Example<\/strong><\/p>\nConverting the following hg16 intervals to hg18 intervals:<\/p>\n
\nchrX 85170 112199 AK002185 0 +\nchrX 110458 112199 AK097346 0 +\nchrX 112203 121212 AK074528 0 -\n<\/pre>\nwill produce the following hg18 intervals:<\/p>\n
\nchrX 132991 160020 AK002185 0 +\nchrX 158279 160020 AK097346 0 +\nchrX 160024 169033 AK074528 0 -\n<\/pre>\n",
+ "edam_operations": [],
+ "form_style": "regular",
+ "edam_topics": [],
+ "panel_section_id": "liftOver",
+ "version": "1.0.6",
+ "link": "/tool_runner?tool_id=liftOver1",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "Tool",
+ "hidden": "",
+ "id": "liftOver1",
+ "name": "Convert genome coordinates"
}
-}
+]
diff --git a/client/src/components/ToolsView/testData/toolsListInPanel.json b/client/src/components/ToolsView/testData/toolsListInPanel.json
index ab5d9aa7090e..b2ca87e36281 100644
--- a/client/src/components/ToolsView/testData/toolsListInPanel.json
+++ b/client/src/components/ToolsView/testData/toolsListInPanel.json
@@ -1,28 +1,26 @@
{
- "default": {
- "collection_operations": {
- "tools": [
- "__UNZIP_COLLECTION__", "__ZIP_COLLECTION__", "__FILTER_FAILED_DATASETS__", "__FILTER_EMPTY_DATASETS__"
- ],
- "model_class": "ToolSection",
- "version": "",
- "id": "collection_operations",
- "name": "Collection Operations"
- },
- "liftOver": {
- "tools": ["liftOver1"],
- "model_class": "ToolSection",
- "version": "",
- "id": "liftOver",
- "name": "Lift-Over"
- },
- "testlabel1": {
- "model_class": "ToolSectionLabel",
- "id": "testlabel1",
- "text": null,
- "version": "",
- "description": null,
- "links": null
- }
+ "collection_operations": {
+ "tools": [
+ "__UNZIP_COLLECTION__", "__ZIP_COLLECTION__", "__FILTER_FAILED_DATASETS__", "__FILTER_EMPTY_DATASETS__"
+ ],
+ "model_class": "ToolSection",
+ "version": "",
+ "id": "collection_operations",
+ "name": "Collection Operations"
+ },
+ "liftOver": {
+ "tools": ["liftOver1"],
+ "model_class": "ToolSection",
+ "version": "",
+ "id": "liftOver",
+ "name": "Lift-Over"
+ },
+ "testlabel1": {
+ "model_class": "ToolSectionLabel",
+ "id": "testlabel1",
+ "text": null,
+ "version": "",
+ "description": null,
+ "links": null
}
}
diff --git a/client/src/components/Toolshed/RepositoryDetails/Index.test.js b/client/src/components/Toolshed/RepositoryDetails/Index.test.js
index e2049ec08aa7..ba48a8ae6901 100644
--- a/client/src/components/Toolshed/RepositoryDetails/Index.test.js
+++ b/client/src/components/Toolshed/RepositoryDetails/Index.test.js
@@ -34,7 +34,7 @@ Services.mockImplementation(() => {
describe("RepositoryDetails", () => {
it("test repository details index", async () => {
const axiosMock = new MockAdapter(axios);
- axiosMock.onGet("api/tool_panel?in_panel=true&view=default").reply(200, {});
+ axiosMock.onGet("api/tool_panels/default").reply(200, {});
mockFetcher.path("/api/configuration").method("get").mock({ data: {} });
const localVue = getLocalVue();
const pinia = createPinia();
diff --git a/client/src/stores/toolStore.ts b/client/src/stores/toolStore.ts
index f6c969cc46c7..122b07db1a25 100644
--- a/client/src/stores/toolStore.ts
+++ b/client/src/stores/toolStore.ts
@@ -156,9 +156,9 @@ export const useToolStore = defineStore("toolStore", () => {
if (!loading.value && !allToolsByIdFetched.value) {
loading.value = true;
await axios
- .get(`${getAppRoot()}api/tool_panel?in_panel=False`)
+ .get(`${getAppRoot()}api/tools?in_panel=False`)
.then(({ data }) => {
- saveAllTools(data.tools);
+ saveAllTools(data as Tool[]);
loading.value = false;
})
.catch((error) => {
@@ -177,10 +177,10 @@ export const useToolStore = defineStore("toolStore", () => {
currentPanelView.value = panelView;
}
await axios
- .get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`)
+ .get(`${getAppRoot()}api/tool_panels/${panelView}`)
.then(({ data }) => {
loading.value = false;
- savePanelView(panelView, data[panelView]);
+ savePanelView(panelView, data);
})
.catch(async (error) => {
loading.value = false;
@@ -199,15 +199,15 @@ export const useToolStore = defineStore("toolStore", () => {
return;
}
loading.value = true;
- const { data } = await axios.get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`);
- savePanelView(panelView, data[panelView]);
+ const { data } = await axios.get(`${getAppRoot()}api/tool_panels/${panelView}`);
+ savePanelView(panelView, data);
loading.value = false;
}
}
async function fetchPanel(panelView: string) {
- const { data } = await axios.get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`);
- savePanelView(panelView, data[panelView]);
+ const { data } = await axios.get(`${getAppRoot()}api/tool_panels/${panelView}`);
+ savePanelView(panelView, data);
}
function saveToolForId(toolId: string, toolData: Tool) {
@@ -218,8 +218,11 @@ export const useToolStore = defineStore("toolStore", () => {
Vue.set(toolResults.value, whooshQuery, toolsData);
}
- function saveAllTools(toolsData: Record) {
- toolsById.value = toolsData;
+ function saveAllTools(toolsData: Tool[]) {
+ toolsById.value = toolsData.reduce((acc, item) => {
+ acc[item.id] = item;
+ return acc;
+ }, {} as Record);
}
function savePanelView(panelView: string, newPanel: { [id: string]: ToolSection | Tool }) {
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 793f200dda55..264b96d26d60 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -1331,38 +1331,24 @@ def to_dict(self, trans, in_panel=True, tool_help=False, view=None, **kwds):
rval.append(self.get_tool_to_dict(trans, tool, tool_help=tool_help))
return rval
- def to_panel_view(self, trans, in_panel=True, tool_help=False, view=None, **kwds):
+ def to_panel_view(self, trans, view="default_panel_view", **kwds):
"""
Create a panel view representation of the toolbox.
- For in_panel=True, uses the structure:
- {view: {section_id: { section but with .tools=List[all tool ids] }, ...}}}
- For in_panel=False, uses the structure:
- {tools: {tool_id: tool.to_dict(), ...}}}
+ Uses the structure:
+ {section_id: { section but with .tools=List[all tool ids] }, ...}}
"""
- rval = {}
- if in_panel:
- if view is None:
- view = self._default_panel_view
- view_contents: Dict[str, Dict] = {}
- rval[view] = view_contents
- panel_elts = self.tool_panel_contents(trans, view=view, **kwds)
- for elt in panel_elts:
- # Only use cache for objects that are Tools.
- if hasattr(elt, "tool_type"):
- view_contents[elt.id] = self.get_tool_to_dict(trans, elt, tool_help=False)
- else:
- kwargs = dict(trans=trans, link_details=True, tool_help=tool_help, toolbox=self, only_ids=True)
- view_contents[elt.id] = elt.to_dict(**kwargs)
- else:
- returned_tools: Dict[str, Dict] = {}
- rval["tools"] = returned_tools
- filter_method = self._build_filter_method(trans)
- for tool in self._tools_by_id.values():
- tool = filter_method(tool, panel_item_types.TOOL)
- if not tool:
- continue
- returned_tools[tool.id] = self.get_tool_to_dict(trans, tool, tool_help=tool_help)
- return rval
+ if view == "default_panel_view":
+ view = self._default_panel_view
+ view_contents: Dict[str, Dict] = {}
+ panel_elts = self.tool_panel_contents(trans, view=view, **kwds)
+ for elt in panel_elts:
+ # Only use cache for objects that are Tools.
+ if hasattr(elt, "tool_type"):
+ view_contents[elt.id] = self.get_tool_to_dict(trans, elt, tool_help=False)
+ else:
+ kwargs = dict(trans=trans, link_details=True, tool_help=False, toolbox=self, only_ids=True)
+ view_contents[elt.id] = elt.to_dict(**kwargs)
+ return view_contents
def _lineage_in_panel(self, panel_dict, tool=None, tool_lineage=None):
"""If tool with same lineage already in panel (or section) - find
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index cbce36d549c2..06763d1fa31f 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -178,56 +178,31 @@ def index(self, trans: GalaxyWebTransaction, **kwds):
raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
@expose_api_anonymous_and_sessionless
- def panel_view(self, trans: GalaxyWebTransaction, **kwds):
+ def panel_views(self, trans: GalaxyWebTransaction, **kwds):
+ """
+ GET /api/tool_panels
+ returns a dictionary of available tool panel views
"""
- GET /api/tool_panel
- returns a dictionary of all tools or panels defined by parameters
+ return self.app.toolbox.panel_view_dicts()
+
+ @expose_api_anonymous_and_sessionless
+ def panel_view(self, trans: GalaxyWebTransaction, view, **kwds):
+ """
+ GET /api/tool_panels/{view}
+
+ returns a dictionary of tools and tool sections for the given view
- :param in_panel: if true, tool sections are returned in panel
- structure, with tool ids 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"))
+ # Read param.
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"))
- view = kwds.get("view", None)
-
- # Find whether to search.
- if q:
- hits = self.service._search(q, view)
- results = []
- if hits:
- for hit in hits:
- try:
- tool = self.service._get_tool(trans, hit, user=trans.user)
- if tool:
- results.append(tool.id)
- except exceptions.AuthenticationFailed:
- pass
- except exceptions.ObjectNotFound:
- pass
- return results
- # Find whether to detect.
- if tool_id:
- detected_versions = self.service._detect(trans, tool_id)
- return detected_versions
-
- # Return everything.
+ # Return panel view.
try:
- return self.app.toolbox.to_panel_view(
- trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help, view=view
- )
+ return self.app.toolbox.to_panel_view(trans, trackster=trackster, view=view)
except exceptions.MessageException:
raise
except Exception:
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 33f1a85e9928..6dcd4c291613 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -367,7 +367,9 @@ def populate_api_routes(webapp, app):
# ====== TOOLS API ======
# =======================
- webapp.mapper.connect("/api/tool_panel", action="panel_view", controller="tools")
+ webapp.mapper.connect("/api/tool_panels", action="panel_views", controller="tools")
+ webapp.mapper.connect("/api/tool_panels/{view}", action="panel_view", controller="tools")
+
webapp.mapper.connect("/api/tools/all_requirements", action="all_requirements", controller="tools")
webapp.mapper.connect("/api/tools/error_stack", action="error_stack", controller="tools")
webapp.mapper.connect("/api/tools/{id:.+?}/build", action="build", controller="tools")
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index a217c572920c..a50f1c36cc21 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -164,11 +164,11 @@ def test_search_grep(self):
assert "Grep1" in get_response
def test_no_panel_index(self):
- index = self._get("tool_panel", data=dict(in_panel=False))
- tools_index = index.json().get("tools", {})
- # No need to flatten out sections, with in_panel=False, only tools by
- # ids are returned.
- tool_ids = list(tools_index.keys())
+ index = self._get("tools", data=dict(in_panel=False))
+ tools_index = index.json()
+ # No need to flatten out sections, with in_panel=False, only tools are
+ # returned.
+ tool_ids = [_["id"] for _ in tools_index]
assert "upload1" in tool_ids
@skip_without_tool("test_sam_to_bam_conversions")
@@ -2640,8 +2640,8 @@ def _run_cat1(self, history_id, inputs, assert_ok=False, **kwargs):
return self._run("cat1", history_id, inputs, assert_ok=assert_ok, **kwargs)
def __tool_ids(self):
- index = self._get("tool_panel")
- tools_index = index.json().get("default", {})
+ index = self._get("tool_panels/default")
+ tools_index = index.json()
# In panels by default, so flatten out sections...
tool_ids = []
for id, tool_or_section in tools_index.items():
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index 1c948bc88508..cd6d72f9388b 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -52,6 +52,7 @@
)
from functools import wraps
from io import StringIO
+from operator import itemgetter
from typing import (
Any,
Callable,
@@ -154,11 +155,11 @@ def skip_without_tool(tool_id: str):
def method_wrapper(method):
def get_tool_ids(api_test_case: HasAnonymousGalaxyInteractor):
interactor = api_test_case.anonymous_galaxy_interactor
- index = interactor.get("tool_panel", data=dict(in_panel=False))
+ index = interactor.get("tools", data=dict(in_panel=False))
api_asserts.assert_status_code_is_ok(index, "Failed to fetch toolbox for target Galaxy.")
- tools = index.json().get("tools", {})
- # `in_panel=False`, so we have a toolsById dict...
- tool_ids = list(tools.keys())
+ tools = index.json()
+ # In panels by default, so flatten out sections...
+ tool_ids = [itemgetter("id")(_) for _ in tools]
return tool_ids
@wraps(method)
@@ -2287,10 +2288,11 @@ def _run_cwl_tool_job(
if os.path.exists(tool_id):
raw_tool_id = os.path.basename(tool_id)
- index = self.dataset_populator._get("tool_panel", data=dict(in_panel=False))
+ index = self.dataset_populator._get("tools", data=dict(in_panel=False))
index.raise_for_status()
- tools = index.json().get("tools", {})
- tool_ids = list(tools.keys())
+ tools = index.json()
+ # In panels by default, so flatten out sections...
+ tool_ids = [itemgetter("id")(_) for _ in tools]
if raw_tool_id in tool_ids:
galaxy_tool_id = raw_tool_id
else:
diff --git a/lib/tool_shed/test/functional/test_galaxy_install.py b/lib/tool_shed/test/functional/test_galaxy_install.py
index 21cc8b1dfc93..227e41aa49c1 100644
--- a/lib/tool_shed/test/functional/test_galaxy_install.py
+++ b/lib/tool_shed/test/functional/test_galaxy_install.py
@@ -10,10 +10,10 @@ def test_install_simple_tool(self):
installable_revisions = populator.get_ordered_installable_revisions(owner, name)
latest_install_revision = installable_revisions.__root__[-1]
self.install_repository(owner, name, latest_install_revision, tool_shed_url=self.url)
- response = self.galaxy_interactor._get("tool_panel?in_panel=False")
+ response = self.galaxy_interactor._get("tools?in_panel=False")
response.raise_for_status()
expected_tool = populator.tool_guid(self, repository, "Add_a_column1", "1.1.0")
- tool_ids = list((response.json().get("tools", {})).keys())
+ tool_ids = [t["id"] for t in response.json()]
assert expected_tool in tool_ids, f"Didn't find {expected_tool} in {tool_ids}"
def test_install_simple_after_repository_metadata_reset(self):
@@ -26,8 +26,8 @@ def test_install_simple_after_repository_metadata_reset(self):
metadata_response = populator.reset_metadata(repository)
assert metadata_response.status == "ok"
self.install_repository(owner, name, latest_install_revision, tool_shed_url=self.url)
- response = self.galaxy_interactor._get("tool_panel?in_panel=False")
+ response = self.galaxy_interactor._get("tools?in_panel=False")
response.raise_for_status()
expected_tool = f"{self.host}:{self.port}/repos/{owner}/{name}/Add_a_column1/1.1.0"
- tool_ids = list((response.json().get("tools", {})).keys())
+ tool_ids = [t["id"] for t in response.json()]
assert expected_tool in tool_ids, f"Didn't find {expected_tool} in {tool_ids}"
diff --git a/test/integration/test_edam_toolbox.py b/test/integration/test_edam_toolbox.py
index 05b923c544ae..33da7f23f176 100644
--- a/test/integration/test_edam_toolbox.py
+++ b/test/integration/test_edam_toolbox.py
@@ -10,9 +10,9 @@ def handle_galaxy_config_kwds(cls, config):
config["edam_panel_views"] = "merged"
def test_edam_toolbox(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="ontology:edam_merged"))
+ index = self.galaxy_interactor.get("tool_panels/ontology:edam_merged")
index.raise_for_status()
- index_panel = index.json().get("ontology:edam_merged", {})
+ index_panel = index.json()
sections = [x for _, x in index_panel.items() if x["model_class"] == "ToolSection"]
section_names = [s["name"] for s in sections]
assert "Mapping" in section_names
@@ -21,9 +21,9 @@ def test_edam_toolbox(self):
# make sure our mapper tool was mapped using Edam correctly...
assert [x for x in mapping_section_tools if x == "mapper"]
- config_index = self.galaxy_interactor.get("configuration")
- config_index.raise_for_status()
- panel_views = config_index.json()["panel_views"]
+ tool_panels = self.galaxy_interactor.get("tool_panels")
+ tool_panels.raise_for_status()
+ panel_views = tool_panels.json()
assert len(panel_views) > 1
assert isinstance(panel_views, dict)
edam_panel_view = panel_views["ontology:edam_merged"]
@@ -40,9 +40,9 @@ def handle_galaxy_config_kwds(cls, config):
config["default_panel_view"] = "ontology:edam_topics"
def test_edam_toolbox(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True))
+ index = self.galaxy_interactor.get("tool_panels/default_panel_view")
index.raise_for_status()
- index_panel = index.json().get("ontology:edam_topics", {})
+ index_panel = index.json()
sections = [x for _, x in index_panel.items() if x["model_class"] == "ToolSection"]
section_names = [s["name"] for s in sections]
assert "Mapping" in section_names
@@ -51,9 +51,9 @@ def test_edam_toolbox(self):
# make sure our mapper tool was mapped using Edam correctly...
assert [x for x in mapping_section_tools if x == "mapper"]
- config_index = self.galaxy_interactor.get("configuration")
- config_index.raise_for_status()
- panel_views = config_index.json()["panel_views"]
+ tool_panels = self.galaxy_interactor.get("tool_panels")
+ tool_panels.raise_for_status()
+ panel_views = tool_panels.json()
assert len(panel_views) > 1
assert isinstance(panel_views, dict)
edam_panel_view = panel_views["ontology:edam_topics"]
diff --git a/test/integration/test_panel_views.py b/test/integration/test_panel_views.py
index e1c60e0cb938..a1b42f3e0d9d 100644
--- a/test/integration/test_panel_views.py
+++ b/test/integration/test_panel_views.py
@@ -16,21 +16,21 @@ def handle_galaxy_config_kwds(cls, config):
config["panel_views_dir"] = PANEL_VIEWS_DIR_1
def test_section_copy(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="filter"))
- index_panel = index.json().get("filter", {})
+ index = self.galaxy_interactor.get("tool_panels/filter")
+ index_panel = index.json()
sections = get_sections(index_panel)
section_names = [s["name"] for s in sections]
assert len(section_names) == 1
assert "For Tours" in section_names
def test_custom_label_order(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="my-custom"))
+ index = self.galaxy_interactor.get("tool_panels/my-custom")
verify_my_custom(index)
def test_filtering_sections_by_tool_id(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_2"))
+ index = self.galaxy_interactor.get("tool_panels/custom_2")
index.raise_for_status()
- index_panel = index.json().get("custom_2", {})
+ index_panel = index.json()
sections = get_sections(index_panel)
assert len(sections) == 1
section = sections[0]
@@ -38,22 +38,22 @@ def test_filtering_sections_by_tool_id(self):
assert len(tools) == 3, len(tools)
def test_filtering_sections_by_tool_id_regex(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_3"))
- verify_custom_regex_filtered(index, "custom_3")
+ index = self.galaxy_interactor.get("tool_panels/custom_3")
+ verify_custom_regex_filtered(index)
def test_filtering_root_by_type(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_4"))
+ index = self.galaxy_interactor.get("tool_panels/custom_4")
index.raise_for_status()
- index_panel = index.json().get("custom_4", {})
+ index_panel = index.json()
assert len(index_panel) == 2
# Labels are filtered out...
assert model_classes(index_panel) == ["Tool", "Tool"]
assert list(index_panel.keys()) == ["empty_list", "count_list"]
def test_custom_section_def(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_6"))
+ index = self.galaxy_interactor.get("tool_panels/custom_6")
index.raise_for_status()
- index_panel = index.json().get("custom_6", {})
+ index_panel = index.json()
assert len(index_panel) == 1
assert model_classes(index_panel) == ["ToolSection"]
section = list(index_panel.values())[0]
@@ -67,13 +67,13 @@ def test_custom_section_def(self):
]
def test_section_embed(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_5"))
- verify_custom_embed(index, "custom_5")
+ index = self.galaxy_interactor.get("tool_panels/custom_5")
+ verify_custom_embed(index)
def test_section_embed_filtering(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_7"))
+ index = self.galaxy_interactor.get("tool_panels/custom_7")
index.raise_for_status()
- index_panel = index.json().get("custom_7", {})
+ index_panel = index.json()
assert len(index_panel) == 1
assert model_classes(index_panel) == ["ToolSection"]
section = list(index_panel.values())[0]
@@ -84,28 +84,28 @@ def test_section_embed_filtering(self):
assert section_elems[3]["model_class"] == "ToolSectionLabel"
def test_section_reference_by_name(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_8"))
- verify_custom_embed(index, "custom_8")
+ index = self.galaxy_interactor.get("tool_panels/custom_8")
+ verify_custom_embed(index)
def test_section_alias(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_9"))
- verify_custom_regex_filtered(index, "custom_9")
+ index = self.galaxy_interactor.get("tool_panels/custom_9")
+ verify_custom_regex_filtered(index)
def test_expand_section_aliases(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_10"))
+ index = self.galaxy_interactor.get("tool_panels/custom_10")
index.raise_for_status()
- index_panel = index.json().get("custom_10", {})
+ index_panel = index.json()
assert len(index_panel) == 2
assert model_classes(index_panel) == ["ToolSection", "ToolSection"]
def test_global_filters(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_11"))
- verify_custom_regex_filtered(index, "custom_11")
+ index = self.galaxy_interactor.get("tool_panels/custom_11")
+ verify_custom_regex_filtered(index)
def test_global_filters_on_integrated_panel(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True, view="custom_12"))
+ index = self.galaxy_interactor.get("tool_panels/custom_12")
index.raise_for_status()
- index_panel = index.json().get("custom_12", {})
+ index_panel = index.json()
sections = get_sections(index_panel)
assert len(sections) == 2
assert "test" in index_panel
@@ -153,13 +153,13 @@ def handle_galaxy_config_kwds(cls, config):
config["default_panel_view"] = "my-custom"
def test_custom_label_order(self):
- index = self.galaxy_interactor.get("tool_panel", data=dict(in_panel=True))
+ index = self.galaxy_interactor.get("tool_panels/default_panel_view")
verify_my_custom(index)
def verify_my_custom(index):
index.raise_for_status()
- index_panel = index.json().get("my-custom", {})
+ index_panel = index.json()
sections = get_sections(index_panel)
assert len(sections) == 0
@@ -167,10 +167,10 @@ def verify_my_custom(index):
assert model_classes(index_panel) == ["ToolSectionLabel", "Tool", "ToolSectionLabel", "Tool", "ToolSectionLabel"]
-def verify_custom_embed(index, view):
+def verify_custom_embed(index):
# custom_5 / custom_8
index.raise_for_status()
- index_panel = index.json().get(view, {})
+ index_panel = index.json()
assert len(index_panel) == 1
assert model_classes(index_panel) == ["ToolSection"]
assert "my-new-section" in index_panel
@@ -188,10 +188,10 @@ def verify_custom_embed(index, view):
]
-def verify_custom_regex_filtered(index, view):
+def verify_custom_regex_filtered(index):
# custom_3 / custom_9
index.raise_for_status()
- index_panel = index.json().get(view, {})
+ index_panel = index.json()
sections = get_sections(index_panel)
assert len(sections) == 1
section = sections[0]