Merge pull request #12783 from jmchilton/type_fixes_managers_3

Type fixes for various visualization backend Python files.

lib/galaxy/visualization/data_providers/basic.py

@@ -1,7 +1,9 @@
 import sys
 from json import loads
+from typing import Iterator
 
 from galaxy.datatypes.tabular import Tabular
+from galaxy.model import DatasetInstance
 
 
 class BaseDataProvider:
@@ -12,6 +14,7 @@ class BaseDataProvider:
     - write subsets of data to new datasets
 
     """
+    original_dataset: DatasetInstance
 
     def __init__(self, converted_dataset=None, original_dataset=None, dependencies=None,
                  error_max_vals="Only the first %i values are returned."):
@@ -28,7 +31,7 @@ class BaseDataProvider:
         """
         raise Exception("Unimplemented Function")
 
-    def get_iterator(self, **kwargs):
+    def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
         """
         Returns an iterator that provides data in the region chrom:start-end
         """

lib/galaxy/visualization/data_providers/genome.py

@@ -10,7 +10,7 @@ import re
 import sys
 from contextlib import contextmanager
 from json import loads
-from typing import Dict, Union
+from typing import Any, Dict, IO, Iterator, List, Optional, Tuple, Union
 
 import pysam
 from bx.bbi.bigbed_file import BigBedFile
@@ -19,6 +19,7 @@ from bx.interval_index_file import Indexes
 
 from galaxy.datatypes.interval import Bed, Gff, Gtf
 from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFFeature, GFFInterval, GFFReaderWrapper, parse_gff_attributes
+from galaxy.model import DatasetInstance
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
 
@@ -30,6 +31,8 @@ from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and
 # Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
 pysam.set_verbosity(0)
 
+PAYLOAD_LIST_TYPE = List[Optional[Union[str, int, float, List[Tuple[int, int]]]]]
+
 
 def float_nan(n):
     '''
@@ -89,9 +92,9 @@ class FeatureLocationIndexDataProvider(BaseDataProvider):
 
         # Find query in file using binary search.
         low = 0
-        high = file_len / line_len
+        high = int(file_len / line_len)
         while low < high:
-            mid = (low + high) // 2
+            mid: int = (low + high) // 2
             position = mid * line_len
             textloc_file.seek(position)
 
@@ -171,7 +174,7 @@ class GenomeDataProvider(BaseDataProvider):
         """
         raise Exception("Unimplemented Function")
 
-    def get_iterator(self, data_file, chrom, start, end, **kwargs):
+    def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
         """
         Returns an iterator that provides data in the region chrom:start-end
         """
@@ -272,6 +275,8 @@ class GenomeDataProvider(BaseDataProvider):
 
 
 class FilterableMixin:
+    original_dataset: DatasetInstance
+
     def get_filters(self):
         """ Returns a dataset's filters. """
         # Get filters.
@@ -329,7 +334,7 @@ class TabixDataProvider(GenomeDataProvider, FilterableMixin):
         with pysam.TabixFile(self.dependencies['bgzip'].file_name, index=index_path) as f:
             yield f
 
-    def get_iterator(self, data_file, chrom, start, end, **kwargs):
+    def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
         # chrom must be a string, start/end integers.
         # in previous versions of pysam, unicode was accepted for chrom, but not in 8.4
         chrom = str(chrom)
@@ -338,7 +343,7 @@ class TabixDataProvider(GenomeDataProvider, FilterableMixin):
         if end >= (2 << 29):
             end = (2 << 29 - 1)  # Tabix-enforced maximum
         # Get iterator using either naming scheme.
-        iterator = iter([])
+        iterator: Iterator[str] = iter([])
         if chrom in data_file.contigs:
             iterator = data_file.fetch(reference=chrom, start=start, end=end)
         else:
@@ -406,7 +411,7 @@ class IntervalDataProvider(GenomeDataProvider):
             feature = line.split()
             length = len(feature)
             # Unique id is just a hash of the line
-            payload = [hash(line), int(feature[start_col]), int(feature[end_col])]
+            payload: PAYLOAD_LIST_TYPE = [hash(line), int(feature[start_col]), int(feature[end_col])]
 
             if no_detail:
                 rval.append(payload)
@@ -484,7 +489,7 @@ class BedDataProvider(GenomeDataProvider):
             feature = line.split()
             length = len(feature)
             # Unique id is just a hash of the line
-            payload = [hash(line), int(feature[1]), int(feature[2])]
+            payload: PAYLOAD_LIST_TYPE = [hash(line), int(feature[1]), int(feature[2])]
 
             if no_detail:
                 rval.append(payload)
@@ -549,7 +554,7 @@ class RawBedDataProvider(BedDataProvider):
     for large datasets.
     """
 
-    def get_iterator(self, data_file, chrom=None, start=None, end=None, **kwargs):
+    def get_iterator(self, data_file, chrom, start, end, **kwargs):
         # Read first line in order to match chrom naming format.
         line = data_file.readline()
         dataset_chrom = line.split()[0]
@@ -677,7 +682,7 @@ class VcfDataProvider(GenomeDataProvider):
 
             if samples_data:
                 # Process and pack samples' genotype and count alleles across samples.
-                alleles_seen = {}
+                alleles_seen: Dict[int, bool] = {}
                 has_alleles = False
 
                 for sample in samples_data:
@@ -685,10 +690,10 @@ class VcfDataProvider(GenomeDataProvider):
                     genotype = sample.split(':')[0]
                     has_alleles = False
                     alleles_seen.clear()
-                    for allele in genotype_re.split(genotype):
+                    for allele_str in genotype_re.split(genotype):
                         try:
                             # This may throw a ValueError if allele is missing.
-                            allele = int(allele)
+                            allele = int(allele_str)
 
                             # Only count allele if it hasn't been seen yet.
                             if allele != 0 and allele not in alleles_seen:
@@ -856,7 +861,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
                                  index_filename=self.converted_dataset.file_name) as f:
             yield f
 
-    def get_iterator(self, data_file, chrom, start, end, **kwargs):
+    def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
         """
         Returns an iterator that provides data in the region chrom:start-end
         """
@@ -873,7 +878,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
             try:
                 data = data_file.fetch(start=start, end=end, reference=chrom)
             except ValueError:
-                return None
+                return iter([])
         return data
 
     def process_data(self, iterator, start_val=0, max_vals=None, ref_seq=None,
@@ -966,7 +971,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
         # Encode reads as list of lists.
         #
         results = []
-        paired_pending = {}
+        paired_pending: Dict[str, Dict[str, Any]] = {}
         unmapped = 0
         message = None
         count = 0
@@ -1110,6 +1115,9 @@ class BBIDataProvider(GenomeDataProvider):
 
     dataset_type = 'bigwig'
 
+    def _get_dataset(self) -> Tuple[IO[bytes], Union[BigBedFile, BigWigFile]]:
+        ...
+
     def valid_chroms(self):
         # No way to return this info as of now
         return None
@@ -1146,7 +1154,7 @@ class BBIDataProvider(GenomeDataProvider):
             min_val = 0
             max_val = 0
             mean = 0
-            sd = 0
+            sd = 0.0
             if summary is not None:
                 # Does the summary contain any defined values?
                 valid_count = summary.valid_count[0]
@@ -1288,7 +1296,7 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
         i = Indexes(self.converted_dataset.file_name)
         yield i
 
-    def get_iterator(self, data_file, chrom, start, end, **kwargs):
+    def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
         """
         Returns an iterator for data in data_file in chrom:start-end
         """
@@ -1406,16 +1414,18 @@ class GtfTabixDataProvider(TabixDataProvider):
         # TODO: extend this code or use code in gff_util to process GFF/3 as well
         # and then create a generic GFFDataProvider that can be used with both
         # raw and tabix datasets.
-        features = {}
+        features: Dict[str, List[GFFInterval]] = {}
+
         for line in iterator:
             line_attrs = parse_gff_attributes(line.split('\t')[8])
             transcript_id = line_attrs['transcript_id']
+            feature_list: List[GFFInterval]
             if transcript_id in features:
-                feature = features[transcript_id]
+                feature_list = features[transcript_id]
             else:
-                feature = []
-                features[transcript_id] = feature
-            feature.append(GFFInterval(None, line.split('\t')))
+                feature_list = []
+                features[transcript_id] = feature_list
+            feature_list.append(GFFInterval(None, line.split('\t')))
 
         # Process data.
         filter_cols = loads(kwargs.get("filter_cols", "[]"))
@@ -1480,7 +1490,7 @@ class ENCODEPeakDataProvider(GenomeDataProvider):
             feature = line.split()
 
             # Feature initialization.
-            payload = [
+            payload: PAYLOAD_LIST_TYPE = [
                 # GUID is just a hash of the line
                 hash(line),
                 # Add start, end.
@@ -1597,7 +1607,7 @@ class ChromatinInteractionsDataProvider(GenomeDataProvider):
 
 
 class ChromatinInteractionsTabixDataProvider(TabixDataProvider, ChromatinInteractionsDataProvider):
-    def get_iterator(self, data_file, chrom, start=0, end=sys.maxsize, interchromosomal=False, **kwargs):
+    def get_iterator(self, data_file, chrom, start=0, end=sys.maxsize, interchromosomal=False, **kwargs) -> Iterator[str]:
         """
         """
         # Modify start as needed to get earlier interactions with start region.
@@ -1625,7 +1635,7 @@ class ChromatinInteractionsTabixDataProvider(TabixDataProvider, ChromatinInterac
 #
 
 
-def package_gff_feature(feature, no_detail=False, filter_cols=None):
+def package_gff_feature(feature, no_detail=False, filter_cols=None) -> PAYLOAD_LIST_TYPE:
     """ Package a GFF feature in an array for data providers. """
     filter_cols = filter_cols or []
     feature = convert_gff_coords_to_bed(feature)

lib/galaxy/visualization/data_providers/phyloviz/__init__.py

@@ -1,4 +1,5 @@
 """ Data providers code for PhyloViz """
+from typing import Any, Dict
 
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.phyloviz.newickparser import Newick_Parser
@@ -23,7 +24,7 @@ class PhylovizDataProvider(BaseDataProvider):
         file_name = self.original_dataset.file_name
         parseMsg = None
         jsonDicts = []
-        rval = {'dataset_type': self.dataset_type}
+        rval: Dict[str, Any] = {'dataset_type': self.dataset_type}
 
         if file_ext in ["newick", "nhx"]:  # parses newick files
             newickParser = Newick_Parser()

lib/galaxy/visualization/data_providers/phyloviz/baseparser.py

@@ -1,4 +1,5 @@
 import json
+from typing import Any, Dict
 
 
 class Node:
@@ -14,6 +15,8 @@ class Node:
         self.length, self.bootstrap = kwargs.get("length", 0), kwargs.get("bootstrap", None)
         self.events = kwargs.get("events", "")
 
+        self.parent = None
+
         # clean up boot strap values
         if self.bootstrap == -1:
             self.bootstrap = None
@@ -28,7 +31,7 @@ class Node:
     def __str__(self):
         return f"{self.name} id:{str(self.id)}, depth: {str(self.depth)}"
 
-    def toJson(self):
+    def toJson(self) -> Dict[str, Any]:
         """Converts the data in the node to a dict representation of json"""
         thisJson = {
             "name": self.name,
@@ -79,7 +82,7 @@ class PhyloTree:
         self.id += 1
         return Node(nodeName, **kwargs)
 
-    def addRoot(self, root):
+    def addRoot(self, root: Node):
         """Creates a root for phyloTree"""
         assert isinstance(root, Node)
         root.parent = None
@@ -88,7 +91,7 @@ class PhyloTree:
     def generateJsonableDict(self):
         """Changes itself into a dictonary by recurssively calling the tojson on all its nodes. Think of it
         as a dict in an array of dict in an array of dict and so on..."""
-        jsonTree = ""
+        jsonTree: Dict[str, Any]
         if self.root:
             assert isinstance(self.root, Node)
             jsonTree = self.root.toJson()

lib/galaxy/visualization/data_providers/phyloviz/newickparser.py

@@ -52,17 +52,17 @@ class Newick_Parser(Base_Parser):
             if len(childString) == 0:
                 continue
             nodeInfo = childString.split(":")
-            name, length, bootstrap = "", None, -1
+            name, length, bootstrap = "", None, -1.0
             if len(nodeInfo) == 2:  # has length info
                 length = nodeInfo[1]
                 # checking for bootstap values
                 name = nodeInfo[0]
                 try:    # Nexus may bootstrap in names position
-                    name = float(name)
-                    if 0 <= name <= 1:
-                        bootstrap = name
-                    elif 1 <= name <= 100:
-                        bootstrap = name / 100
+                    name_as_float = float(name)
+                    if 0 <= name_as_float <= 1:
+                        bootstrap = name_as_float
+                    elif 1 <= name_as_float <= 100:
+                        bootstrap = name_as_float / 100
                     name = ""
                 except ValueError:
                     name = nodeInfo[0]

lib/galaxy/visualization/data_providers/registry.py

@@ -1,4 +1,8 @@
-from galaxy.datatypes.data import Newick, Nexus
+from typing import Dict, Optional, Type, Union
+
+from typing_extensions import Literal
+
+from galaxy.datatypes.data import Data, Newick, Nexus
 from galaxy.datatypes.interval import (
     Bed,
     ChromatinInteractions,
@@ -11,10 +15,15 @@ from galaxy.datatypes.tabular import Tabular, Vcf
 from galaxy.datatypes.xml import Phyloxml
 from galaxy.model import NoConverterException
 from galaxy.visualization.data_providers import genome
-from galaxy.visualization.data_providers.basic import ColumnDataProvider
+from galaxy.visualization.data_providers.basic import BaseDataProvider, ColumnDataProvider
 from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
 
 
+# a dict keyed on datatype with a 'default' string key.
+PROVIDER_BY_DATATYPE_CLASS_DICT = Dict[Union[Literal["default"], Type[Data]], Type[BaseDataProvider]]
+DATA_PROVIDER_BY_TYPE_NAME_DICT = Dict[str, Union[Type[BaseDataProvider], PROVIDER_BY_DATATYPE_CLASS_DICT]]
+
+
 class DataProviderRegistry:
     """
     Registry for data providers that enables listing and lookup.
@@ -24,7 +33,7 @@ class DataProviderRegistry:
         # Mapping from dataset type name to a class that can fetch data from a file of that
         # type. First key is converted dataset type; if result is another dict, second key
         # is original dataset type.
-        self.dataset_type_name_to_data_provider = {
+        self.dataset_type_name_to_data_provider: DATA_PROVIDER_BY_TYPE_NAME_DICT = {
             "tabix": {
                 Vcf: genome.VcfTabixDataProvider,
                 Bed: genome.BedTabixDataProvider,
@@ -49,7 +58,9 @@ class DataProviderRegistry:
         sources, source parameter is ignored.
         """
 
-        data_provider = None
+        data_provider: Optional[BaseDataProvider]
+        data_provider_class: Type[BaseDataProvider]
+
         if raw:
             # Working with raw data.
             if isinstance(original_dataset.datatype, Gff):
@@ -72,9 +83,12 @@ class DataProviderRegistry:
                 # Provider requested by name; get from mappings.
                 value = self.dataset_type_name_to_data_provider[name]
                 if isinstance(value, dict):
+                    # value is a PROVIDER_BY_DATATYPE_CLASS_DICT
                     # Get converter by dataset extension; if there is no data provider,
                     # get the default.
-                    data_provider_class = value.get(original_dataset.datatype.__class__, value.get("default"))
+                    default_type = value.get("default")
+                    assert default_type
+                    data_provider_class = value.get(original_dataset.datatype.__class__, default_type)
                 else:
                     data_provider_class = value
 

lib/galaxy/visualization/genomes.py

@@ -11,7 +11,7 @@ from galaxy.exceptions import (
     ObjectNotFound,
     ReferenceDataError,
 )
-from galaxy.structured_app import MinimalManagerApp
+from galaxy.structured_app import StructuredApp
 from galaxy.util.bunch import Bunch
 
 log = logging.getLogger(__name__)
@@ -197,7 +197,7 @@ class Genomes:
     Provides information about available genome data and methods for manipulating that data.
     """
 
-    def __init__(self, app: MinimalManagerApp):
+    def __init__(self, app: StructuredApp):
         self.app = app
         # Create list of genomes from app.genome_builds
         self.genomes: Dict[str, Genome] = {}

lib/galaxy/visualization/plugins/config_parser.py

@@ -1,5 +1,5 @@
 import logging
-
+from typing import Any, Dict, List
 
 import galaxy.model
 from galaxy.util import asbool
@@ -108,7 +108,7 @@ class VisualizationsConfigParser:
         # param modifiers provide extra information for other params (e.g. hda_ldda='hda' -> dataset_id is an hda id)
         # store these modifiers in a 2-level dictionary { target_param: { param_modifier_key: { param_mod_data }
         # ugh - wish we didn't need these
-        param_modifiers = {}
+        param_modifiers: Dict[str, Any] = {}
         param_modifier_elements = param_confs.findall('param_modifier') if param_confs is not None else []
         for param_modifier_conf in param_modifier_elements:
             param_modifier = self.param_modifier_parser.parse(param_modifier_conf)
@@ -287,7 +287,7 @@ class DataSourceParser:
         # tests should NOT include expensive operations: reading file data, running jobs, etc.
         # do as much here as possible to reduce the overhead of seeing if a visualization is applicable
         # currently tests are or'd only (could be and'd or made into compound boolean tests)
-        tests = []
+        tests: List[Dict[str, Any]] = []
         if not xml_tree_list:
             return tests
 
@@ -354,7 +354,7 @@ class DataSourceParser:
         the registry to convert the data_source into one or more appropriate
         params for the visualization.
         """
-        to_param_dict = {}
+        to_param_dict: Dict[str, Any] = {}
         if not xml_tree_list:
             return to_param_dict
 
@@ -419,13 +419,15 @@ class DictParser(dict):
             self.update(dict(parent_element.items()))
         for element in parent_element:
             if len(element) > 0:
+                asJson: Any
                 if element.tag == element[0].tag:
-                    aDict = ListParser(element)
+                    asJson = ListParser(element)
                 else:
                     aDict = DictParser(element)
-                if element.items():
-                    aDict.update(dict(element.items()))
-                self.update({element.tag: aDict})
+                    if element.items():
+                        aDict.update(dict(element.items()))
+                    asJson = aDict
+                self.update({element.tag: asJson})
             elif element.items():
                 self.update({element.tag: dict(element.items())})
             else:

lib/galaxy/visualization/plugins/plugin.py

@@ -5,6 +5,7 @@ from a query string and render a webpage based on those data.
 import copy
 import logging
 import os
+from typing import Any, Dict
 
 import mako.lookup
 
@@ -23,6 +24,7 @@ class ServesTemplatesPluginMixin:
     """
     An object that renders (mako) template files from the server.
     """
+    path: str
 
     #: default number of templates to search for plugin template lookup
     DEFAULT_TEMPLATE_COLLECTION_SIZE = 10
@@ -85,9 +87,8 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         Render and return the text of the non-saved plugin webpage/fragment.
         """
         # not saved - no existing config
-        config = {}
         # set up render vars based on plugin.config and kwargs
-        render_vars = self._build_render_vars(config, trans=trans, **kwargs)
+        render_vars = self._build_render_vars({}, trans=trans, **kwargs)
         return self._render(render_vars, trans=trans, embedded=embedded)
 
     def render_saved(self, visualization, trans=None, embedded=None, **kwargs):
@@ -95,7 +96,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         Render and return the text of the plugin webpage/fragment using the
         config/data of a saved visualization.
         """
-        config = self._get_saved_visualization_config(visualization, **kwargs)
+        config: Dict[str, Any] = self._get_saved_visualization_config(visualization, **kwargs)
         # pass the saved visualization config for parsing into render vars
         render_vars = self._build_render_vars(config, trans=trans, **kwargs)
         # update any values that were loaded from the saved Visualization
@@ -134,7 +135,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         else:
             log.debug(f'Visualization has no static path: {path}.')
 
-    def _get_saved_visualization_config(self, visualization, revision=None, **kwargs):
+    def _get_saved_visualization_config(self, visualization, revision=None, **kwargs) -> Dict[str, Any]:
         """
         Return the config of a saved visualization and revision.
 
@@ -144,11 +145,11 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         return copy.copy(visualization.latest_revision.config)
 
     # ---- non-public
-    def _build_render_vars(self, config, trans=None, **kwargs):
+    def _build_render_vars(self, config: Dict[str, Any], trans=None, **kwargs) -> Dict[str, Any]:
         """
         Build all the variables that will be passed into the renderer.
         """
-        render_vars = {}
+        render_vars: Dict[str, Any] = {}
         # Meta variables passed to the template/renderer to describe the visualization being rendered.
         render_vars.update(
             visualization_name=self.name,
@@ -161,14 +162,14 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
             query=kwargs,
         )
         # config based on existing or kwargs
-        config = self._build_config(config, trans=trans, **kwargs)
-        render_vars['config'] = config
+        render_config = self._build_config(config, trans=trans, **kwargs)
+        render_vars['config'] = render_config
         # further parse config to resources (models, etc.) used in template based on registry config
-        resources = self._config_to_resources(trans, config)
+        resources = self._config_to_resources(trans, render_config)
         render_vars.update(resources)
         return render_vars
 
-    def _build_config(self, config, trans=None, **kwargs):
+    def _build_config(self, config, trans=None, **kwargs) -> utils.OpenObject:
         """
         Build the configuration for this new/saved visualization by combining
         any existing config and the kwargs (gen. from the url query).

lib/galaxy/visualization/plugins/resource_parser.py

@@ -5,6 +5,7 @@ a dictionary of string data/ids (often from a query string).
 import json
 import logging
 import weakref
+from typing import Callable, Dict, Optional, Union
 
 import galaxy.exceptions
 import galaxy.util
@@ -12,11 +13,16 @@ from galaxy.managers import (
     hdas as hda_manager,
     visualizations as visualization_manager
 )
+from galaxy.model import HistoryDatasetAssociation, LibraryDatasetDatasetAssociation, Visualization
 from galaxy.util import bunch
 
 log = logging.getLogger(__name__)
 
 
+ParameterPrimitiveType = Union[int, float, str]
+ParameterType = Union[ParameterPrimitiveType, HistoryDatasetAssociation, LibraryDatasetDatasetAssociation, Visualization]
+
+
 class ResourceParser:
     """
     Given a parameter dictionary (often a converted query string) and a
@@ -28,7 +34,7 @@ class ResourceParser:
     The keys used to store the new values can optionally be re-mapped to
     new keys (e.g. dataset_id="NNN" -> hda=<HistoryDatasetAssociation>).
     """
-    primitive_parsers = {
+    primitive_parsers: Dict[str, Callable[[str], ParameterPrimitiveType]] = {
         'str': lambda param: galaxy.util.sanitize_html.sanitize_html(param),
         'bool': lambda param: galaxy.util.string_as_bool(param),
         'int': int,
@@ -127,20 +133,21 @@ class ResourceParser:
         return config
 
     # TODO: I would LOVE to rip modifiers out completely
-    def parse_parameter_modifiers(self, trans, param_modifiers, query_params):
+    def parse_parameter_modifiers(self, trans, param_modifiers, query_params) -> Dict[str, Dict[str, Optional[ParameterType]]]:
         """
         Parse and return parameters that are meant to modify other parameters,
         be grouped with them, or are needed to successfully parse other parameters.
         """
         # only one level of modification - down that road lies madness
         # parse the modifiers out of query_params first since they modify the other params coming next
-        parsed_modifiers = {}
+        parsed_modifiers: Dict[str, Dict[str, Optional[ParameterType]]] = {}
         if not param_modifiers:
             return parsed_modifiers
         # precondition: expects a two level dictionary
         # { target_param_name -> { param_modifier_name -> { param_modifier_data }}}
         for target_param_name, modifier_dict in param_modifiers.items():
-            parsed_modifiers[target_param_name] = target_modifiers = {}
+            target_modifiers: Dict[str, Optional[ParameterType]] = {}
+            parsed_modifiers[target_param_name] = target_modifiers
 
             for modifier_name, modifier_config in modifier_dict.items():
                 query_val = query_params.get(modifier_name, None)
@@ -153,7 +160,7 @@ class ResourceParser:
 
         return parsed_modifiers
 
-    def parse_parameter_default(self, trans, param_config):
+    def parse_parameter_default(self, trans, param_config) -> Optional[ParameterType]:
         """
         Parse any default values for the given param, defaulting the default
         to `None`.
@@ -175,18 +182,7 @@ class ResourceParser:
         a resource usable directly by a template.
         """
         param_type = expected_param_data.get('type')
-        # constrain_to = expected_param_data.get( 'constrain_to' )
-        csv = expected_param_data.get('csv')
-
-        parsed_param = None
-
-        # handle recursion for csv values
-        if csv and recurse:
-            parsed_param = []
-            query_param_list = galaxy.util.listify(query_param)
-            for query_param in query_param_list:
-                parsed_param.append(self._parse_param(trans, expected_param_data, query_param, recurse=False))
-            return parsed_param
+        parsed_param: Optional[ParameterType] = None
 
         if param_type in self.primitive_parsers:
             # TODO: what about param modifiers on primitives?

lib/galaxy/webapps/galaxy/controllers/visualization.py

@@ -18,14 +18,12 @@ from sqlalchemy import (
 from sqlalchemy.orm import eagerload, undefer
 
 from galaxy import model, util, web
-from galaxy.datatypes.interval import Bed
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.sharable import SlugBuilder
 from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
 from galaxy.structured_app import StructuredApp
 from galaxy.util import sanitize_text, unicodify
 from galaxy.util.sanitize_html import sanitize_html
-from galaxy.visualization.data_providers.genome import RawBedDataProvider
 from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
 from galaxy.visualization.genomes import decode_dbkey
 from galaxy.visualization.genomes import GenomeRegion
@@ -879,26 +877,3 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         if len(args) > 0:
             nargs += args
         return os.path.join(*nargs)
-
-    @web.json
-    def bookmarks_from_dataset(self, trans, hda_id=None, ldda_id=None):
-        if hda_id:
-            hda_ldda = "hda"
-            dataset_id = hda_id
-        elif ldda_id:
-            hda_ldda = "ldda"
-            dataset_id = ldda_id
-        dataset = self.get_hda_or_ldda(trans, hda_ldda, dataset_id)
-
-        rows = []
-        if isinstance(dataset.datatype, Bed):
-            data = RawBedDataProvider(original_dataset=dataset).get_iterator()
-            for i, line in enumerate(data):
-                if (i > 500):
-                    break
-                fields = line.split()
-                location = name = f"{fields[0]}:{fields[1]}-{fields[2]}"
-                if len(fields) > 3:
-                    name = fields[4]
-                rows.append([location, name])
-        return {'data': rows}

setup.cfg

@@ -80,10 +80,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.web.framework.middleware.error]
 check_untyped_defs = False
-[mypy-galaxy.visualization.genomes]
-check_untyped_defs = False
-[mypy-galaxy.visualization.data_providers.phyloviz.baseparser]
-check_untyped_defs = False
 [mypy-galaxy.util.topsort]
 check_untyped_defs = False
 [mypy-galaxy.util.submodules]
@@ -135,8 +131,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.containers.docker_decorators]
 check_untyped_defs = False
-[mypy-galaxy.visualization.data_providers.phyloviz.newickparser]
-check_untyped_defs = False
 [mypy-galaxy.tools.bundled.maf.maf_to_interval]
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.maf.maf_stats]
@@ -373,8 +367,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-tool_shed.repository_types.registry]
 check_untyped_defs = False
-[mypy-galaxy.visualization.plugins.config_parser]
-check_untyped_defs = False
 [mypy-galaxy.util.pastescript.serve]
 check_untyped_defs = False
 [mypy-galaxy.tools.errors]
@@ -511,14 +503,8 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-tool_shed.utility_containers]
 check_untyped_defs = False
-[mypy-galaxy.visualization.data_providers.genome]
-check_untyped_defs = False
-[mypy-galaxy.visualization.data_providers.phyloviz]
-check_untyped_defs = False
 [mypy-galaxy.datatypes.registry]
 check_untyped_defs = False
-[mypy-galaxy.visualization.data_providers.registry]
-check_untyped_defs = False
 [mypy-galaxy.tools.data_fetch]
 check_untyped_defs = False
 [mypy-galaxy.tools.parameters.dynamic_options]
@@ -599,16 +585,12 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.queue_worker]
 check_untyped_defs = False
-[mypy-galaxy.visualization.plugins.resource_parser]
-check_untyped_defs = False
 [mypy-galaxy.tools]
 check_untyped_defs = False
 [mypy-galaxy.jobs.mapper]
 check_untyped_defs = False
 [mypy-galaxy.workflow.modules]
 check_untyped_defs = False
-[mypy-galaxy.visualization.plugins.plugin]
-check_untyped_defs = False
 [mypy-galaxy.tools.evaluation]
 check_untyped_defs = False
 [mypy-galaxy.managers.history_contents]