Ontologies (#1110)

* add sample ontologies file

* add ontologies reducer

* Move select category to own component

* Dialog and Input factored out

* refactoring categorical, partway

* validationn

* anno

* suggest  populates input

* frontend for ontology working

* initial implementation of back-end support for ontologies

* edit is now dialog again

* autosuggest working on edit

* part way through create arbitrary label

* handle choice in function

* pass duplicate cat  prop

* editing works

* update test to match new CLI params

* fix occupancy alignment

* edit category as dialogue

* secondary button

* remove stubbed out ontologies

* add label setting upon new label creation

* Update legal characters for labels (#1119)

* Allow any term in the ontology (bypass legal name check)

* Add hyphens and parens to legal characters in names

* improve performance for large ontologies

* correctly handle case where ontologies are disabled

* fix logic error in CLI

Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>

* PR cleanup 1

* lint

* validate user generated labels

* finish hooking up connected suggest component

* protect against undefined callbacks

* Fix illegal characters error message

* break out npm run commands

* fix error detection on label edit

Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>
Co-authored-by: Sidney Bell <sidneymbell@users.noreply.github.com>

server/cli/launch.py

@@ -15,6 +15,7 @@ from server.app.util.errors import ScanpyFileError
 from server.app.util.utils import custom_format_warning
 from server.utils.utils import find_available_port, is_port_available, sort_options
 from server.app.util.data_locator import DataLocator
+from server.app.util.ontology import load_obo, OntologyLoadFailure
 
 # anything bigger than this will generate a special message
 BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20  # 100MB
@@ -94,6 +95,18 @@ def common_args(func):
         help="Directory of where to save output annotations; filename will be specified in the application. "
         "Incompatible with --annotations-input-file.",
     )
+    @click.option(
+        "--experimental-annotations-ontology",
+        is_flag=True,
+        default=False,
+        show_default=True,
+        help="When creating annotations, optionally autocomplete names from ontology terms.",)
+    @click.option(
+        "--experimental-annotations-ontology-obo",
+        default=None,
+        show_default=True,
+        metavar="<path or url>",
+        help="Location of OBO file defining cell annotatoin autosuggest terms.",)
     @click.option(
         "--backed",
         "-b",
@@ -127,9 +140,15 @@ def parse_engine_args(
     experimental_annotations_output_dir,
     backed,
     disable_diffexp,
+    experimental_annotations_ontology,
+    experimental_annotations_ontology_obo
 ):
     annotations_file = experimental_annotations_file if experimental_annotations else None
     annotations_output_dir = experimental_annotations_output_dir if experimental_annotations else None
+    annotations_cell_ontology_enabled = experimental_annotations and (
+        experimental_annotations_ontology or bool(experimental_annotations_ontology_obo)
+    )
+    annotations_ontology_obopath = experimental_annotations_ontology_obo if annotations_cell_ontology_enabled else None
     return {
         "layout": embedding,
         "max_category_items": max_category_items,
@@ -139,6 +158,9 @@ def parse_engine_args(
         "annotations": experimental_annotations,
         "annotations_file": annotations_file,
         "annotations_output_dir": annotations_output_dir,
+        "annotations_cell_ontology_enabled": annotations_cell_ontology_enabled,
+        "annotations_cell_ontology_obopath": annotations_ontology_obopath,
+        "annotations_cell_ontology_terms": None,
         "backed": backed,
         "disable_diffexp": disable_diffexp,
     }
@@ -222,6 +244,8 @@ def launch(
     experimental_annotations_output_dir,
     backed,
     disable_diffexp,
+    experimental_annotations_ontology,
+    experimental_annotations_ontology_obo
 ):
     """Launch the cellxgene data viewer.
     This web app lets you explore single-cell expression data.
@@ -248,6 +272,8 @@ def launch(
         experimental_annotations_output_dir,
         backed,
         disable_diffexp,
+        experimental_annotations_ontology,
+        experimental_annotations_ontology_obo,
     )
     try:
         data_locator = DataLocator(data)
@@ -314,6 +340,10 @@ def launch(
             click.echo("Warning: --experimental-annotations-file ignored as --annotations not enabled.")
         if experimental_annotations_output_dir is not None:
             click.echo("Warning: --experimental-annotations-output-dir ignored as --annotations not enabled.")
+        if experimental_annotations_ontology:
+            click.echo("Warning: --experimental-annotations-ontology ignored as --annotations not enabled.")
+        if experimental_annotations_ontology_obo is not None:
+            click.echo("Warning: --experimental-annotations-ontology-obo ignored as --annotations not enabled.")
     else:
         if experimental_annotations_file is not None and experimental_annotations_output_dir is not None:
             raise click.ClickException(
@@ -333,6 +363,14 @@ def launch(
                     "Unable to create directory specified by " "--experimental-annotations-output-dir"
                 )
 
+        if e_args.get('annotations_cell_ontology_enabled', False):
+            try:
+                e_args['annotations_cell_ontology_terms'] = load_obo(
+                    e_args.get('annotations_cell_ontology_obopath', None)
+                )
+            except OntologyLoadFailure as e:
+                raise click.ClickException("Unable to load ontology terms\n" + str(e))
+
     if about:
 
         def url_check(url):