From 72b221fd8b787ccee08105252834bd2c8c3ed0b3 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Tue, 16 Aug 2022 12:15:16 +0200
Subject: [PATCH 01/26] add detailed edam_formats and edam_data apis

---
 lib/galaxy/datatypes/_schema.py            | 26 +++++++++++++++++++
 lib/galaxy/datatypes/registry.py           | 10 ++++++++
 lib/galaxy/managers/datatypes.py           | 29 ++++++++++++++++++++++
 lib/galaxy/tool_util/edam_util.py          | 16 ++++++------
 lib/galaxy/tool_util/toolbox/views/edam.py | 10 +++++---
 lib/galaxy/webapps/galaxy/api/datatypes.py | 23 ++++++++++++++---
 6 files changed, 98 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/datatypes/_schema.py b/lib/galaxy/datatypes/_schema.py
index 50c1774b614..d9b7ea5cfaf 100644
--- a/lib/galaxy/datatypes/_schema.py
+++ b/lib/galaxy/datatypes/_schema.py
@@ -98,3 +98,29 @@ class DatatypeConverter(BaseModel):
 
 class DatatypeConverterList(BaseModel):
     __root__: List[DatatypeConverter] = Field(title="List of data type converters", default=[])
+
+
+class DatatypeEDAMDetails(BaseModel):
+    prefix_IRI: str = Field(
+        ...,  # Mark this field as required
+        title="Prefix IRI",
+        description="The EDAM prefixed Resource Identifier",
+        example="format_1782",
+    )
+    label: Optional[str] = Field(
+        title="Label",
+        description="The EDAM label",
+        example="NCBI gene report format",
+    )
+    definition: Optional[str] = Field(
+        title="Definition",
+        description="The EDAM definition",
+        example="Entry (gene) format of the NCBI database.",
+    )
+
+
+class DatatypeEDAMDetailsDict(BaseModel):
+    __root__: Dict[str, DatatypeEDAMDetails] = Field(
+        title="Dict of EDAM details for formats",
+        default={},
+    )
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 4ac590c55f1..ba061710bee 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -21,6 +21,7 @@ import yaml
 import galaxy.util
 from galaxy.util import RW_R__R__
 from galaxy.util.bunch import Bunch
+from galaxy.tool_util.edam_util import load_edam_tree
 from . import (
     binary,
     coverage,
@@ -46,9 +47,18 @@ class ConfigurationError(Exception):
 
 class Registry:
     def __init__(self, config=None):
+        edam_ontology_path = config.edam_toolbox_ontology_path
+
+        edam = load_edam_tree(
+            None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,
+            "format_",
+            "data_",
+        )
+
         self.log = logging.getLogger(__name__)
         self.log.addHandler(logging.NullHandler())
         self.config = config
+        self.edam = edam
         self.datatypes_by_extension = {}
         self.datatypes_by_suffix_inferences = {}
         self.mimetypes_by_extension = {}
diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index 9b5a6450670..95c46e19d36 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -12,6 +12,7 @@ from galaxy.datatypes._schema import (
     DatatypeDetails,
     DatatypesCombinedMap,
     DatatypesMap,
+    DatatypeEDAMDetailsDict,
 )
 from galaxy.datatypes.data import Data
 from galaxy.datatypes.registry import Registry
@@ -89,6 +90,34 @@ def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     return parse_obj_as(DatatypeConverterList, converters)
 
 
+def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
+    details_dict = {}
+    for (format, edam_iri) in edam_ids.items():
+        edam_details = datatypes_registry.edam.get(edam_iri, {})
+
+        details_dict[format] = {
+            "prefix_IRI": edam_iri,
+            "label": edam_details.get("label", None),
+            "definition": edam_details.get("definition", None),
+        }
+
+    return details_dict
+
+
+def view_edam_formats(datatypes_registry: Registry, id_only: Optional[bool] = True) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
+    if id_only:
+        return datatypes_registry.edam_formats
+    else:
+        return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
+
+
+def view_edam_data(datatypes_registry: Registry, id_only: Optional[bool] = True) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
+    if id_only:
+        return datatypes_registry.edam_data
+    else:
+        return _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
+
+
 __all__ = (
     "DatatypeConverterList",
     "DatatypeDetails",
diff --git a/lib/galaxy/tool_util/edam_util.py b/lib/galaxy/tool_util/edam_util.py
index 26102b1ae37..da4d0560bbd 100644
--- a/lib/galaxy/tool_util/edam_util.py
+++ b/lib/galaxy/tool_util/edam_util.py
@@ -16,19 +16,19 @@ ROOT_OPERATION = "operation_0004"
 ROOT_TOPIC = "topic_0003"
 
 
-def load_edam_tree(path: Optional[str] = None):
+def load_edam_tree(path: Optional[str] = None, *included_terms: str):
     if path is not None:
         assert os.path.exists(path), f"Failed to load EDAM tabular data at [{path}] path does not exist."
         handle = open(path)
     else:
         assert (
             tabular_stream is not None
-        ), "Failed to load optional import from edam-onotology package, install using [pip install edam-ontology]."
+        ), "Failed to load optional import from edam-ontology package, install using [pip install edam-ontology]."
         handle = tabular_stream()
-    return load_edam_tree_from_tsv_stream(handle)
+    return load_edam_tree_from_tsv_stream(handle, *included_terms)
 
 
-def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
+def load_edam_tree_from_tsv_stream(tsv_stream: TextIO, *included_terms: str):
     edam: Dict[str, Dict] = {}
 
     def _recurse_edam_parents(term, path=None):
@@ -47,7 +47,7 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
                 columns[field] = i
             is_first = False
 
-            defintion_column = columns["http://www.geneontology.org/formats/oboInOwl#hasDefinition"]
+            definition_column = columns["http://www.geneontology.org/formats/oboInOwl#hasDefinition"]
             term_column = columns["Class ID"]
             label_column = columns["Preferred Label"]
             parents_column = columns["Parents"]
@@ -59,14 +59,14 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
 
         term_id = term[len(EDAM_PREFIX) :]
 
-        # Only care about formats and operations
-        if not (term_id.startswith("operation_") or term_id.startswith("topic_")):
+        # Only care about included terms
+        if (included_terms is not None) and not (term_id.startswith(included_terms)):
             continue
 
         parents = fields[parents_column].split("|")
         edam[term_id] = {
             "label": fields[label_column],
-            "definition": fields[defintion_column].strip('"'),
+            "definition": fields[definition_column].strip('"'),
             "parents": [x[len(EDAM_PREFIX) :] for x in parents if x.startswith(EDAM_PREFIX)],
         }
 
diff --git a/lib/galaxy/tool_util/toolbox/views/edam.py b/lib/galaxy/tool_util/toolbox/views/edam.py
index 89ec2fa1e49..8049e07a0f0 100644
--- a/lib/galaxy/tool_util/toolbox/views/edam.py
+++ b/lib/galaxy/tool_util/toolbox/views/edam.py
@@ -38,7 +38,9 @@ class EdamPanelMode(str, Enum):
 class EdamToolPanelView(ToolPanelView):
     def __init__(self, edam_ontology_path: Optional[str], mode: EdamPanelMode = EdamPanelMode.merged):
         edam = load_edam_tree(
-            None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path
+            None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,
+            "operation_",
+            "topic_",
         )
         self.edam = edam
         self.mode = mode
@@ -162,15 +164,15 @@ class EdamToolPanelView(ToolPanelView):
         if mode == EdamPanelMode.merged:
             model_id = "ontology:edam_merged"
             name = "EDAM Operations and Topics"
-            description = "Tools are grouped using both annotated operation and topic information (if availabled)."
+            description = "Tools are grouped using both annotated operation and topic information (if available)."
         elif mode == EdamPanelMode.operations:
             model_id = "ontology:edam_operations"
             name = "EDAM Operations"
-            description = "Tools are grouped using annotated EDAM operation information (if availabled)."
+            description = "Tools are grouped using annotated EDAM operation information (if available)."
         elif mode == EdamPanelMode.topics:
             model_id = "ontology:edam_topics"
             name = "EDAM Topics"
-            description = "Tools are grouped using annotated EDAM topic information (if availabled)."
+            description = "Tools are grouped using annotated EDAM topic information (if available)."
         else:
             raise AssertionError(f"Invalid EDAM mode encountered {mode}")
         model_class = self.__class__.__name__
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index c91f2bb90be..9e31f74d615 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -17,10 +17,13 @@ from galaxy.managers.datatypes import (
     DatatypeDetails,
     DatatypesCombinedMap,
     DatatypesMap,
+    DatatypeEDAMDetailsDict,
     view_converters,
     view_index,
     view_mapping,
     view_sniffers,
+    view_edam_formats,
+    view_edam_data,
 )
 from . import (
     depends,
@@ -43,6 +46,12 @@ UploadOnlyQueryParam: Optional[bool] = Query(
     description="Whether to return only datatypes which can be uploaded",
 )
 
+IdentifierOnly: Optional[bool] = Query(
+    default=True,
+    title="prefixIRI only",
+    description="Whether to return only the EDAM prefixIRI rather than the EDAM details",
+)
+
 
 @router.cbv
 class FastAPIDatatypes:
@@ -111,15 +120,21 @@ class FastAPIDatatypes:
         summary="Returns a dictionary/map of datatypes and EDAM formats",
         response_description="Dictionary/map of datatypes and EDAM formats",
     )
-    async def edam_formats(self) -> Dict[str, str]:
+    async def edam_formats(
+        self,
+        id_only: Optional[bool] = IdentifierOnly,
+    ) -> Union[DatatypeEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
-        return self.datatypes_registry.edam_formats
+        return view_edam_formats(self.datatypes_registry, id_only)
 
     @router.get(
         "/api/datatypes/edam_data",
         summary="Returns a dictionary/map of datatypes and EDAM data",
         response_description="Dictionary/map of datatypes and EDAM data",
     )
-    async def edam_data(self) -> Dict[str, str]:
+    async def edam_data(
+        self,
+        id_only: Optional[bool] = IdentifierOnly,
+    ) -> Union[DatatypeEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM data."""
-        return self.datatypes_registry.edam_data
+        return view_edam_data(self.datatypes_registry, id_only)

From cb3c2942810512383e45e79c23bde215b7896ad8 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Tue, 16 Aug 2022 15:47:18 +0200
Subject: [PATCH 02/26] add tests for new apis

---
 lib/galaxy_test/api/test_datatypes.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/lib/galaxy_test/api/test_datatypes.py b/lib/galaxy_test/api/test_datatypes.py
index e3e4a21b250..84886e2bb0b 100644
--- a/lib/galaxy_test/api/test_datatypes.py
+++ b/lib/galaxy_test/api/test_datatypes.py
@@ -89,6 +89,15 @@ class DatatypesApiTestCase(ApiTestCase):
         edam_formats = response.json()
         assert isinstance(edam_formats, dict)
         assert edam_formats["ab1"] == "format_3000"
+        time.sleep(2)
+
+        response = self._get("datatypes/edam_formats?id_only=false")
+        self._assert_status_code_is(response, 200)
+        edam_formats = response.json()
+        assert isinstance(edam_formats, dict)
+        assert isinstance(edam_formats["afg"], dict)
+        assert edam_formats["afg"]["prefix_IRI"] == "format_3582"
+        assert edam_formats["afg"]["label"] == "afg"
 
     def test_edam_data(self):
         response = self._get("datatypes/edam_data")
@@ -96,6 +105,14 @@ class DatatypesApiTestCase(ApiTestCase):
         edam_data = response.json()
         assert isinstance(edam_data, dict)
         assert edam_data["ab1"] == "data_0924"
+        time.sleep(2)
+
+        response = self._get("datatypes/edam_data?id_only=false")
+        edam_data = response.json()
+        assert isinstance(edam_data, dict)
+        assert isinstance(edam_data["afg"], dict)
+        assert edam_data["afg"]["prefix_IRI"] == "data_0925"
+        assert edam_data["afg"]["label"] == "Sequence assembly"
 
     def _index_datatypes(self, data=None):
         data = data or {}

From da66f75a1e3c0592bc32243a109633cbed76a38d Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Tue, 16 Aug 2022 17:48:32 +0200
Subject: [PATCH 03/26] fix optional included_terms in load_edam_tree

---
 lib/galaxy/tool_util/edam_util.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/edam_util.py b/lib/galaxy/tool_util/edam_util.py
index da4d0560bbd..788cfa86c15 100644
--- a/lib/galaxy/tool_util/edam_util.py
+++ b/lib/galaxy/tool_util/edam_util.py
@@ -60,7 +60,7 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO, *included_terms: str):
         term_id = term[len(EDAM_PREFIX) :]
 
         # Only care about included terms
-        if (included_terms is not None) and not (term_id.startswith(included_terms)):
+        if included_terms and not (term_id.startswith(included_terms)):
             continue
 
         parents = fields[parents_column].split("|")

From 712dd45328434ab35e6432e83112a0ff286a10a3 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 09:57:19 +0200
Subject: [PATCH 04/26] fix no config breaks registry

---
 lib/galaxy/datatypes/registry.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index ba061710bee..06f48efed06 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -47,7 +47,7 @@ class ConfigurationError(Exception):
 
 class Registry:
     def __init__(self, config=None):
-        edam_ontology_path = config.edam_toolbox_ontology_path
+        edam_ontology_path = config.edam_toolbox_ontology_path if config is not None else None
 
         edam = load_edam_tree(
             None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,

From 744b8128e0eae04399c2abefb9384a29a729cad3 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 10:15:59 +0200
Subject: [PATCH 05/26] fix edam_toolbox_ontology_path not in config causes
 crash

---
 lib/galaxy/datatypes/registry.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 06f48efed06..ae714731efb 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -47,7 +47,7 @@ class ConfigurationError(Exception):
 
 class Registry:
     def __init__(self, config=None):
-        edam_ontology_path = config.edam_toolbox_ontology_path if config is not None else None
+        edam_ontology_path = config.get("edam_toolbox_ontology_path", None) if config is not None else None
 
         edam = load_edam_tree(
             None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,

From 85c6045248e796fc455a97523cf5bd329a752b99 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 10:29:39 +0200
Subject: [PATCH 06/26] explicitly reexport DatatypeEDAMDetailsDict

---
 lib/galaxy/managers/datatypes.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index 95c46e19d36..9b8cc2559a1 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -104,14 +104,18 @@ def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
     return details_dict
 
 
-def view_edam_formats(datatypes_registry: Registry, id_only: Optional[bool] = True) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
+def view_edam_formats(
+    datatypes_registry: Registry, id_only: Optional[bool] = True
+) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_formats
     else:
         return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
 
 
-def view_edam_data(datatypes_registry: Registry, id_only: Optional[bool] = True) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
+def view_edam_data(
+    datatypes_registry: Registry, id_only: Optional[bool] = True
+) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_data
     else:
@@ -123,6 +127,7 @@ __all__ = (
     "DatatypeDetails",
     "DatatypesCombinedMap",
     "DatatypesMap",
+    "DatatypeEDAMDetailsDict",
     "view_index",
     "view_mapping",
     "view_types_and_mapping",

From 83e1db6404c2f67334edfd723e173aec6b2583e7 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 10:48:33 +0200
Subject: [PATCH 07/26] rename DatatypesEDAMDetailsDict sort imports

---
 lib/galaxy/datatypes/_schema.py            |  2 +-
 lib/galaxy/managers/datatypes.py           |  8 ++++----
 lib/galaxy/webapps/galaxy/api/datatypes.py | 10 +++++-----
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/datatypes/_schema.py b/lib/galaxy/datatypes/_schema.py
index d9b7ea5cfaf..6b618e77d0f 100644
--- a/lib/galaxy/datatypes/_schema.py
+++ b/lib/galaxy/datatypes/_schema.py
@@ -119,7 +119,7 @@ class DatatypeEDAMDetails(BaseModel):
     )
 
 
-class DatatypeEDAMDetailsDict(BaseModel):
+class DatatypesEDAMDetailsDict(BaseModel):
     __root__: Dict[str, DatatypeEDAMDetails] = Field(
         title="Dict of EDAM details for formats",
         default={},
diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index 9b8cc2559a1..bb962439a62 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -11,8 +11,8 @@ from galaxy.datatypes._schema import (
     DatatypeConverterList,
     DatatypeDetails,
     DatatypesCombinedMap,
+    DatatypesEDAMDetailsDict,
     DatatypesMap,
-    DatatypeEDAMDetailsDict,
 )
 from galaxy.datatypes.data import Data
 from galaxy.datatypes.registry import Registry
@@ -106,7 +106,7 @@ def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
 
 def view_edam_formats(
     datatypes_registry: Registry, id_only: Optional[bool] = True
-) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
+) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_formats
     else:
@@ -115,7 +115,7 @@ def view_edam_formats(
 
 def view_edam_data(
     datatypes_registry: Registry, id_only: Optional[bool] = True
-) -> Union[Dict[str, str], DatatypeEDAMDetailsDict]:
+) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_data
     else:
@@ -126,8 +126,8 @@ __all__ = (
     "DatatypeConverterList",
     "DatatypeDetails",
     "DatatypesCombinedMap",
+    "DatatypesEDAMDetailsDict",
     "DatatypesMap",
-    "DatatypeEDAMDetailsDict",
     "view_index",
     "view_mapping",
     "view_types_and_mapping",
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index 9e31f74d615..dec29010bd2 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -16,14 +16,14 @@ from galaxy.managers.datatypes import (
     DatatypeConverterList,
     DatatypeDetails,
     DatatypesCombinedMap,
+    DatatypesEDAMDetailsDict,
     DatatypesMap,
-    DatatypeEDAMDetailsDict,
     view_converters,
+    view_edam_data,
+    view_edam_formats,
     view_index,
     view_mapping,
     view_sniffers,
-    view_edam_formats,
-    view_edam_data,
 )
 from . import (
     depends,
@@ -123,7 +123,7 @@ class FastAPIDatatypes:
     async def edam_formats(
         self,
         id_only: Optional[bool] = IdentifierOnly,
-    ) -> Union[DatatypeEDAMDetailsDict, Dict[str, str]]:
+    ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
         return view_edam_formats(self.datatypes_registry, id_only)
 
@@ -135,6 +135,6 @@ class FastAPIDatatypes:
     async def edam_data(
         self,
         id_only: Optional[bool] = IdentifierOnly,
-    ) -> Union[DatatypeEDAMDetailsDict, Dict[str, str]]:
+    ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM data."""
         return view_edam_data(self.datatypes_registry, id_only)

From 474b25c15b4884eec329963dc747794624f503ec Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 11:14:45 +0200
Subject: [PATCH 08/26] add new `datatypes` client route

---
 client/src/components/Datatypes.vue   | 10 ++++++++++
 client/src/entry/analysis/router.js   |  5 +++++
 lib/galaxy/webapps/galaxy/buildapp.py |  1 +
 3 files changed, 16 insertions(+)
 create mode 100644 client/src/components/Datatypes.vue

diff --git a/client/src/components/Datatypes.vue b/client/src/components/Datatypes.vue
new file mode 100644
index 00000000000..ba2703cea5e
--- /dev/null
+++ b/client/src/components/Datatypes.vue
@@ -0,0 +1,10 @@
+<script setup>
+
+</script>
+
+<template>
+    <span>Datatypes</span>
+</template>
+
+<style scoped>
+</style>
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 483e67a1e87..509f49a3732 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -52,6 +52,7 @@ import { CloudAuth } from "components/User/CloudAuth";
 import { ExternalIdentities } from "components/User/ExternalIdentities";
 import { HistoryExport } from "components/HistoryExport/index";
 import { StorageDashboardRouter } from "components/User/DiskUsage";
+import Datatypes from "components/Datatypes";
 
 Vue.use(VueRouter);
 
@@ -418,6 +419,10 @@ export function getRouter(Galaxy) {
                         component: StoredWorkflowInvocations,
                         props: true,
                     },
+                    {
+                        path: "datatypes",
+                        component: Datatypes,
+                    },
                 ],
             },
             { path: "/login/start", component: Login },
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index ec95f7f87fa..968815b1a2c 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -262,6 +262,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route("/interactivetool_entry_points/list")
     webapp.add_client_route("/libraries{path:.*?}")
     webapp.add_client_route("/storage{path:.*?}")
+    webapp.add_client_route("/datatypes")
 
     # ==== Done
     # Indicate that all configuration settings have been provided

From fc1c06bf88821c10d09ec7308eba5e9c828ad359 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 11:57:48 +0200
Subject: [PATCH 09/26] resolve datatypes name conflict

---
 .../{Datatypes.vue => AvailableDatatypes.vue}          |  8 ++++----
 client/src/entry/analysis/router.js                    | 10 +++++-----
 lib/galaxy/webapps/galaxy/buildapp.py                  |  1 -
 3 files changed, 9 insertions(+), 10 deletions(-)
 rename client/src/components/{Datatypes.vue => AvailableDatatypes.vue} (76%)

diff --git a/client/src/components/Datatypes.vue b/client/src/components/AvailableDatatypes.vue
similarity index 76%
rename from client/src/components/Datatypes.vue
rename to client/src/components/AvailableDatatypes.vue
index ba2703cea5e..4b7184f0784 100644
--- a/client/src/components/Datatypes.vue
+++ b/client/src/components/AvailableDatatypes.vue
@@ -1,10 +1,10 @@
-<script setup>
-
-</script>
-
 <template>
     <span>Datatypes</span>
 </template>
 
+<script>
+export default {}
+</script>
+
 <style scoped>
 </style>
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 509f49a3732..e5be32725b1 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -22,6 +22,7 @@ import DatasetAttributes from "components/DatasetInformation/DatasetAttributes";
 import DatasetDetails from "components/DatasetInformation/DatasetDetails";
 import DatasetError from "components/DatasetInformation/DatasetError";
 import DatasetList from "components/Dataset/DatasetList";
+import AvailableDatatypes from "components/AvailableDatatypes";
 import DisplayStructured from "components/DisplayStructured";
 import FormGeneric from "components/Form/FormGeneric";
 import Grid from "components/Grid/Grid";
@@ -52,7 +53,6 @@ import { CloudAuth } from "components/User/CloudAuth";
 import { ExternalIdentities } from "components/User/ExternalIdentities";
 import { HistoryExport } from "components/HistoryExport/index";
 import { StorageDashboardRouter } from "components/User/DiskUsage";
-import Datatypes from "components/Datatypes";
 
 Vue.use(VueRouter);
 
@@ -141,6 +141,10 @@ export function getRouter(Galaxy) {
                         component: DatasetError,
                         props: true,
                     },
+                    {
+                        path: "available_datatypes",
+                        component: AvailableDatatypes,
+                    },
                     {
                         path: "histories/import",
                         component: HistoryImport,
@@ -419,10 +423,6 @@ export function getRouter(Galaxy) {
                         component: StoredWorkflowInvocations,
                         props: true,
                     },
-                    {
-                        path: "datatypes",
-                        component: Datatypes,
-                    },
                 ],
             },
             { path: "/login/start", component: Login },
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 968815b1a2c..ec95f7f87fa 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -262,7 +262,6 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route("/interactivetool_entry_points/list")
     webapp.add_client_route("/libraries{path:.*?}")
     webapp.add_client_route("/storage{path:.*?}")
-    webapp.add_client_route("/datatypes")
 
     # ==== Done
     # Indicate that all configuration settings have been provided

From d78f0186818b8a4277773a93fe8c367b7f9e1db7 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 12:34:08 +0200
Subject: [PATCH 10/26] format python

---
 lib/galaxy/datatypes/registry.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index ae714731efb..689c5642dec 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -19,9 +19,9 @@ from typing import (
 import yaml
 
 import galaxy.util
+from galaxy.tool_util.edam_util import load_edam_tree
 from galaxy.util import RW_R__R__
 from galaxy.util.bunch import Bunch
-from galaxy.tool_util.edam_util import load_edam_tree
 from . import (
     binary,
     coverage,

From c22011ed3e4da78556811d71e68d230eb546c79b Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 16:11:44 +0200
Subject: [PATCH 11/26] basic layout and filtering

---
 client/src/components/AvailableDatatypes.vue | 29 +++++++++---
 client/src/composables/datatypes.js          | 46 ++++++++++++++++++++
 client/src/composables/filter.js             | 28 ++++++++++++
 client/src/entry/analysis/router.js          |  2 +-
 lib/galaxy/webapps/galaxy/buildapp.py        |  1 +
 5 files changed, 98 insertions(+), 8 deletions(-)
 create mode 100644 client/src/composables/datatypes.js
 create mode 100644 client/src/composables/filter.js

diff --git a/client/src/components/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes.vue
index 4b7184f0784..9f1c0e8d037 100644
--- a/client/src/components/AvailableDatatypes.vue
+++ b/client/src/components/AvailableDatatypes.vue
@@ -1,10 +1,25 @@
-<template>
-    <span>Datatypes</span>
-</template>
+<script setup>
+import { ref } from "vue";
+import { useGetDetailedDatatypes } from "composables/datatypes";
+import { useFilterObjectArray } from "composables/filter";
+import DelayedInput from "components/Common/DelayedInput";
 
-<script>
-export default {}
+const fields = ["extension"];
+
+const filter = ref("");
+
+const { datatypes } = useGetDetailedDatatypes();
+const filteredArray = useFilterObjectArray(datatypes, filter, fields);
 </script>
 
-<style scoped>
-</style>
+<template>
+    <div>
+        <h1>Datatypes</h1>
+        <DelayedInput :delay="200" @change="(val) => (filter = val)" />
+        <div v-for="datatype in filteredArray" :key="datatype.extension">
+            <div>{{ datatype.extension }}</div>
+        </div>
+    </div>
+</template>
+
+<style scoped></style>
diff --git a/client/src/composables/datatypes.js b/client/src/composables/datatypes.js
new file mode 100644
index 00000000000..4d5baf56a91
--- /dev/null
+++ b/client/src/composables/datatypes.js
@@ -0,0 +1,46 @@
+import { ref } from "vue";
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+
+export function useGetDetailedDatatypes() {
+    const datatypesLoading = ref(true);
+    const datatypes = ref([]);
+
+    async function getDatatypes() {
+        const datatypesPromise = axios.get(`${getAppRoot()}api/datatypes?extension_only=false`);
+        const datatypeEDAMFormatsPromise = axios.get(`${getAppRoot()}api/datatypes/edam_formats?id_only=false`);
+        const datatypeEDAMDataPromise = axios.get(`${getAppRoot()}api/datatypes/edam_data?id_only=false`);
+
+        const [baseTypes, datatypeEDAMFormats, datatypeEDAMData] = await Promise.all([
+            datatypesPromise,
+            datatypeEDAMFormatsPromise,
+            datatypeEDAMDataPromise,
+        ]);
+
+        datatypes.value = baseTypes.data.map((type, i) => {
+            const typeEDAMFormat = datatypeEDAMFormats.data[type.extension] ?? null;
+            const typeEDAMData = datatypeEDAMData.data[type.extension] ?? null;
+
+            return {
+                extension: type.extension,
+                description: type.description,
+                edamFormat: typeEDAMFormat.prefix_IRI,
+                edamFormatLabel: typeEDAMFormat.label,
+                edamFormatDefinition: typeEDAMFormat.definition,
+                edamData: typeEDAMData.prefix_IRI,
+                edamDataLabel: typeEDAMData.label,
+                edamDataDefinition: typeEDAMData.definition,
+            };
+        });
+
+        datatypesLoading.value = false;
+    }
+
+    try {
+        getDatatypes();
+    } catch (e) {
+        console.error("unable to fetch available datatypes\n", e);
+    }
+
+    return { datatypes, datatypesLoading };
+}
diff --git a/client/src/composables/filter.js b/client/src/composables/filter.js
new file mode 100644
index 00000000000..4af74f49e1b
--- /dev/null
+++ b/client/src/composables/filter.js
@@ -0,0 +1,28 @@
+import { computed, unref } from "vue";
+
+/**
+ * Filter array of objects, by comparing `filter` to all `fields`
+ */
+export function useFilterObjectArray(array, filter, objectFields) {
+    const filtered = computed(() => {
+        const f = unref(filter);
+        const arr = unref(array);
+        const fields = unref(objectFields);
+
+        if (f === "") {
+            return arr;
+        } else {
+            return arr.filter((obj) => {
+                for (const field of fields) {
+                    if (obj[field].toLowerCase().includes(f)) {
+                        return true;
+                    }
+                }
+
+                return false;
+            });
+        }
+    });
+
+    return filtered;
+}
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index e5be32725b1..03714392483 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -142,7 +142,7 @@ export function getRouter(Galaxy) {
                         props: true,
                     },
                     {
-                        path: "available_datatypes",
+                        path: "datatypes",
                         component: AvailableDatatypes,
                     },
                     {
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index ec95f7f87fa..f1a689fe2c7 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -208,6 +208,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route("/admin/quotas")
     webapp.add_client_route("/admin/form/{form_id}")
     webapp.add_client_route("/admin/api_keys")
+    webapp.add_client_route("/datatypes")
     webapp.add_client_route("/login/start")
     webapp.add_client_route("/login/confirm")
     webapp.add_client_route("/tools/view")

From 73cc49e6a7b89d182af3b68b13b5fa7d293698d2 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 17 Aug 2022 18:02:39 +0200
Subject: [PATCH 12/26] add table to render datatypes

---
 client/src/components/AvailableDatatypes.vue | 60 +++++++++++++++++---
 1 file changed, 52 insertions(+), 8 deletions(-)

diff --git a/client/src/components/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes.vue
index 9f1c0e8d037..b867dfb3bf6 100644
--- a/client/src/components/AvailableDatatypes.vue
+++ b/client/src/components/AvailableDatatypes.vue
@@ -4,22 +4,66 @@ import { useGetDetailedDatatypes } from "composables/datatypes";
 import { useFilterObjectArray } from "composables/filter";
 import DelayedInput from "components/Common/DelayedInput";
 
-const fields = ["extension"];
-
 const filter = ref("");
+const filterFields = ["extension"];
 
 const { datatypes } = useGetDetailedDatatypes();
-const filteredArray = useFilterObjectArray(datatypes, filter, fields);
+const filteredDatatypes = useFilterObjectArray(datatypes, filter, filterFields);
+
+const fields = [
+    {
+        key: "extension",
+    },
+    {
+        key: "edamFormatLabel",
+        label: "EDAM Format",
+    },
+    {
+        key: "edamDataLabel",
+        label: "EDAM Data",
+    },
+];
+
+const edamLink = (edamIRI) => `https://edamontology.github.io/edam-browser/#${edamIRI}`;
 </script>
 
 <template>
     <div>
         <h1>Datatypes</h1>
-        <DelayedInput :delay="200" @change="(val) => (filter = val)" />
-        <div v-for="datatype in filteredArray" :key="datatype.extension">
-            <div>{{ datatype.extension }}</div>
-        </div>
+        <p>All Datatypes supported by this Galaxy instance. Hover over an item for more information.</p>
+        <DelayedInput placeholder="filter extensions" class="mb-3" :delay="200" @change="(val) => (filter = val)" />
+        <b-table striped small :items="filteredDatatypes" :fields="fields">
+            <template v-slot:cell(extension)="row">
+                <span v-b-tooltip.hover :title="row.item.description">
+                    {{ row.item.extension }}
+                </span>
+            </template>
+
+            <template v-slot:cell(edamFormatLabel)="row">
+                <a
+                    v-b-tooltip.hover
+                    target="_blank"
+                    :href="edamLink(row.item.edamFormat)"
+                    :title="row.item.edamFormatDefinition">
+                    {{ row.item.edamFormatLabel }}
+                </a>
+            </template>
+
+            <template v-slot:cell(edamDataLabel)="row">
+                <a
+                    v-b-tooltip.hover
+                    target="_blank"
+                    :href="edamLink(row.item.edamData)"
+                    :title="row.item.edamDataDefinition">
+                    {{ row.item.edamDataLabel }}
+                </a>
+            </template>
+        </b-table>
     </div>
 </template>
 
-<style scoped></style>
+<style scoped>
+table {
+    cursor: default;
+}
+</style>

From 8296b27230ceb7692e1450b8e34942fbcd5eb4d5 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Thu, 18 Aug 2022 09:37:13 +0200
Subject: [PATCH 13/26] rename move and fix composables document composables

---
 client/src/components/AvailableDatatypes.vue |  6 +-
 client/src/composables/datatypes.js          | 64 +++++++++++---------
 client/src/composables/{ => utils}/filter.js |  8 ++-
 3 files changed, 43 insertions(+), 35 deletions(-)
 rename client/src/composables/{ => utils}/filter.js (65%)

diff --git a/client/src/components/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes.vue
index b867dfb3bf6..dc1ea0aed2b 100644
--- a/client/src/components/AvailableDatatypes.vue
+++ b/client/src/components/AvailableDatatypes.vue
@@ -1,13 +1,13 @@
 <script setup>
 import { ref } from "vue";
-import { useGetDetailedDatatypes } from "composables/datatypes";
-import { useFilterObjectArray } from "composables/filter";
+import { useDetailedDatatypes } from "composables/datatypes";
+import { useFilterObjectArray } from "composables/utils/filter";
 import DelayedInput from "components/Common/DelayedInput";
 
 const filter = ref("");
 const filterFields = ["extension"];
 
-const { datatypes } = useGetDetailedDatatypes();
+const { datatypes } = useDetailedDatatypes();
 const filteredDatatypes = useFilterObjectArray(datatypes, filter, filterFields);
 
 const fields = [
diff --git a/client/src/composables/datatypes.js b/client/src/composables/datatypes.js
index 4d5baf56a91..d83459aec68 100644
--- a/client/src/composables/datatypes.js
+++ b/client/src/composables/datatypes.js
@@ -2,45 +2,49 @@ import { ref } from "vue";
 import axios from "axios";
 import { getAppRoot } from "onload/loadConfig";
 
-export function useGetDetailedDatatypes() {
+/**
+ * Fetches a detailed array of datatypes available on this galaxy instance.
+ * Does not cache the result or use a store.
+ */
+export function useDetailedDatatypes() {
     const datatypesLoading = ref(true);
     const datatypes = ref([]);
 
     async function getDatatypes() {
-        const datatypesPromise = axios.get(`${getAppRoot()}api/datatypes?extension_only=false`);
-        const datatypeEDAMFormatsPromise = axios.get(`${getAppRoot()}api/datatypes/edam_formats?id_only=false`);
-        const datatypeEDAMDataPromise = axios.get(`${getAppRoot()}api/datatypes/edam_data?id_only=false`);
+        try {
+            const datatypesPromise = axios.get(`${getAppRoot()}api/datatypes?extension_only=false`);
+            const datatypeEDAMFormatsPromise = axios.get(`${getAppRoot()}api/datatypes/edam_formats?id_only=false`);
+            const datatypeEDAMDataPromise = axios.get(`${getAppRoot()}api/datatypes/edam_data?id_only=false`);
 
-        const [baseTypes, datatypeEDAMFormats, datatypeEDAMData] = await Promise.all([
-            datatypesPromise,
-            datatypeEDAMFormatsPromise,
-            datatypeEDAMDataPromise,
-        ]);
+            const [baseTypes, datatypeEDAMFormats, datatypeEDAMData] = await Promise.all([
+                datatypesPromise,
+                datatypeEDAMFormatsPromise,
+                datatypeEDAMDataPromise,
+            ]);
 
-        datatypes.value = baseTypes.data.map((type, i) => {
-            const typeEDAMFormat = datatypeEDAMFormats.data[type.extension] ?? null;
-            const typeEDAMData = datatypeEDAMData.data[type.extension] ?? null;
+            datatypes.value = baseTypes.data.map((type, i) => {
+                const typeEDAMFormat = datatypeEDAMFormats.data[type.extension] ?? null;
+                const typeEDAMData = datatypeEDAMData.data[type.extension] ?? null;
 
-            return {
-                extension: type.extension,
-                description: type.description,
-                edamFormat: typeEDAMFormat.prefix_IRI,
-                edamFormatLabel: typeEDAMFormat.label,
-                edamFormatDefinition: typeEDAMFormat.definition,
-                edamData: typeEDAMData.prefix_IRI,
-                edamDataLabel: typeEDAMData.label,
-                edamDataDefinition: typeEDAMData.definition,
-            };
-        });
-
-        datatypesLoading.value = false;
+                return {
+                    extension: type.extension,
+                    description: type.description,
+                    edamFormat: typeEDAMFormat.prefix_IRI,
+                    edamFormatLabel: typeEDAMFormat.label,
+                    edamFormatDefinition: typeEDAMFormat.definition,
+                    edamData: typeEDAMData.prefix_IRI,
+                    edamDataLabel: typeEDAMData.label,
+                    edamDataDefinition: typeEDAMData.definition,
+                };
+            });
+        } catch (e) {
+            console.error("unable to fetch available datatypes\n", e);
+        } finally {
+            datatypesLoading.value = false;
+        }
     }
 
-    try {
-        getDatatypes();
-    } catch (e) {
-        console.error("unable to fetch available datatypes\n", e);
-    }
+    getDatatypes();
 
     return { datatypes, datatypesLoading };
 }
diff --git a/client/src/composables/filter.js b/client/src/composables/utils/filter.js
similarity index 65%
rename from client/src/composables/filter.js
rename to client/src/composables/utils/filter.js
index 4af74f49e1b..9cc90750eb0 100644
--- a/client/src/composables/filter.js
+++ b/client/src/composables/utils/filter.js
@@ -1,11 +1,15 @@
 import { computed, unref } from "vue";
 
 /**
- * Filter array of objects, by comparing `filter` to all `fields`
+ * Reactively filter an array of objects, by comparing `filter` to all `fields`.
+ * All parameters can optionally be refs.
+ * @param array array of objects to filter
+ * @param filter string to filter by
+ * @param objectFields string array of fields to filter by on each object
  */
 export function useFilterObjectArray(array, filter, objectFields) {
     const filtered = computed(() => {
-        const f = unref(filter);
+        const f = unref(filter).toLowerCase();
         const arr = unref(array);
         const fields = unref(objectFields);
 

From 6ee735b31e835a877cbad4d1e9ec74010c04fe28 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Thu, 18 Aug 2022 09:51:31 +0200
Subject: [PATCH 14/26] make rows sortable add history filter hint

---
 client/src/components/AvailableDatatypes.vue | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/client/src/components/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes.vue
index dc1ea0aed2b..5cd55e3f101 100644
--- a/client/src/components/AvailableDatatypes.vue
+++ b/client/src/components/AvailableDatatypes.vue
@@ -13,14 +13,17 @@ const filteredDatatypes = useFilterObjectArray(datatypes, filter, filterFields);
 const fields = [
     {
         key: "extension",
+        sortable: true,
     },
     {
         key: "edamFormatLabel",
         label: "EDAM Format",
+        sortable: true,
     },
     {
         key: "edamDataLabel",
         label: "EDAM Data",
+        sortable: true,
     },
 ];
 
@@ -30,9 +33,12 @@ const edamLink = (edamIRI) => `https://edamontology.github.io/edam-browser/#${ed
 <template>
     <div>
         <h1>Datatypes</h1>
-        <p>All Datatypes supported by this Galaxy instance. Hover over an item for more information.</p>
+        <p>
+            All Datatypes supported by this Galaxy instance. Hover over an item for more information. These extensions
+            can be filtered by in the History, by expanding "search datasets".
+        </p>
         <DelayedInput placeholder="filter extensions" class="mb-3" :delay="200" @change="(val) => (filter = val)" />
-        <b-table striped small :items="filteredDatatypes" :fields="fields">
+        <b-table striped small sort-icon-left :items="filteredDatatypes" :fields="fields">
             <template v-slot:cell(extension)="row">
                 <span v-b-tooltip.hover :title="row.item.description">
                     {{ row.item.extension }}

From 113c45961b588f8de7bb3b93a04fd1dfb9079a8f Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 12:19:46 +0200
Subject: [PATCH 15/26] remove sleep from tests

---
 lib/galaxy_test/api/test_datatypes.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/lib/galaxy_test/api/test_datatypes.py b/lib/galaxy_test/api/test_datatypes.py
index 84886e2bb0b..09e9f34fb91 100644
--- a/lib/galaxy_test/api/test_datatypes.py
+++ b/lib/galaxy_test/api/test_datatypes.py
@@ -89,8 +89,6 @@ class DatatypesApiTestCase(ApiTestCase):
         edam_formats = response.json()
         assert isinstance(edam_formats, dict)
         assert edam_formats["ab1"] == "format_3000"
-        time.sleep(2)
-
         response = self._get("datatypes/edam_formats?id_only=false")
         self._assert_status_code_is(response, 200)
         edam_formats = response.json()
@@ -105,8 +103,6 @@ class DatatypesApiTestCase(ApiTestCase):
         edam_data = response.json()
         assert isinstance(edam_data, dict)
         assert edam_data["ab1"] == "data_0924"
-        time.sleep(2)
-
         response = self._get("datatypes/edam_data?id_only=false")
         edam_data = response.json()
         assert isinstance(edam_data, dict)

From fab5c5fd699d096872a72c4c87ad24026bcb6206 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 12:19:59 +0200
Subject: [PATCH 16/26] sort extension by default

---
 client/src/components/AvailableDatatypes.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes.vue
index 5cd55e3f101..a8dcfb7bba5 100644
--- a/client/src/components/AvailableDatatypes.vue
+++ b/client/src/components/AvailableDatatypes.vue
@@ -38,7 +38,7 @@ const edamLink = (edamIRI) => `https://edamontology.github.io/edam-browser/#${ed
             can be filtered by in the History, by expanding "search datasets".
         </p>
         <DelayedInput placeholder="filter extensions" class="mb-3" :delay="200" @change="(val) => (filter = val)" />
-        <b-table striped small sort-icon-left :items="filteredDatatypes" :fields="fields">
+        <b-table striped small sort-icon-left sort-by="extension" :items="filteredDatatypes" :fields="fields">
             <template v-slot:cell(extension)="row">
                 <span v-b-tooltip.hover :title="row.item.description">
                     {{ row.item.extension }}

From 976ca36b345684668bb7e161d595891fcdd93277 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 13:18:53 +0200
Subject: [PATCH 17/26] load edam ontology only once

---
 lib/galaxy/datatypes/registry.py           |  2 ++
 lib/galaxy/tool_util/toolbox/base.py       |  2 +-
 lib/galaxy/tool_util/toolbox/views/edam.py | 13 +++----------
 3 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 689c5642dec..c7431d846d2 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -53,6 +53,8 @@ class Registry:
             None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,
             "format_",
             "data_",
+            "operation_",
+            "topic_",
         )
 
         self.log = logging.getLogger(__name__)
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index d606a493cdf..0ac52890acd 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -193,7 +193,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
 
         for edam_view in listify(self.app.config.edam_panel_views):
             mode = EdamPanelMode[edam_view]
-            tool_panel_views_list.append(EdamToolPanelView(self.app.config.edam_toolbox_ontology_path, mode=mode))
+            tool_panel_views_list.append(EdamToolPanelView(self.app.datatypes_registry, mode=mode))
 
         if view_sources is not None:
             for definition in view_sources.get_definitions():
diff --git a/lib/galaxy/tool_util/toolbox/views/edam.py b/lib/galaxy/tool_util/toolbox/views/edam.py
index 8049e07a0f0..ae3eccdf3f7 100644
--- a/lib/galaxy/tool_util/toolbox/views/edam.py
+++ b/lib/galaxy/tool_util/toolbox/views/edam.py
@@ -1,15 +1,13 @@
 import logging
-import os
 from enum import Enum
 from typing import (
     Dict,
     List,
-    Optional,
     Tuple,
 )
+from galaxy.datatypes.registry import Registry
 
 from galaxy.tool_util.edam_util import (
-    load_edam_tree,
     ROOT_OPERATION,
     ROOT_TOPIC,
 )
@@ -36,13 +34,8 @@ class EdamPanelMode(str, Enum):
 
 
 class EdamToolPanelView(ToolPanelView):
-    def __init__(self, edam_ontology_path: Optional[str], mode: EdamPanelMode = EdamPanelMode.merged):
-        edam = load_edam_tree(
-            None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path,
-            "operation_",
-            "topic_",
-        )
-        self.edam = edam
+    def __init__(self, datatypes_registry: Registry, mode: EdamPanelMode = EdamPanelMode.merged):
+        self.edam = datatypes_registry.edam
         self.mode = mode
         self.include_topics = mode in [EdamPanelMode.merged, EdamPanelMode.topics]
         self.include_operations = mode in [EdamPanelMode.merged, EdamPanelMode.operations]

From 3e5c726ecbbffa0200163df8cbcaffa7226834dd Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 13:19:32 +0200
Subject: [PATCH 18/26] make datatypes manager functions async

---
 lib/galaxy/managers/datatypes.py           | 20 ++++++++++----------
 lib/galaxy/webapps/galaxy/api/datatypes.py | 16 ++++++++--------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index bb962439a62..fc199ed9d35 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -18,7 +18,7 @@ from galaxy.datatypes.data import Data
 from galaxy.datatypes.registry import Registry
 
 
-def view_index(
+async def view_index(
     datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
 ) -> Union[List[DatatypeDetails], List[str]]:
     if extension_only:
@@ -35,7 +35,7 @@ def view_index(
         return rval
 
 
-def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
+async def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
     ext_to_class_name: Dict[str, str] = {}
     classes = []
     for k, v in datatypes_registry.datatypes_by_extension.items():
@@ -58,7 +58,7 @@ def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
     return DatatypesMap(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
 
 
-def view_types_and_mapping(
+async def view_types_and_mapping(
     datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
 ) -> DatatypesCombinedMap:
     return DatatypesCombinedMap(
@@ -67,7 +67,7 @@ def view_types_and_mapping(
     )
 
 
-def view_sniffers(datatypes_registry: Registry) -> List[str]:
+async def view_sniffers(datatypes_registry: Registry) -> List[str]:
     rval: List[str] = []
     for sniffer_elem in datatypes_registry.sniffer_elems:
         datatype = sniffer_elem.get("type")
@@ -76,7 +76,7 @@ def view_sniffers(datatypes_registry: Registry) -> List[str]:
     return rval
 
 
-def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
+async def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     converters = []
     for (source_type, targets) in datatypes_registry.datatype_converters.items():
         for target_type in targets:
@@ -90,7 +90,7 @@ def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     return parse_obj_as(DatatypeConverterList, converters)
 
 
-def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
+async def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
     details_dict = {}
     for (format, edam_iri) in edam_ids.items():
         edam_details = datatypes_registry.edam.get(edam_iri, {})
@@ -104,22 +104,22 @@ def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
     return details_dict
 
 
-def view_edam_formats(
+async def view_edam_formats(
     datatypes_registry: Registry, id_only: Optional[bool] = True
 ) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_formats
     else:
-        return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
+        return await _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
 
 
-def view_edam_data(
+async def view_edam_data(
     datatypes_registry: Registry, id_only: Optional[bool] = True
 ) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_data
     else:
-        return _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
+        return await _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
 
 
 __all__ = (
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index dec29010bd2..bba28b26afe 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -68,7 +68,7 @@ class FastAPIDatatypes:
         upload_only: Optional[bool] = UploadOnlyQueryParam,
     ) -> Union[List[DatatypeDetails], List[str]]:
         """Gets the list of all available data types."""
-        return view_index(self.datatypes_registry, extension_only, upload_only)
+        return await view_index(self.datatypes_registry, extension_only, upload_only)
 
     @router.get(
         "/api/datatypes/mapping",
@@ -77,7 +77,7 @@ class FastAPIDatatypes:
     )
     async def mapping(self) -> DatatypesMap:
         """Gets mappings for data types."""
-        return view_mapping(self.datatypes_registry)
+        return await view_mapping(self.datatypes_registry)
 
     @router.get(
         "/api/datatypes/types_and_mapping",
@@ -93,8 +93,8 @@ class FastAPIDatatypes:
         mapping information from (/api/datatypes/mapping) into a single
         response."""
         return DatatypesCombinedMap(
-            datatypes=view_index(self.datatypes_registry, extension_only, upload_only),
-            datatypes_mapping=view_mapping(self.datatypes_registry),
+            datatypes=await view_index(self.datatypes_registry, extension_only, upload_only),
+            datatypes_mapping=await view_mapping(self.datatypes_registry),
         )
 
     @router.get(
@@ -104,7 +104,7 @@ class FastAPIDatatypes:
     )
     async def sniffers(self) -> List[str]:
         """Gets the list of all installed data type sniffers."""
-        return view_sniffers(self.datatypes_registry)
+        return await view_sniffers(self.datatypes_registry)
 
     @router.get(
         "/api/datatypes/converters",
@@ -113,7 +113,7 @@ class FastAPIDatatypes:
     )
     async def converters(self) -> DatatypeConverterList:
         """Gets the list of all installed converters."""
-        return view_converters(self.datatypes_registry)
+        return await view_converters(self.datatypes_registry)
 
     @router.get(
         "/api/datatypes/edam_formats",
@@ -125,7 +125,7 @@ class FastAPIDatatypes:
         id_only: Optional[bool] = IdentifierOnly,
     ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
-        return view_edam_formats(self.datatypes_registry, id_only)
+        return await view_edam_formats(self.datatypes_registry, id_only)
 
     @router.get(
         "/api/datatypes/edam_data",
@@ -137,4 +137,4 @@ class FastAPIDatatypes:
         id_only: Optional[bool] = IdentifierOnly,
     ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM data."""
-        return view_edam_data(self.datatypes_registry, id_only)
+        return await view_edam_data(self.datatypes_registry, id_only)

From b137efb23af7afddaaec6349ef67c96eba5f6538 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 13:32:08 +0200
Subject: [PATCH 19/26] format imports

---
 lib/galaxy/tool_util/toolbox/views/edam.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/toolbox/views/edam.py b/lib/galaxy/tool_util/toolbox/views/edam.py
index ae3eccdf3f7..0f5a7b25005 100644
--- a/lib/galaxy/tool_util/toolbox/views/edam.py
+++ b/lib/galaxy/tool_util/toolbox/views/edam.py
@@ -5,8 +5,8 @@ from typing import (
     List,
     Tuple,
 )
-from galaxy.datatypes.registry import Registry
 
+from galaxy.datatypes.registry import Registry
 from galaxy.tool_util.edam_util import (
     ROOT_OPERATION,
     ROOT_TOPIC,

From 3d1325c2de6d0829b29a9fb5fa258a65d4af853c Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 15:23:17 +0200
Subject: [PATCH 20/26] remove async

---
 lib/galaxy/managers/datatypes.py           | 20 ++++++++++----------
 lib/galaxy/webapps/galaxy/api/datatypes.py | 16 ++++++++--------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index fc199ed9d35..bb962439a62 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -18,7 +18,7 @@ from galaxy.datatypes.data import Data
 from galaxy.datatypes.registry import Registry
 
 
-async def view_index(
+def view_index(
     datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
 ) -> Union[List[DatatypeDetails], List[str]]:
     if extension_only:
@@ -35,7 +35,7 @@ async def view_index(
         return rval
 
 
-async def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
+def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
     ext_to_class_name: Dict[str, str] = {}
     classes = []
     for k, v in datatypes_registry.datatypes_by_extension.items():
@@ -58,7 +58,7 @@ async def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
     return DatatypesMap(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
 
 
-async def view_types_and_mapping(
+def view_types_and_mapping(
     datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
 ) -> DatatypesCombinedMap:
     return DatatypesCombinedMap(
@@ -67,7 +67,7 @@ async def view_types_and_mapping(
     )
 
 
-async def view_sniffers(datatypes_registry: Registry) -> List[str]:
+def view_sniffers(datatypes_registry: Registry) -> List[str]:
     rval: List[str] = []
     for sniffer_elem in datatypes_registry.sniffer_elems:
         datatype = sniffer_elem.get("type")
@@ -76,7 +76,7 @@ async def view_sniffers(datatypes_registry: Registry) -> List[str]:
     return rval
 
 
-async def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
+def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     converters = []
     for (source_type, targets) in datatypes_registry.datatype_converters.items():
         for target_type in targets:
@@ -90,7 +90,7 @@ async def view_converters(datatypes_registry: Registry) -> DatatypeConverterList
     return parse_obj_as(DatatypeConverterList, converters)
 
 
-async def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
+def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
     details_dict = {}
     for (format, edam_iri) in edam_ids.items():
         edam_details = datatypes_registry.edam.get(edam_iri, {})
@@ -104,22 +104,22 @@ async def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, st
     return details_dict
 
 
-async def view_edam_formats(
+def view_edam_formats(
     datatypes_registry: Registry, id_only: Optional[bool] = True
 ) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_formats
     else:
-        return await _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
+        return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
 
 
-async def view_edam_data(
+def view_edam_data(
     datatypes_registry: Registry, id_only: Optional[bool] = True
 ) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
     if id_only:
         return datatypes_registry.edam_data
     else:
-        return await _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
+        return _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
 
 
 __all__ = (
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index bba28b26afe..dec29010bd2 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -68,7 +68,7 @@ class FastAPIDatatypes:
         upload_only: Optional[bool] = UploadOnlyQueryParam,
     ) -> Union[List[DatatypeDetails], List[str]]:
         """Gets the list of all available data types."""
-        return await view_index(self.datatypes_registry, extension_only, upload_only)
+        return view_index(self.datatypes_registry, extension_only, upload_only)
 
     @router.get(
         "/api/datatypes/mapping",
@@ -77,7 +77,7 @@ class FastAPIDatatypes:
     )
     async def mapping(self) -> DatatypesMap:
         """Gets mappings for data types."""
-        return await view_mapping(self.datatypes_registry)
+        return view_mapping(self.datatypes_registry)
 
     @router.get(
         "/api/datatypes/types_and_mapping",
@@ -93,8 +93,8 @@ class FastAPIDatatypes:
         mapping information from (/api/datatypes/mapping) into a single
         response."""
         return DatatypesCombinedMap(
-            datatypes=await view_index(self.datatypes_registry, extension_only, upload_only),
-            datatypes_mapping=await view_mapping(self.datatypes_registry),
+            datatypes=view_index(self.datatypes_registry, extension_only, upload_only),
+            datatypes_mapping=view_mapping(self.datatypes_registry),
         )
 
     @router.get(
@@ -104,7 +104,7 @@ class FastAPIDatatypes:
     )
     async def sniffers(self) -> List[str]:
         """Gets the list of all installed data type sniffers."""
-        return await view_sniffers(self.datatypes_registry)
+        return view_sniffers(self.datatypes_registry)
 
     @router.get(
         "/api/datatypes/converters",
@@ -113,7 +113,7 @@ class FastAPIDatatypes:
     )
     async def converters(self) -> DatatypeConverterList:
         """Gets the list of all installed converters."""
-        return await view_converters(self.datatypes_registry)
+        return view_converters(self.datatypes_registry)
 
     @router.get(
         "/api/datatypes/edam_formats",
@@ -125,7 +125,7 @@ class FastAPIDatatypes:
         id_only: Optional[bool] = IdentifierOnly,
     ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
-        return await view_edam_formats(self.datatypes_registry, id_only)
+        return view_edam_formats(self.datatypes_registry, id_only)
 
     @router.get(
         "/api/datatypes/edam_data",
@@ -137,4 +137,4 @@ class FastAPIDatatypes:
         id_only: Optional[bool] = IdentifierOnly,
     ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
         """Gets a map of datatypes and their corresponding EDAM data."""
-        return await view_edam_data(self.datatypes_registry, id_only)
+        return view_edam_data(self.datatypes_registry, id_only)

From 8cbc5978a777c625c2741982910b57eac10d40b3 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 15:23:42 +0200
Subject: [PATCH 21/26] pass edam to EdamToolPanelView directly

---
 lib/galaxy/tool_util/toolbox/base.py       | 2 +-
 lib/galaxy/tool_util/toolbox/views/edam.py | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 0ac52890acd..ee9af7eed53 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -193,7 +193,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
 
         for edam_view in listify(self.app.config.edam_panel_views):
             mode = EdamPanelMode[edam_view]
-            tool_panel_views_list.append(EdamToolPanelView(self.app.datatypes_registry, mode=mode))
+            tool_panel_views_list.append(EdamToolPanelView(self.app.datatypes_registry.edam, mode=mode))
 
         if view_sources is not None:
             for definition in view_sources.get_definitions():
diff --git a/lib/galaxy/tool_util/toolbox/views/edam.py b/lib/galaxy/tool_util/toolbox/views/edam.py
index 0f5a7b25005..0df472e592f 100644
--- a/lib/galaxy/tool_util/toolbox/views/edam.py
+++ b/lib/galaxy/tool_util/toolbox/views/edam.py
@@ -6,7 +6,6 @@ from typing import (
     Tuple,
 )
 
-from galaxy.datatypes.registry import Registry
 from galaxy.tool_util.edam_util import (
     ROOT_OPERATION,
     ROOT_TOPIC,
@@ -34,8 +33,8 @@ class EdamPanelMode(str, Enum):
 
 
 class EdamToolPanelView(ToolPanelView):
-    def __init__(self, datatypes_registry: Registry, mode: EdamPanelMode = EdamPanelMode.merged):
-        self.edam = datatypes_registry.edam
+    def __init__(self, edam: Dict[str, Dict], mode: EdamPanelMode = EdamPanelMode.merged):
+        self.edam = edam
         self.mode = mode
         self.include_topics = mode in [EdamPanelMode.merged, EdamPanelMode.topics]
         self.include_operations = mode in [EdamPanelMode.merged, EdamPanelMode.operations]

From 1d34d6eb9220f8497fa9aff4916bb72db250af38 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 24 Aug 2022 16:25:06 +0200
Subject: [PATCH 22/26] move detailed datatypes api to separate route

---
 client/src/composables/datatypes.js        |  4 +--
 lib/galaxy/managers/datatypes.py           | 16 +++++-----
 lib/galaxy/webapps/galaxy/api/datatypes.py | 34 +++++++++++++++-------
 3 files changed, 34 insertions(+), 20 deletions(-)

diff --git a/client/src/composables/datatypes.js b/client/src/composables/datatypes.js
index d83459aec68..e9b71b467bd 100644
--- a/client/src/composables/datatypes.js
+++ b/client/src/composables/datatypes.js
@@ -13,8 +13,8 @@ export function useDetailedDatatypes() {
     async function getDatatypes() {
         try {
             const datatypesPromise = axios.get(`${getAppRoot()}api/datatypes?extension_only=false`);
-            const datatypeEDAMFormatsPromise = axios.get(`${getAppRoot()}api/datatypes/edam_formats?id_only=false`);
-            const datatypeEDAMDataPromise = axios.get(`${getAppRoot()}api/datatypes/edam_data?id_only=false`);
+            const datatypeEDAMFormatsPromise = axios.get(`${getAppRoot()}api/datatypes/edam_formats/detailed`);
+            const datatypeEDAMDataPromise = axios.get(`${getAppRoot()}api/datatypes/edam_data/detailed`);
 
             const [baseTypes, datatypeEDAMFormats, datatypeEDAMData] = await Promise.all([
                 datatypesPromise,
diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index bb962439a62..1b9964bc475 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -105,21 +105,21 @@ def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
 
 
 def view_edam_formats(
-    datatypes_registry: Registry, id_only: Optional[bool] = True
+    datatypes_registry: Registry, detailed: Optional[bool] = False
 ) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
-    if id_only:
-        return datatypes_registry.edam_formats
-    else:
+    if detailed:
         return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
+    else:
+        return datatypes_registry.edam_formats
 
 
 def view_edam_data(
-    datatypes_registry: Registry, id_only: Optional[bool] = True
+    datatypes_registry: Registry, detailed: Optional[bool] = False
 ) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
-    if id_only:
-        return datatypes_registry.edam_data
-    else:
+    if detailed:
         return _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
+    else:
+        return datatypes_registry.edam_data
 
 
 __all__ = (
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index dec29010bd2..9c50254d216 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -120,21 +120,35 @@ class FastAPIDatatypes:
         summary="Returns a dictionary/map of datatypes and EDAM formats",
         response_description="Dictionary/map of datatypes and EDAM formats",
     )
-    async def edam_formats(
-        self,
-        id_only: Optional[bool] = IdentifierOnly,
-    ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
+    async def edam_formats(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
-        return view_edam_formats(self.datatypes_registry, id_only)
+        return view_edam_formats(self.datatypes_registry)
+
+    @router.get(
+        "/api/datatypes/edam_formats/detailed",
+        summary="Returns a dictionary of datatypes and EDAM format details",
+        response_description="Dictionary of EDAM format details containing the EDAM iri, label, and definition",
+    )
+    async def edam_formats_detailed(self) -> DatatypesEDAMDetailsDict:
+        """Gets a map of datatypes and their corresponding EDAM formats.
+        EDAM formats contain the EDAM iri, label, and definition."""
+        return view_edam_formats(self.datatypes_registry, True)
 
     @router.get(
         "/api/datatypes/edam_data",
         summary="Returns a dictionary/map of datatypes and EDAM data",
         response_description="Dictionary/map of datatypes and EDAM data",
     )
-    async def edam_data(
-        self,
-        id_only: Optional[bool] = IdentifierOnly,
-    ) -> Union[DatatypesEDAMDetailsDict, Dict[str, str]]:
+    async def edam_data(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM data."""
-        return view_edam_data(self.datatypes_registry, id_only)
+        return view_edam_data(self.datatypes_registry)
+
+    @router.get(
+        "/api/datatypes/edam_data/detailed",
+        summary="Returns a dictionary of datatypes and EDAM data details",
+        response_description="Dictionary of EDAM data details containing the EDAM iri, label, and definition",
+    )
+    async def edam_data_detailed(self) -> DatatypesEDAMDetailsDict:
+        """Gets a map of datatypes and their corresponding EDAM data.
+        EDAM data contains the EDAM iri, label, and definition."""
+        return view_edam_data(self.datatypes_registry, True)

From d2163273c52567e5e2cf699c38fbf8af426bad2a Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Thu, 25 Aug 2022 16:26:28 +0200
Subject: [PATCH 23/26] update tests

---
 lib/galaxy_test/api/test_datatypes.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/api/test_datatypes.py b/lib/galaxy_test/api/test_datatypes.py
index 09e9f34fb91..37be3e06a3b 100644
--- a/lib/galaxy_test/api/test_datatypes.py
+++ b/lib/galaxy_test/api/test_datatypes.py
@@ -89,7 +89,7 @@ class DatatypesApiTestCase(ApiTestCase):
         edam_formats = response.json()
         assert isinstance(edam_formats, dict)
         assert edam_formats["ab1"] == "format_3000"
-        response = self._get("datatypes/edam_formats?id_only=false")
+        response = self._get("datatypes/edam_formats/detailed")
         self._assert_status_code_is(response, 200)
         edam_formats = response.json()
         assert isinstance(edam_formats, dict)
@@ -103,7 +103,7 @@ class DatatypesApiTestCase(ApiTestCase):
         edam_data = response.json()
         assert isinstance(edam_data, dict)
         assert edam_data["ab1"] == "data_0924"
-        response = self._get("datatypes/edam_data?id_only=false")
+        response = self._get("datatypes/edam_data/detailed")
         edam_data = response.json()
         assert isinstance(edam_data, dict)
         assert isinstance(edam_data["afg"], dict)

From d76d34529847a142fe76ea7cd01a0c8610b1fba1 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 29 Aug 2022 12:00:18 +0200
Subject: [PATCH 24/26] fix wrong type annotations

---
 lib/galaxy/managers/datatypes.py           |  6 +++---
 lib/galaxy/webapps/galaxy/api/datatypes.py | 11 +++++++----
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index 1b9964bc475..8ed5d033edc 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -90,7 +90,7 @@ def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     return parse_obj_as(DatatypeConverterList, converters)
 
 
-def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
+def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]) -> Dict[str, Dict]:
     details_dict = {}
     for (format, edam_iri) in edam_ids.items():
         edam_details = datatypes_registry.edam.get(edam_iri, {})
@@ -106,7 +106,7 @@ def _get_edam_details(datatypes_registry: Registry, edam_ids: Dict[str, str]):
 
 def view_edam_formats(
     datatypes_registry: Registry, detailed: Optional[bool] = False
-) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
+) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
     if detailed:
         return _get_edam_details(datatypes_registry, datatypes_registry.edam_formats)
     else:
@@ -115,7 +115,7 @@ def view_edam_formats(
 
 def view_edam_data(
     datatypes_registry: Registry, detailed: Optional[bool] = False
-) -> Union[Dict[str, str], DatatypesEDAMDetailsDict]:
+) -> Union[Dict[str, str], Dict[str, Dict[str, str]]]:
     if detailed:
         return _get_edam_details(datatypes_registry, datatypes_registry.edam_data)
     else:
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index 9c50254d216..7a35bc4b0a6 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -3,6 +3,7 @@ API operations allowing clients to determine datatype supported by Galaxy.
 """
 import logging
 from typing import (
+    cast,
     Dict,
     List,
     Optional,
@@ -122,14 +123,15 @@ class FastAPIDatatypes:
     )
     async def edam_formats(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
-        return view_edam_formats(self.datatypes_registry)
+        return cast(Dict[str, str], view_edam_formats(self.datatypes_registry))
 
     @router.get(
         "/api/datatypes/edam_formats/detailed",
         summary="Returns a dictionary of datatypes and EDAM format details",
         response_description="Dictionary of EDAM format details containing the EDAM iri, label, and definition",
+        response_model=DatatypesEDAMDetailsDict,
     )
-    async def edam_formats_detailed(self) -> DatatypesEDAMDetailsDict:
+    async def edam_formats_detailed(self):
         """Gets a map of datatypes and their corresponding EDAM formats.
         EDAM formats contain the EDAM iri, label, and definition."""
         return view_edam_formats(self.datatypes_registry, True)
@@ -141,14 +143,15 @@ class FastAPIDatatypes:
     )
     async def edam_data(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM data."""
-        return view_edam_data(self.datatypes_registry)
+        return cast(Dict[str, str], view_edam_data(self.datatypes_registry))
 
     @router.get(
         "/api/datatypes/edam_data/detailed",
         summary="Returns a dictionary of datatypes and EDAM data details",
         response_description="Dictionary of EDAM data details containing the EDAM iri, label, and definition",
+        response_model=DatatypesEDAMDetailsDict,
     )
-    async def edam_data_detailed(self) -> DatatypesEDAMDetailsDict:
+    async def edam_data_detailed(self):
         """Gets a map of datatypes and their corresponding EDAM data.
         EDAM data contains the EDAM iri, label, and definition."""
         return view_edam_data(self.datatypes_registry, True)

From 7cab02a3341cb41fee4da0153a5cc7b22906f2fe Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 29 Aug 2022 16:48:52 +0200
Subject: [PATCH 25/26] add link to description url

---
 client/src/components/AvailableDatatypes.vue | 10 +++++++++-
 client/src/composables/datatypes.js          |  1 +
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/client/src/components/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes.vue
index a8dcfb7bba5..7724806a42a 100644
--- a/client/src/components/AvailableDatatypes.vue
+++ b/client/src/components/AvailableDatatypes.vue
@@ -40,7 +40,15 @@ const edamLink = (edamIRI) => `https://edamontology.github.io/edam-browser/#${ed
         <DelayedInput placeholder="filter extensions" class="mb-3" :delay="200" @change="(val) => (filter = val)" />
         <b-table striped small sort-icon-left sort-by="extension" :items="filteredDatatypes" :fields="fields">
             <template v-slot:cell(extension)="row">
-                <span v-b-tooltip.hover :title="row.item.description">
+                <a
+                    v-if="row.item.descriptionUrl"
+                    v-b-tooltip.hover
+                    target="_blank"
+                    :title="row.item.description"
+                    :href="row.item.descriptionUrl">
+                    {{ row.item.extension }}
+                </a>
+                <span v-else v-b-tooltip.hover :title="row.item.description">
                     {{ row.item.extension }}
                 </span>
             </template>
diff --git a/client/src/composables/datatypes.js b/client/src/composables/datatypes.js
index e9b71b467bd..15aa61ce8cd 100644
--- a/client/src/composables/datatypes.js
+++ b/client/src/composables/datatypes.js
@@ -29,6 +29,7 @@ export function useDetailedDatatypes() {
                 return {
                     extension: type.extension,
                     description: type.description,
+                    descriptionUrl: type.description_url,
                     edamFormat: typeEDAMFormat.prefix_IRI,
                     edamFormatLabel: typeEDAMFormat.label,
                     edamFormatDefinition: typeEDAMFormat.definition,

From 5f7a422f28374b1dfa8831155f623e738dadcf6f Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 31 Aug 2022 10:51:22 +0200
Subject: [PATCH 26/26] move AvailableDatatypes to subfolder

---
 .../components/{ => AvailableDatatypes}/AvailableDatatypes.vue  | 0
 client/src/entry/analysis/router.js                             | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename client/src/components/{ => AvailableDatatypes}/AvailableDatatypes.vue (100%)

diff --git a/client/src/components/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes/AvailableDatatypes.vue
similarity index 100%
rename from client/src/components/AvailableDatatypes.vue
rename to client/src/components/AvailableDatatypes/AvailableDatatypes.vue
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 03714392483..987ba1ee0f8 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -22,7 +22,7 @@ import DatasetAttributes from "components/DatasetInformation/DatasetAttributes";
 import DatasetDetails from "components/DatasetInformation/DatasetDetails";
 import DatasetError from "components/DatasetInformation/DatasetError";
 import DatasetList from "components/Dataset/DatasetList";
-import AvailableDatatypes from "components/AvailableDatatypes";
+import AvailableDatatypes from "components/AvailableDatatypes/AvailableDatatypes";
 import DisplayStructured from "components/DisplayStructured";
 import FormGeneric from "components/Form/FormGeneric";
 import Grid from "components/Grid/Grid";