Remove trackster traces completely?

guerler · guerler · commit 47fd4458be4b · 2025-10-07T07:33:38.000+03:00
diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -407,7 +407,6 @@ def user_vault(self):
 
 
 class MockVisualizationsRegistry:
-    BUILT_IN_VISUALIZATIONS = ["trackster"]
 
     def get_visualizations(self, trans, target):
         return []
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -855,8 +855,7 @@ galaxy:
   # <tool_data_path>.
   #builds_file_path: shared/ucsc/builds.txt
 
-  # Directory where chrom len files are kept, currently mainly used by
-  # trackster.
+  # Directory where chrom len files are kept.
   # The value of this option will be resolved with respect to
   # <tool_data_path>.
   #len_file_path: shared/ucsc/chrom
diff --git a/lib/galaxy/config/sample/job_conf.sample.yml b/lib/galaxy/config/sample/job_conf.sample.yml
@@ -1156,11 +1156,6 @@ tools:
   id: baz
   handler: special_handlers
   environment: bigmem
--
-  # legacy trackerster parameter for tool mapping
-  id: foo
-  handler: handler0
-  source: trackster
 -
   # Classes can be used to map groups of tools - the current classes include
   # - local (these special tools that aren't parameterized for remote execution - expression tools, upload, etc..)
diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -1232,9 +1232,6 @@
         <tool id="longbar" destination="dynamic" resources="all" />
         <!-- Pick a handler randomly from those declaring this tag. -->
         <tool id="baz" handler="special_handlers" destination="bigmem"/>
-        <tool id="foo" handler="handler0">
-            <param id="source">trackster</param>
-        </tool>
     </tools>
     <limits>
         <!-- Certain limits can be defined. The 'concurrent_jobs' limits all
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
@@ -765,7 +765,7 @@ mapping:
         default: shared/ucsc/chrom
         required: false
         desc: |
-          Directory where chrom len files are kept, currently mainly used by trackster.
+          Directory where chrom len files are kept.
 
           The value of this option will be resolved with respect to <tool_data_path>.
 
diff --git a/lib/galaxy/datatypes/_schema.py b/lib/galaxy/datatypes/_schema.py
@@ -159,7 +159,7 @@ class DatatypeVisualizationMapping(BaseModel):
         ...,  # Mark this field as required
         title="Visualization",
         description="The visualization plugin to use",
-        examples=["igv", "trackster", "vitessce"],
+        examples=["igv", "vitessce"],
     )
 
 
diff --git a/lib/galaxy/tool_util/toolbox/filters/__init__.py b/lib/galaxy/tool_util/toolbox/filters/__init__.py
@@ -17,8 +17,7 @@ def __init__(self, toolbox):
         self.toolbox = toolbox
 
         # Prepopulate dict containing filters that are always checked,
-        # other filters that get checked depending on context (e.g. coming from
-        # trackster or no user found are added in build filters).
+        # other filters that get checked depending on context.
         self.default_filters = dict(tool=[_not_hidden, _handle_authorization], section=[], label=[])
         # Add dynamic filters to these default filters.
         config = toolbox.app.config
@@ -48,8 +47,6 @@ def build_filters(self, trans, **kwds):
                     if category:
                         validate = getattr(trans.app.config, f"user_tool_{category}_filters", [])
                         self.__init_filters(category, user_filters, filters, validate=validate)
-        if kwds.get("trackster", False):
-            filters["tool"].append(_has_trackster_conf)
 
         return filters
 
@@ -104,6 +101,3 @@ def _handle_authorization(context, tool):
         return False
     return True
 
-
-def _has_trackster_conf(context, tool):
-    return tool.trackster_conf
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -139,7 +139,6 @@ the tool menu immediately following the hyperlink for the tool (based on the
         <xs:element name="code" type="Code" minOccurs="0"/>
         <xs:element name="uihints" type="UIhints" minOccurs="0"/>
         <xs:element name="options" type="Options" minOccurs="0"/>
-        <xs:element name="trackster_conf" type="TracksterConf" minOccurs="0"/>
         <xs:element name="citations" type="Citations" minOccurs="0"/>
       </xs:all>
       <xs:attribute name="id" type="xs:string" use="required">
@@ -1047,29 +1046,6 @@ The content of ``stdout`` and ``stderr`` are strings containing the output of th
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-  <xs:complexType name="TracksterConf">
-    <xs:annotation>
-      <xs:documentation xml:lang="en">This directive is used to specify some rarely modified trackster options.</xs:documentation>
-    </xs:annotation>
-    <xs:sequence>
-      <xs:element name="action" type="TracksterAction" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-  <xs:complexType name="TracksterAction">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"/>
-    </xs:annotation>
-    <xs:attribute name="name" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en"/>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="output_name" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en"/>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
   <xs:complexType name="Tests">
     <xs:annotation gxdocs:best_practices="tests">
       <xs:documentation xml:lang="en"><![CDATA[
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -1494,7 +1494,6 @@ def parse(self, tool_source: ToolSource, guid: Optional[str] = None, dynamic: bo
             self.edam_operations = None
             self.edam_topics = None
 
-        self.__parse_trackster_conf(tool_source)
         # Record macro paths so we can reload a tool if any of its macro has changes
         self._macro_paths = tool_source.macro_paths
         self.ports = tool_source.parse_interactivetool()
@@ -1555,15 +1554,6 @@ def __parse_config_files(self, tool_source: ToolSource):
         self.config_files.extend(tool_source.parse_template_configfiles())
         self.config_files.extend(tool_source.parse_file_sources())
 
-    def __parse_trackster_conf(self, tool_source):
-        self.trackster_conf = None
-        if not hasattr(tool_source, "root"):
-            return
-
-        # Trackster configuration.
-        if (trackster_conf := tool_source.root.find("trackster_conf")) is not None:
-            self.trackster_conf = TracksterConfig.parse(trackster_conf)
-
     def parse_tests(self):
         if self.tool_source:
             test_descriptions = parse_tool_test_descriptions(self.tool_source, self.id)
@@ -4598,20 +4588,6 @@ def _rerun_remap_job_id(trans, incoming, tool_id: Optional[str]) -> Optional[int
     return rerun_remap_job_id
 
 
-class TracksterConfig:
-    """Trackster configuration encapsulation."""
-
-    def __init__(self, actions):
-        self.actions = actions
-
-    @staticmethod
-    def parse(root):
-        actions = []
-        for action_elt in root.findall("action"):
-            actions.append(SetParamAction.parse(action_elt))
-        return TracksterConfig(actions)
-
-
 class SetParamAction:
     """Set parameter action."""
 
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
@@ -1629,14 +1629,6 @@ def package_gff_feature(feature, no_detail=False, filter_cols=None) -> PAYLOAD_L
         feature.end,
     ]
 
-    # HACK: ignore interval with name 'transcript' from feature.
-    # Cufflinks puts this interval in each of its transcripts,
-    # and they mess up trackster by covering the feature's blocks.
-    # This interval will always be a feature's first interval,
-    # and the GFF's third column is its feature name.
-    feature_intervals = feature.intervals
-    if feature.intervals[0].fields[2] == "transcript":
-        feature_intervals = feature.intervals[1:]
     # Add blocks.
     block_sizes = [(interval.end - interval.start) for interval in feature_intervals]
     block_starts = [(interval.start - feature.start) for interval in feature_intervals]
diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
@@ -127,8 +127,6 @@ def to_dict(self):
         }
 
     def _get_url(self):
-        if self.name in self.app.visualizations_registry.BUILT_IN_VISUALIZATIONS:
-            return url_for(controller="visualization", action=self.name)
         return url_for("visualization_plugin", visualization_name=self.name)
 
     def _get_saved_visualization_config(self, visualization, revision=None, **kwargs) -> dict[str, Any]:
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
@@ -36,8 +36,6 @@ class VisualizationsRegistry:
     BASE_DIR = "static/plugins/visualizations"
     #: base url to controller endpoint
     BASE_URL = "visualizations"
-    #: built-in visualizations
-    BUILT_IN_VISUALIZATIONS = ["trackster"]
 
     def __str__(self):
         return self.__class__.__name__
diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py
@@ -612,151 +612,12 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
 
     slug_builder = SlugBuilder()
 
-    def get_tool_def(self, trans, hda):
-        """Returns definition of an interactive tool for an HDA."""
-
-        # Get dataset's job.
-        job = None
-        for job_output_assoc in hda.creating_job_associations:
-            job = job_output_assoc.job
-            break
-        if not job:
-            return None
-
-        tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version)
-        if not tool:
-            return None
-
-        # Tool must have a Trackster configuration.
-        if not tool.trackster_conf:
-            return None
-
-        # -- Get tool definition and add input values from job. --
-        tool_dict = tool.to_dict(trans, io_details=True)
-        tool_param_values = {p.name: p.value for p in job.parameters}
-        tool_param_values = tool.params_from_strings(tool_param_values, ignore_errors=True)
-
-        # Only get values for simple inputs for now.
-        inputs_dict = [i for i in tool_dict["inputs"] if i["type"] not in ["data", "hidden_data", "conditional"]]
-        for t_input in inputs_dict:
-            # Add value to tool.
-            if "name" in t_input:
-                name = t_input["name"]
-                if name in tool_param_values:
-                    value = tool_param_values[name]
-                    if isinstance(value, Dictifiable):
-                        value = value.to_dict()
-                    t_input["value"] = value
-
-        return tool_dict
-
     def get_visualization_config(self, trans, visualization):
-        """Returns a visualization's configuration. Only works for trackster visualizations right now."""
-        config = None
-        if visualization.type in ["trackster", "genome"]:
-            # Unpack Trackster config.
-            latest_revision = visualization.latest_revision
-            bookmarks = latest_revision.config.get("bookmarks", [])
-
-            def pack_track(track_dict):
-                if unencoded_id := track_dict.get("dataset_id"):
-                    encoded_id = trans.security.encode_id(unencoded_id)
-                else:
-                    encoded_id = track_dict["dataset"]["id"]
-                hda_ldda = track_dict.get("hda_ldda", "hda")
-
-                dataset = self.get_hda_or_ldda(trans, hda_ldda, encoded_id)
-                try:
-                    prefs = track_dict["prefs"]
-                except KeyError:
-                    prefs = {}
-                track_data_provider = trans.app.data_provider_registry.get_data_provider(
-                    trans, original_dataset=dataset, source="data"
-                )
-                return {
-                    "track_type": dataset.datatype.track_type,
-                    "dataset": trans.security.encode_dict_ids(dataset.to_dict()),
-                    "prefs": prefs,
-                    "mode": track_dict.get("mode", "Auto"),
-                    "filters": track_dict.get("filters", {"filters": track_data_provider.get_filters()}),
-                    "tool": self.get_tool_def(trans, dataset),
-                    "tool_state": track_dict.get("tool_state", {}),
-                }
-
-            def pack_collection(collection_dict):
-                drawables = []
-                for drawable_dict in collection_dict["drawables"]:
-                    if "track_type" in drawable_dict:
-                        drawables.append(pack_track(drawable_dict))
-                    else:
-                        drawables.append(pack_collection(drawable_dict))
-                return {
-                    "obj_type": collection_dict["obj_type"],
-                    "drawables": drawables,
-                    "prefs": collection_dict.get("prefs", []),
-                    "filters": collection_dict.get("filters", {}),
-                }
-
-            def encode_dbkey(dbkey):
-                """
-                Encodes dbkey as needed. For now, prepends user's public name
-                to custom dbkey keys.
-                """
-                encoded_dbkey = dbkey
-                user = visualization.user
-                if "dbkeys" in user.preferences and str(dbkey) in user.preferences["dbkeys"]:
-                    encoded_dbkey = f"{user.username}:{dbkey}"
-                return encoded_dbkey
-
-            # Set tracks.
-            tracks = []
-            if "tracks" in latest_revision.config:
-                # Legacy code.
-                for track_dict in visualization.latest_revision.config["tracks"]:
-                    tracks.append(pack_track(track_dict))
-            elif "view" in latest_revision.config:
-                for drawable_dict in visualization.latest_revision.config["view"]["drawables"]:
-                    if "track_type" in drawable_dict:
-                        tracks.append(pack_track(drawable_dict))
-                    else:
-                        tracks.append(pack_collection(drawable_dict))
-
-            config = {
-                "title": visualization.title,
-                "vis_id": trans.security.encode_id(visualization.id) if visualization.id is not None else None,
-                "tracks": tracks,
-                "bookmarks": bookmarks,
-                "chrom": "",
-                "dbkey": encode_dbkey(visualization.dbkey),
-            }
-
-            if "viewport" in latest_revision.config:
-                config["viewport"] = latest_revision.config["viewport"]
-        else:
-            # Default action is to return config unaltered.
-            latest_revision = visualization.latest_revision
-            config = latest_revision.config
-
+        """Returns a visualization's configuration."""
+        latest_revision = visualization.latest_revision
+        config = latest_revision.config
         return config
 
-    def get_new_track_config(self, trans, dataset):
-        """
-        Returns track configuration dict for a dataset.
-        """
-        # Get data provider.
-        track_data_provider = trans.app.data_provider_registry.get_data_provider(trans, original_dataset=dataset)
-
-        # Get track definition.
-        return {
-            "track_type": dataset.datatype.track_type,
-            "name": dataset.name,
-            "dataset": trans.security.encode_dict_ids(dataset.to_dict()),
-            "prefs": {},
-            "filters": {"filters": track_data_provider.get_filters()},
-            "tool": self.get_tool_def(trans, dataset),
-            "tool_state": {},
-        }
-
     def get_hda_or_ldda(self, trans, hda_ldda, dataset_id):
         """Returns either HDA or LDDA for hda/ldda and id combination."""
         if hda_ldda == "hda":
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -310,16 +310,13 @@ def index(self, trans: GalaxyWebTransaction, **kwds):
         :param in_panel: if true, tools are returned in panel structure,
                          including sections and labels
         :param view: ToolBox view to apply (default is 'default')
-        :param trackster: if true, only tools that are compatible with
-                          Trackster are returned
         :param q: if present search on the given query will be performed
         :param tool_id: if present the given tool_id will be searched for
                         all installed versions
         """
 
         # Read params.
         in_panel = util.string_as_bool(kwds.get("in_panel", "True"))
-        trackster = util.string_as_bool(kwds.get("trackster", "False"))
         q = kwds.get("q", "")
         tool_id = kwds.get("tool_id", "")
         tool_help = util.string_as_bool(kwds.get("tool_help", "False"))
@@ -356,7 +353,7 @@ def index(self, trans: GalaxyWebTransaction, **kwds):
         # Return everything.
         try:
             return self.app.toolbox.to_dict(
-                trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help, view=view
+                trans, in_panel=in_panel, tool_help=tool_help, view=view
             )
         except exceptions.MessageException:
             raise
@@ -384,16 +381,11 @@ def panel_view(self, trans: GalaxyWebTransaction, view, **kwds):
 
         returns a dictionary of tools and tool sections for the given view
 
-        :param trackster: if true, only tools that are compatible with
-                          Trackster are returned
         """
 
-        # Read param.
-        trackster = util.string_as_bool(kwds.get("trackster", "False"))
-
         # Return panel view.
         try:
-            return self.app.toolbox.to_panel_view(trans, trackster=trackster, view=view)
+            return self.app.toolbox.to_panel_view(trans, view=view)
         except exceptions.MessageException:
             raise
         except Exception:
diff --git a/lib/galaxy/webapps/galaxy/services/datasets.py b/lib/galaxy/webapps/galaxy/services/datasets.py

Original file line number	Diff line number	Diff line change
`@@ -159,7 +159,7 @@ class DatatypeVisualizationMapping(BaseModel):`
`159`	`159`	`..., # Mark this field as required`
`160`	`160`	`title="Visualization",`
`161`	`161`	`description="The visualization plugin to use",`
`162`		`- examples=["igv", "trackster", "vitessce"],`
	`162`	`+ examples=["igv", "vitessce"],`
`163`	`163`	`)`
`164`	`164`
`165`	`165`