_name = p.stem + p.suffix
                 subcollection_name = p.parent
 
-                collection_path = f"{self.home}/{str(subcollection_name)}"
-                data_object_path = f"{collection_path}/{str(data_object_name)}"
+                collection_path = f"{self.home}/{subcollection_name}"
+                data_object_path = f"{collection_path}/{data_object_name}"
 
                 try:
                     data_obj = self.session.data_objects.get(data_object_path, **options)
@@ -682,7 +682,7 @@ def _get_filename(self, obj, **kwargs):
         # if dir_only:
         #     return cache_path
         log.debug("irods_pt _get_filename: %s", ipt_timer)
-        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}")
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -709,9 +709,7 @@ def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
             self._push_to_irods(rel_path, source_file)
         else:
             log.debug("irods_pt _update_from_file: %s", ipt_timer)
-            raise ObjectNotFound(
-                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
-            )
+            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, kwargs: {kwargs}")
         log.debug("irods_pt _update_from_file: %s", ipt_timer)
 
     # Unlike S3, url is not really applicable to iRODS
@@ -723,8 +721,8 @@ def _get_object_url(self, obj, **kwargs):
             data_object_name = p.stem + p.suffix
             subcollection_name = p.parent
 
-            collection_path = f"{self.home}/{str(subcollection_name)}"
-            data_object_path = f"{collection_path}/{str(data_object_name)}"
+            collection_path = f"{self.home}/{subcollection_name}"
+            data_object_path = f"{collection_path}/{data_object_name}"
 
             return data_object_path
 

lib/galaxy/objectstore/s3.py

@@ -626,7 +626,7 @@ def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}")
 
     def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
@@ -723,7 +723,7 @@ def _get_filename(self, obj, **kwargs):
         # even if it does not exist.
         # if dir_only:
         #     return cache_path
-        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}")
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -748,9 +748,7 @@ def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
             # Update the file on S3
             self._push_to_os(rel_path, source_file)
         else:
-            raise ObjectNotFound(
-                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
-            )
+            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, kwargs: {kwargs}")
 
     def _get_object_url(self, obj, **kwargs):
         if self._exists(obj, **kwargs):

lib/galaxy/queue_worker.py

@@ -298,9 +298,7 @@ def admin_job_lock(app, **kwargs):
     # job_queue is exposed in the root app, but this will be 'fixed' at some
     # point, so we're using the reference from the handler.
     app.job_manager.job_lock = job_lock
-    log.info(
-        "Administrative Job Lock is now set to %s. Jobs will %s dispatch." % (job_lock, "not" if job_lock else "now")
-    )
+    log.info(f"Administrative Job Lock is now set to {job_lock}. Jobs will {'not' if job_lock else 'now'} dispatch.")
 
 
 control_message_to_task = {