Merge pull request #9337 from mvdbeek/various_python3_fixes

[20.01] Various python 3 fixes from sentry

client/galaxy/scripts/viz/trackster.js

@@ -154,7 +154,12 @@ export class TracksterUI extends Backbone.Model {
                     icon_class: "globe",
                     title: _l("Circster"),
                     on_click: () => {
-                        window.top.location = `${this.baseURL}visualization/circster?id=${this.view.vis_id}`;
+                        const vis_id = this.view.vis_id;
+                        var circster_q = "id=" + vis_id;
+                        if (vis_id == undefined) {
+                            circster_q = `dataset_id=${this.view.drawables[0].dataset.id}&hda_ldda=${this.view.drawables[0].dataset.attributes.hda_ldda}`;
+                        }
+                        window.top.location = `${this.baseURL}visualization/circster?${circster_q}`;
                     }
                 },
                 {

lib/galaxy/datatypes/dataproviders/dataset.py

@@ -52,7 +52,8 @@ class DatasetDataProvider(base.DataProvider):
         self.dataset = dataset
         # this dataset file is obviously the source
         # TODO: this might be a good place to interface with the object_store...
-        super(DatasetDataProvider, self).__init__(open(dataset.file_name, 'rb'))
+        mode = 'rb' if dataset.datatype.is_binary else 'r'
+        super(DatasetDataProvider, self).__init__(open(dataset.file_name, mode))
 
     # TODO: this is a bit of a mess
     @classmethod

lib/galaxy/datatypes/interval.py

@@ -210,7 +210,7 @@ class Interval(Tabular):
 
     def as_ucsc_display_file(self, dataset, **kwd):
         """Returns file contents with only the bed data"""
-        with tempfile.NamedTemporaryFile(delete=False) as fh:
+        with tempfile.NamedTemporaryFile(delete=False, mode='w') as fh:
             c, s, e, t, n = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol, dataset.metadata.strandCol or 0, dataset.metadata.nameCol or 0
             c, s, e, t, n = int(c) - 1, int(s) - 1, int(e) - 1, int(t) - 1, int(n) - 1
             if t >= 0:  # strand column (should) exists

lib/galaxy/openid/openid_manager.py

@@ -47,12 +47,12 @@ class OpenIDManager(object):
     def get_session(self, trans):
         session_file = os.path.join(self.session_path, str(trans.galaxy_session.id))
         if not os.path.exists(session_file):
-            pickle.dump(dict(), open(session_file, 'w'))
-        return pickle.load(open(session_file))
+            pickle.dump(dict(), open(session_file, 'wb'))
+        return pickle.load(open(session_file, 'rb'))
 
     def persist_session(self, trans, oidconsumer):
         session_file = os.path.join(self.session_path, str(trans.galaxy_session.id))
-        pickle.dump(oidconsumer.session, open(session_file, 'w'))
+        pickle.dump(oidconsumer.session, open(session_file, 'wb'))
 
     def get_consumer(self, trans):
         return consumer.Consumer(self.get_session(trans), self.store)

lib/galaxy/tools/data/__init__.py

@@ -352,7 +352,7 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
                 # Handle URLs as files
                 filename = file_element.get('url', None)
                 if filename:
-                    tmp_file = NamedTemporaryFile(prefix='TTDT_URL_%s-' % self.name)
+                    tmp_file = NamedTemporaryFile(prefix='TTDT_URL_%s-' % self.name, mode='w')
                     try:
                         tmp_file.write(requests.get(filename, timeout=url_timeout).text)
                     except Exception as e:

lib/galaxy/visualization/data_providers/genome.py

@@ -1223,11 +1223,11 @@ class BBIDataProvider(GenomeDataProvider):
 
             # Start with N samples.
             num_points = num_samples
-            step_size = (end - start) / num_points
+            step_size = (end - start) // num_points
             # Add additional points to sample in the remainder not covered by
             # the initial N samples.
             remainder_start = start + step_size * num_points
-            additional_points = (end - remainder_start) / step_size
+            additional_points = (end - remainder_start) // step_size
             num_points += additional_points
 
         result = summarize_region(bbi, chrom, start, end, num_points)
@@ -1243,7 +1243,7 @@ class BBIDataProvider(GenomeDataProvider):
 class BigBedDataProvider(BBIDataProvider):
     def _get_dataset(self):
         # Nothing converts to bigBed so we don't consider converted dataset
-        f = open(self.original_dataset.file_name)
+        f = open(self.original_dataset.file_name, 'rb')
         return f, BigBedFile(file=f)
 
 
@@ -1255,9 +1255,9 @@ class BigWigDataProvider(BBIDataProvider):
 
     def _get_dataset(self):
         if self.converted_dataset is not None:
-            f = open(self.converted_dataset.file_name)
+            f = open(self.converted_dataset.file_name, 'rb')
         else:
-            f = open(self.original_dataset.file_name)
+            f = open(self.original_dataset.file_name, 'rb')
         return f, BigWigFile(file=f)
 
 

lib/galaxy/webapps/base/controller.py

@@ -905,11 +905,12 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
             bookmarks = unpack_bookmarks(config['bookmarks'])
             vis_rev.config = {"view": view_content, "bookmarks": bookmarks}
             # Viewport from payload
-            if 'viewport' in config:
-                chrom = config['viewport']['chrom']
-                start = config['viewport']['start']
-                end = config['viewport']['end']
-                overview = config['viewport']['overview']
+            viewport = config.get('viewport')
+            if viewport:
+                chrom = viewport['chrom']
+                start = viewport['start']
+                end = viewport['end']
+                overview = viewport['overview']
                 vis_rev.config["viewport"] = {'chrom': chrom, 'start': start, 'end': end, 'overview': overview}
         else:
             # Default action is to save the config as is with no validation.
@@ -1028,7 +1029,7 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
                         tracks.append(pack_collection(drawable_dict))
 
             config = {"title": visualization.title,
-                      "vis_id": trans.security.encode_id(visualization.id),
+                      "vis_id": trans.security.encode_id(visualization.id) if visualization.id is not None else None,
                       "tracks": tracks,
                       "bookmarks": bookmarks,
                       "chrom": "",

lib/galaxy/webapps/galaxy/api/library_datasets.py

@@ -7,6 +7,10 @@ import string
 import tempfile
 import zipfile
 from json import dumps
+try:
+    from string import maketrans
+except ImportError:
+    maketrans = str.maketrans
 
 from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
 
@@ -575,7 +579,7 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
         if format in ['zip', 'tgz', 'tbz']:
             # error = False
             killme = string.punctuation + string.whitespace
-            trantab = string.maketrans(killme, '_' * len(killme))
+            trantab = maketrans(killme, '_' * len(killme))
             try:
                 outext = 'zip'
                 if format == 'zip':