{datedCellLabel(focusedEpoch)}
{humanize(focusedEpoch.protocol_name?.split('.').at(-1)) || 'Protocol not recorded'} · Epoch {focusedEpoch.epoch_number ?? '—'} within block · {focusedEpoch.start_time?.split(/[T ]/)[1]?.slice(0,8) || 'Time not recorded'}
From 8050bcd93d75892e30ee85682d5ecad4194947ae Mon Sep 17 00:00:00 2001
From: arthurh <49833088+maxwellsdm1867@users.noreply.github.com>
Date: Tue, 29 Sep 2026 15:43:08 -0700
Subject: [PATCH 3/9] Share compact inclusion controls between epoch and tree
views
---
workspace-app/src/components/EpochInclusionToggle.css | 4 ++++
workspace-app/src/components/EpochInclusionToggle.jsx | 7 +++++++
workspace-app/src/components/HierarchyTree.css | 5 +----
workspace-app/src/components/HierarchyTree.jsx | 5 +++--
workspace-app/src/components/InspectionCellTree.css | 3 ---
workspace-app/src/components/InspectionCellTree.jsx | 4 ++--
6 files changed, 17 insertions(+), 11 deletions(-)
create mode 100644 workspace-app/src/components/EpochInclusionToggle.css
create mode 100644 workspace-app/src/components/EpochInclusionToggle.jsx
diff --git a/workspace-app/src/components/EpochInclusionToggle.css b/workspace-app/src/components/EpochInclusionToggle.css
new file mode 100644
index 0000000..3301e40
--- /dev/null
+++ b/workspace-app/src/components/EpochInclusionToggle.css
@@ -0,0 +1,4 @@
+.inspector button.epoch-inclusion-toggle{display:inline-flex;flex:0 0 23px;width:23px;min-height:23px;align-items:center;justify-content:center;gap:0;padding:3px;border:1px solid transparent;border-radius:4px;background:transparent;color:#397267}
+.inspector button.epoch-inclusion-toggle[aria-pressed=false]{color:#945541;background:#f8eee9}
+.inspector button.epoch-inclusion-toggle:hover{border-color:var(--border);background:var(--surface-subtle)}
+.inspector button.epoch-inclusion-toggle:focus-visible{outline:2px solid var(--accent);outline-offset:2px}
diff --git a/workspace-app/src/components/EpochInclusionToggle.jsx b/workspace-app/src/components/EpochInclusionToggle.jsx
new file mode 100644
index 0000000..8414678
--- /dev/null
+++ b/workspace-app/src/components/EpochInclusionToggle.jsx
@@ -0,0 +1,7 @@
+import {Check,X} from 'lucide-react';
+import './EpochInclusionToggle.css';
+
+export default function EpochInclusionToggle({epoch,label,onToggle,disabled=false,className=''}){
+ const included=epoch.curation?.included!==false;
+ return
;
+}
diff --git a/workspace-app/src/components/HierarchyTree.css b/workspace-app/src/components/HierarchyTree.css
index 2a5a33c..152d426 100644
--- a/workspace-app/src/components/HierarchyTree.css
+++ b/workspace-app/src/components/HierarchyTree.css
@@ -23,9 +23,6 @@
.ht-leaf{display:grid;grid-template-columns:minmax(0,1fr) auto auto;align-items:center;gap:4px}
.ht-leaf>button:first-child{min-width:0;flex-wrap:wrap}
.ht-leaf .annotation-row-pills{max-width:100%;flex-wrap:wrap}
-.ht-leaf>button.ht-tag-action,.ht-leaf>button.ht-inclusion-action{width:auto;min-height:28px;padding:5px 6px;gap:4px;justify-content:center;font-size:10px;white-space:nowrap}
+.ht-leaf>button.ht-tag-action{width:auto;min-height:28px;padding:5px 6px;gap:4px;justify-content:center;font-size:10px;white-space:nowrap}
.ht-leaf>button.ht-tag-action{color:var(--accent);border:1px solid var(--border)}
-.ht-leaf>button.ht-inclusion-action,.ht-inclusion-state{color:#467554;background:#edf5ef;border-radius:5px}
-.ht-leaf>button.ht-inclusion-action.excluded,.ht-inclusion-state.excluded{color:#9b6255;background:#faf0ec}
.ht-inclusion-state{font-size:10px;padding:5px}
-.ht-inclusion-action[aria-pressed=false]{text-decoration:none}
diff --git a/workspace-app/src/components/HierarchyTree.jsx b/workspace-app/src/components/HierarchyTree.jsx
index 359f9ab..246be46 100644
--- a/workspace-app/src/components/HierarchyTree.jsx
+++ b/workspace-app/src/components/HierarchyTree.jsx
@@ -1,6 +1,7 @@
+import EpochInclusionToggle from './EpochInclusionToggle.jsx';
import {revealWithin} from '../epochListScroll.js';
import {useCallback,useEffect,useRef,useState} from 'react';
-import {Check,X,Tag,Activity,ArrowLeft,ArrowRight,ChevronDown,ChevronRight,Folder,FolderOpen,LoaderCircle,RefreshCw} from 'lucide-react';
+import {Tag,Activity,ArrowLeft,ArrowRight,ChevronDown,ChevronRight,Folder,FolderOpen,LoaderCircle,RefreshCw} from 'lucide-react';
import {api,number,duration} from '../api.js';
import {treePageRequest} from '../pagedTreeRequest.js';
import {branchLabel,branchTooltip,componentLabel,componentValue,epochLeafLabel,readableField} from '../treeBranchPresentation.js';
@@ -98,7 +99,7 @@ export default function HierarchyTree(props){
const label=page.kind==='epochs'?'Epochs':readableField(field?.label,field?.field);
return
)}
{page.data&&
{page.data.total?offset+1:0}–{Math.min(offset+60,page.data.total)} of {number(page.data.total)}
}
;
From 7d49db259b964cf45b8d0f9893bb0c814ef19ba4 Mon Sep 17 00:00:00 2001
From: arthurh <49833088+maxwellsdm1867@users.noreply.github.com>
Date: Tue, 29 Sep 2026 15:46:05 -0700
Subject: [PATCH 4/9] Keep manually collapsed split-tree branches closed
---
workspace-app/src/components/HierarchyTree.jsx | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/workspace-app/src/components/HierarchyTree.jsx b/workspace-app/src/components/HierarchyTree.jsx
index 246be46..25dc9e7 100644
--- a/workspace-app/src/components/HierarchyTree.jsx
+++ b/workspace-app/src/components/HierarchyTree.jsx
@@ -79,15 +79,23 @@ export default function HierarchyTree(props){
},[state.pages,state.expanded,state.loading,state.error]);
useEffect(()=>{if(!state.loading&&focusScroll.current){const node=container.current?.querySelector(`[data-epoch-uuid="${focusScroll.current}"]`);if(node){revealWithin(scroll.current,node);focusScroll.current=null;}}},[selected,state.pages,state.loading]);
function toggle(branch){
- if(current.current.error)return;
+ if(current.current.error)return false;
const key=hierarchyKey(branch.path),opened=current.current.expanded.some(path=>hierarchyKey(path)===key);
if(opened){
+ revealSelected.current=null;focusScroll.current=null;
if(current.current.loadingPath&&pathContains(branch.path,current.current.loadingPath)){controller.current?.abort();serial.current++;callbacks.current.onStatus?.({loading:false,error:null});}
commit(old=>({...collapseHierarchy(old,branch.path),loading:old.loadingPath&&pathContains(branch.path,old.loadingPath)?false:old.loading,loadingPath:old.loadingPath&&pathContains(branch.path,old.loadingPath)?null:old.loadingPath}));
}else{
commit(old=>expandHierarchy(old,branch.path));
if(!current.current.pages.some(page=>hierarchyKey(page.path)===key))load({path:branch.path});
}
+ return !opened;
+ }
+ function collapseAll(){
+ controller.current?.abort();serial.current++;
+ revealSelected.current=null;focusScroll.current=null;
+ commit(old=>({...old,expanded:[],loading:false,loadingPath:null}));
+ callbacks.current.onStatus?.({loading:false,error:null});
}
function branchKeys(event,branch,opened){
if(event.key==='ArrowRight'){event.preventDefault();event.stopPropagation();if(!opened)toggle(branch);else event.currentTarget.closest('li')?.querySelector('ul button')?.focus({preventScroll:true});}
@@ -101,7 +109,7 @@ export default function HierarchyTree(props){
{entries.map((item,index)=>{
if(page.kind==='epochs')return
{props.onTagEpoch&&}{props.onToggleInclusion&&}{!props.onToggleInclusion&&{item.curation?.included===false?'Excluded':'Included'}};
const key=hierarchyKey(item.path),opened=state.expanded.some(path=>hierarchyKey(path)===key),children=state.pages.find(child=>hierarchyKey(child.path)===key),loading=state.loading&&hierarchyKey(state.loadingPath||[])===key;
- return
{opened&&(children?renderPage(children):{loading?'Loading branch…':'Branch is not loaded.'}
)};
+ return
{opened&&(children?renderPage(children):{loading?'Loading branch…':'Branch is not loaded.'}
)};
})}
{!entries.length&&
No matching epochs.}
{(page.offset>0||page.has_more)&&
{page.offset+1}–{page.offset+entries.length} / {number(page.total)}}
@@ -113,6 +121,6 @@ export default function HierarchyTree(props){
{state.error&&
{state.error}
}
{state.notice&&
{state.notice}
}
{if(!scrollFrame.current)scrollFrame.current=requestAnimationFrame(()=>{scrollFrame.current=null;remember();});}}>{root?renderPage(root,true):!state.error&&
Loading tree…
}
-
+
;
}
From 80c1db6839cc0becf1824285711df9a06133abb7 Mon Sep 17 00:00:00 2001
From: arthurh <49833088+maxwellsdm1867@users.noreply.github.com>
Date: Tue, 29 Sep 2026 16:00:32 -0700
Subject: [PATCH 5/9] Unify epoch views and add protocol-local multi-tag
filters
---
python/tests/test_workspace_annotations.py | 104 ++++++++++++++++++
python/workspace_api.py | 8 +-
python/workspace_service.py | 63 +++++++++--
workspace-app/src/App.jsx | 5 +-
.../src/components/EpochBrowserChrome.jsx | 8 +-
.../src/components/HierarchyTree.css | 33 +++++-
.../src/components/HierarchyTree.jsx | 7 +-
.../src/components/InspectionCellTree.css | 24 ++++
.../src/components/InspectionCellTree.jsx | 9 +-
workspace-app/src/components/Inspector.css | 4 +
workspace-app/src/components/Inspector.jsx | 13 ++-
.../src/components/ProtocolViewFilter.css | 20 ++++
.../src/components/ProtocolViewFilter.jsx | 15 +++
workspace-app/src/protocolViewFilter.js | 22 ++++
workspace-app/src/protocolViewFilter.test.js | 18 +++
15 files changed, 320 insertions(+), 33 deletions(-)
create mode 100644 workspace-app/src/components/ProtocolViewFilter.css
create mode 100644 workspace-app/src/components/ProtocolViewFilter.jsx
create mode 100644 workspace-app/src/protocolViewFilter.js
create mode 100644 workspace-app/src/protocolViewFilter.test.js
diff --git a/python/tests/test_workspace_annotations.py b/python/tests/test_workspace_annotations.py
index a36432d..9dd49b2 100644
--- a/python/tests/test_workspace_annotations.py
+++ b/python/tests/test_workspace_annotations.py
@@ -221,6 +221,110 @@ def test_forged_cell_link_and_oversized_tag_sets_fail_closed(self):
for raw in ('limit=true','limit=1.5','limit=-1','limit=1&limit=2','limit=%D9%A1'):
with self.subTest(raw=raw):self.assertEqual(self.client.get('/api/annotation-tags?'+raw).status_code,400)
+ def test_protocol_local_tag_filter_matches_inherited_and_direct_tags_across_views_and_export(self):
+ base = '/api/protocols/' + self.service.protocol_id
+ original = copy.deepcopy(self.service.query_result(self.service.protocol_id))
+ self.edit('cell', self.cell, ['selected'])
+ self.edit('epoch', self.second, ['other'])
+ summary = self.client.get(base + '?tag=selected').get_json()
+ self.assertEqual(summary['counts']['epochs'], 1)
+ self.assertEqual([cell['cell_uuid'] for cell in summary['cells']], [self.cell])
+ page = self.client.get(base + '/epochs?tag=selected').get_json()
+ self.assertEqual([row['epoch_uuid'] for row in page['epochs']], [self.first])
+ tree = self.client.get(base + '/tree?tag=selected&splits=cell')
+ self.assertEqual(tree.status_code, 200, tree.get_json())
+ self.assertEqual(tree.get_json()['count'], 1)
+ self.assertEqual(tree.get_json()['children'][0]['epoch_uuids'], [self.first])
+ fields = self.client.get(base + '/tree-fields?tag=selected')
+ self.assertEqual(fields.status_code, 200, fields.get_json())
+ paged = self.client.post('/api/tree-pages', json={
+ 'protocol_uuid': self.service.protocol_id, 'filters': {'tag': 'selected'},
+ 'splits': 'cell'}, headers=self.headers).get_json()
+ self.assertEqual(paged['total_epochs'], 1)
+ leaf = self.client.post('/api/tree-pages', json={
+ 'protocol_uuid': self.service.protocol_id, 'filters': {'tag': 'selected'},
+ 'splits': 'cell', 'path': paged['branches'][0]['path'],
+ 'revision': paged['revision']}, headers=self.headers).get_json()
+ self.assertEqual([row['epoch_uuid'] for row in leaf['epochs']], [self.first])
+ self.assertEqual(self.client.get(base + '/epochs?tagged=true').get_json()['total'], 2)
+ self.assertEqual(self.client.get(base + '/epochs?tag=Selected').get_json()['total'], 0)
+ exported = self.client.post(base + '/exports', json={
+ 'query_revision': summary['query_revision'], 'filters': {'tag': 'selected'}}, headers=self.headers)
+ self.assertEqual(exported.status_code, 201, exported.get_json())
+ response = self.client.get(exported.get_json()['download_url'])
+ package = json.loads(response.data); response.close()
+ self.assertEqual([row['epoch_uuid'] for row in package['epochs']], [self.first])
+ self.assertEqual(package['recipe']['options']['filters'], {'tag': 'selected'})
+ self.assertEqual(self.service.query_result(self.service.protocol_id), original)
+
+ def test_protocol_tag_predicate_all_any_and_negation_keep_tree_and_exports_consistent(self):
+ base = '/api/protocols/' + self.service.protocol_id
+ original = copy.deepcopy(self.service.query_result(self.service.protocol_id))
+ self.edit('cell', self.cell, ['good'])
+ self.edit('epoch', self.first, ['inspect'])
+ self.edit('epoch', self.second, ['reject'])
+ def rule(tag, field='annotations/effective/tags'):
+ return {'field': field, 'operator': 'contains', 'value': tag}
+ cases = [({'all': [rule('good'), rule('inspect'), {'not': rule('reject')}]}, [self.first]),
+ ({'any': [rule('good'), rule('reject')]}, [self.first, self.second]),
+ ({'all': [rule('good', 'annotations/epoch/tags')]}, []),
+ ({'all': [{'not': rule('reject')}]}, [self.first])]
+ for predicate, expected in cases:
+ with self.subTest(predicate=predicate):
+ filters = {'tag_predicate': json.dumps(predicate)}
+ response = self.client.get(base, query_string=filters)
+ self.assertEqual(response.status_code, 200, response.get_json())
+ summary = response.get_json()
+ self.assertEqual(summary['counts']['epochs'], len(expected))
+ page = self.client.get(base + '/epochs', query_string=filters).get_json()
+ self.assertEqual([row['epoch_uuid'] for row in page['epochs']], expected)
+ tree = self.client.get(base + '/tree', query_string={**filters, 'splits': 'cell'}).get_json()
+ self.assertEqual(tree['count'], len(expected))
+ paged = self.client.post('/api/tree-pages', json={
+ 'protocol_uuid': self.service.protocol_id, 'filters': filters,
+ 'splits': 'cell'}, headers=self.headers).get_json()
+ self.assertEqual(paged['total_epochs'], len(expected))
+ if expected:
+ exported = self.client.post(base + '/exports', json={
+ 'query_revision': summary['query_revision'], 'filters': filters}, headers=self.headers)
+ self.assertEqual(exported.status_code, 201, exported.get_json())
+ download = self.client.get(exported.get_json()['download_url'])
+ package = json.loads(download.data); download.close()
+ self.assertEqual([row['epoch_uuid'] for row in package['epochs']], expected)
+ self.assertEqual(self.service.query_result(self.service.protocol_id), original)
+
+ def test_protocol_tag_predicate_rejects_non_tag_fields_and_invalid_ast(self):
+ base = '/api/protocols/' + self.service.protocol_id
+ predicates = ['{', 'null', json.dumps({'field': 'parameters/example', 'operator': 'eq', 'value': 1}),
+ json.dumps({'field': 'annotations/effective/tags', 'operator': 'contains', 'value': 3}),
+ json.dumps({'field': 'annotations/effective/tags', 'operator': 'unknown', 'value': 'x'}),
+ json.dumps({'all': [], 'extra': True}), json.dumps({'not': {'all': []}, 'extra': True})]
+ for predicate in predicates:
+ with self.subTest(predicate=predicate):
+ filters = {'tag_predicate': predicate}
+ self.assertEqual(self.client.get(base + '/epochs', query_string=filters).status_code, 400)
+ self.assertEqual(self.client.post('/api/tree-pages', json={
+ 'protocol_uuid': self.service.protocol_id, 'filters': filters}, headers=self.headers).status_code, 400)
+
+ def test_tag_filter_tree_fields_refresh_after_annotation_change_and_reject_malformed_filters(self):
+ base = '/api/protocols/' + self.service.protocol_id
+ self.edit('epoch', self.first, ['selected'])
+ before = self.service._tree_fields(self.service.protocol_id, {'tag': 'selected'})
+ self.edit('epoch', self.first, remove=['selected'], revision=1)
+ self.edit('epoch', self.second, ['selected'])
+ after = self.service._tree_fields(self.service.protocol_id, {'tag': 'selected'})
+ self.assertNotEqual(before[1], after[1])
+ self.assertEqual([row['epoch_uuid'] for row in self.service.filtered_rows(
+ self.service.protocol_id, {'tag': 'selected'})], [self.second])
+ for query in ('tagged=false', 'tagged=1', 'tag=', 'tag=%20selected', 'tag=selected%0A', 'tag=selected&tag=other', 'tagged=true&tagged=false'):
+ with self.subTest(query=query):
+ self.assertEqual(self.client.get(base + '/epochs?' + query).status_code, 400)
+ for filters in ({'tag': True}, {'tagged': True}, {'tag': ['selected']}, {'tagged': ''}):
+ with self.subTest(filters=filters):
+ response = self.client.post('/api/tree-pages', json={
+ 'protocol_uuid': self.service.protocol_id, 'filters': filters}, headers=self.headers)
+ self.assertEqual(response.status_code, 400)
+
def test_protocol_export_freezes_annotations_and_stale_tags_reject_old_revision(self):
base='/api/protocols/'+self.service.protocol_id
previous=self.client.get(base).get_json()['query_revision']
diff --git a/python/workspace_api.py b/python/workspace_api.py
index 332475b..deebe32 100644
--- a/python/workspace_api.py
+++ b/python/workspace_api.py
@@ -129,10 +129,12 @@ def create_app(project_dir, retinanalysis_dir, *, service=None, store=None, expl
app.extensions["curation_store"] = store
def filters(allowed=()):
- if set(request.args) - {"cell_uuid", "cell_type", "group_label", "offset", "limit", "splits"} - set(allowed):
+ if any(len(request.args.getlist(key)) != 1 for key in ('tag', 'tagged', 'tag_predicate') if key in request.args):
+ raise ValueError('Tag filters must be specified once')
+ if set(request.args) - {"cell_uuid", "cell_type", "group_label", "tag", "tagged", "tag_predicate", "offset", "limit", "splits"} - set(allowed):
raise ValueError("Unknown query filter; no unrestricted fallback was applied")
- return {key: request.args[key] for key in ("cell_uuid", "cell_type", "group_label")
- if request.args.get(key)}
+ return {key: request.args[key] for key in ("cell_uuid", "cell_type", "group_label", "tag", "tagged", "tag_predicate")
+ if key in request.args}
def state(protocol_uuid):
result = service.query_result(protocol_uuid)
diff --git a/python/workspace_service.py b/python/workspace_service.py
index 0630993..c34e7ea 100644
--- a/python/workspace_service.py
+++ b/python/workspace_service.py
@@ -52,16 +52,40 @@ def _fingerprint(epoch):
def validate_filters(filters):
filters = {} if filters is None else filters
- if not isinstance(filters, dict) or set(filters) - {'cell_uuid', 'cell_type', 'group_label'}:
- raise ValueError('Unsupported filter; use cell_uuid, cell_type, or group_label')
+ if not isinstance(filters, dict) or set(filters) - {'cell_uuid', 'cell_type', 'group_label', 'tag', 'tagged', 'tag_predicate'}:
+ raise ValueError('Unsupported filter; use cell_uuid, cell_type, group_label, tag, tagged, or tag_predicate')
if any(not isinstance(value, str) for value in filters.values()):
raise ValueError('Filter values must be text')
+ if 'tag' in filters:
+ from workspace_annotations import text
+ text(filters['tag'])
+ if 'tagged' in filters and filters['tagged'] != 'true':
+ raise ValueError('The tagged filter must be the text true')
+ if 'tag_predicate' in filters:
+ predicate = validate_tag_filter_predicate(filters['tag_predicate'])
+ filters = {**filters, 'tag_predicate': json.dumps(predicate, sort_keys=True, separators=(',', ':'), allow_nan=False)}
cleaned = {k: v for k, v in filters.items() if v}
if 'cell_uuid' in cleaned:
cleaned['cell_uuid'] = _uuid(cleaned['cell_uuid'])
return cleaned
+TAG_FILTER_FIELDS = ('annotations/cell/tags', 'annotations/epoch/tags', 'annotations/effective/tags')
+
+
+def validate_tag_filter_predicate(value):
+ """Use the regular bounded predicate grammar, limited to shared tag arrays."""
+ if not isinstance(value, str) or len(value) > 65536:
+ raise ValueError('Tag predicate must be JSON text up to 65536 characters')
+ try:
+ predicate = json.loads(value)
+ except (ValueError, RecursionError) as error:
+ raise ValueError('Malformed tag predicate JSON') from error
+ from workspace_predicates import validate
+ return validate(predicate, {'fields': [{'id': key} for key in TAG_FILTER_FIELDS]},
+ {'tag_schema': {key: ['example tag'] for key in TAG_FILTER_FIELDS}})
+
+
def bounded_window(start, count, total, maximum=100000):
if isinstance(start, bool) or isinstance(count, bool) or not isinstance(start, int) or not isinstance(count, int):
raise ValueError('Sample offset and count must be integers')
@@ -581,8 +605,32 @@ def filtered_rows(self, protocol_uuid, filters=None):
result = self.query_result(protocol_uuid)
curation = self._curation(protocol_uuid)
rows = [self._decorate(self.rows[member['uuid']], curation) for member in result['epochs']]
- return sorted((row for row in rows if all(row.get(k) == v for k, v in filters.items())),
- key=lambda row: (row['date'], row['start_time'], row['epoch_uuid']))
+ return self._filter_rows(rows, filters)
+
+ def _filter_rows(self, rows, filters):
+ """Narrow the current dataset without changing membership or annotations.
+
+ Shared cell tags inherit to epochs. Protocol curation tags are a distinct
+ scope and do not satisfy these shared annotation filters.
+ """
+ ordinary = {key: value for key, value in filters.items() if key not in {'tag', 'tagged', 'tag_predicate'}}
+ rows = [row for row in rows if all(row.get(key) == value for key, value in ordinary.items())]
+ if any(key in filters for key in ('tag', 'tagged', 'tag_predicate')):
+ shared = getattr(self, 'shared_annotations', None)
+ annotations = shared.for_epochs(rows) if shared else {}
+ from workspace_predicates import matches
+ predicate = validate_tag_filter_predicate(filters['tag_predicate']) if 'tag_predicate' in filters else None
+ selected = []
+ for row in rows:
+ tags = {chip['tag'] for chip in annotations.get(row['epoch_uuid'], {}).get('effective_tags', [])}
+ if ('tag' not in filters or filters['tag'] in tags) and ('tagged' not in filters or tags):
+ annotation = annotations.get(row['epoch_uuid'], {})
+ current = {field: sorted({chip['tag'] for chip in annotation.get(scope, [])})
+ for field, scope in zip(TAG_FILTER_FIELDS, ('cell_tags', 'epoch_tags', 'effective_tags'))}
+ if predicate is None or matches(predicate, current):
+ selected.append(row)
+ rows = selected
+ return sorted(rows, key=lambda row: (row['date'], row['start_time'], row['epoch_uuid']))
@staticmethod
def _counts(rows):
@@ -681,7 +729,9 @@ def _tree_fields(self, protocol_uuid, filters=None):
binding = self.binding(protocol_uuid) if protocol_uuid else None
scope = self.source_scope() if protocol_uuid is None else None
scope_revision = scope['revision'] if scope else None
- key = (protocol_uuid, binding['version'] if binding else 0, scope_revision, tuple(sorted(filters.items())))
+ shared = getattr(self, 'shared_annotations', None)
+ tag_revision = shared.snapshot()['revision'] if shared and any(key in filters for key in ('tag', 'tagged', 'tag_predicate')) else None
+ key = (protocol_uuid, binding['version'] if binding else 0, scope_revision, tuple(sorted(filters.items())), tag_revision)
if key in cache:
result = cache.pop(key)
cache[key] = result # Most recently used, without recomputation.
@@ -713,8 +763,7 @@ def _tree_rows(self, protocol_uuid, filters=None):
self._ready()
filters = validate_filters(filters)
active = set(self.source_scope()['active_source_revisions'])
- return sorted((row for row in self.rows.values() if row['source_sha256'] in active and all(row.get(key) == value for key, value in filters.items())),
- key=lambda row: (row['date'], row['start_time'], row['epoch_uuid']))
+ return self._filter_rows([row for row in self.rows.values() if row['source_sha256'] in active], filters)
def validate_tree_splits(self, protocol_uuid, splits):
fields = self.tree_fields(protocol_uuid)['fields']
diff --git a/workspace-app/src/App.jsx b/workspace-app/src/App.jsx
index 7bafbb8..151c8cd 100644
--- a/workspace-app/src/App.jsx
+++ b/workspace-app/src/App.jsx
@@ -1,3 +1,4 @@
+import {tagFilterLabel} from './protocolViewFilter.js';
import H5Inbox from './components/H5Inbox.jsx';
import ProjectClosedNotice from './components/ProjectClosedNotice.jsx';
import AppUpdates from './components/AppUpdates.jsx';
@@ -73,7 +74,7 @@ function Protocol({id,revision,onChange,onTagFilter,initialRecipe,initialInspect
function filter(key,value){setResult(null);setError('');setFilters(old=>{const next={...old};if(value)next[key]=value;else delete next[key];return next;});}
async function refreshQuery(){setRefreshing(true);setError('');try{setDiff(await api(`/protocols/${id}/refresh`,{method:'POST',body:{filters}}));protocol.reload();onChange();}catch(e){setError(e.message);}finally{setRefreshing(false);}}
async function saveExport(){setExporting(true);setError('');try{const r=await api(`/protocols/${id}/exports`,{method:'POST',body:{format,name:exportName || data.definition.name,review_policy:policy,filters,query_revision:data.query_revision,split_order:splitOrder.join(', ')}});if(!validExportReceipt(r,format)){onChange();throw new Error('The server did not return a complete export receipt. Check this protocol’s Exports and Activity & logs before retrying.');}setResult(r);onChange();}catch(e){setError(e.message);}finally{setExporting(false);}}
- const exportPanel=data&&(<>
{setFormat(value);setResult(null);setError('');}}/>{EXPORT_FORMATS[format]?.description || 'Choose a supported output format to continue. The saved export keeps its original format.'}
Export scope · {number(counts.cells)} matching cells
Uses this protocol’s saved query and current filters. Focusing a cell or checking bulk-action targets does not restrict this export.
{filters.cell_type || 'All cell types'}{filters.group_label ? `Group: ${filters.group_label}` : 'All source groups'}{filters.cell_uuid&&Cell: {datedCellLabel(data.cells?.find(c=>c.cell_uuid===filters.cell_uuid) || {},true)}}
- Matching epochs
- {number(counts.epochs)}
- Included
- {number(counts.included)}
- Excluded
- {number(counts.excluded)}
- Already in saved exports
- {number(counts.exported ?? 0)}
{policy==='approved_only'&&- Not marked reviewed
- {number(held)}
}- Ready to export
- {exportBlocked?'Source update needed':Number.isFinite(eligible)?number(eligible):'Loading…'}
{exportBlocked?
This retained dataset includes sources excluded from queries. Open Data stores and propagate the proposed changes before exporting.
:eligible===0?
{policy==='approved_only'&&counts.included>0?'No included epochs are marked reviewed. Choose “Included epochs” to export without a review requirement, or mark review status during inspection.':'No epochs are included in this query. Change the query scope or include the epochs you want to export.'}
:
{policy==='include_unreviewed'?'All included epochs are eligible; review is not required.':'Only included epochs marked reviewed are eligible.'} The server rechecks membership before saving. Each export remains a separate saved revision.
}
{error}
}{result&&}Previous exports
);
+ const exportPanel=data&&(<>
{setFormat(value);setResult(null);setError('');}}/>{EXPORT_FORMATS[format]?.description || 'Choose a supported output format to continue. The saved export keeps its original format.'}
Export scope · {number(counts.cells)} matching cells
Uses this protocol’s saved query and current filters. Focusing a cell or checking bulk-action targets does not restrict this export.
{filters.cell_type || 'All cell types'}{tagFilterLabel(filters)&&{tagFilterLabel(filters)}}{filters.group_label ? `Group: ${filters.group_label}` : 'All source groups'}{filters.cell_uuid&&Cell: {datedCellLabel(data.cells?.find(c=>c.cell_uuid===filters.cell_uuid) || {},true)}}
- Matching epochs
- {number(counts.epochs)}
- Included
- {number(counts.included)}
- Excluded
- {number(counts.excluded)}
- Already in saved exports
- {number(counts.exported ?? 0)}
{policy==='approved_only'&&- Not marked reviewed
- {number(held)}
}- Ready to export
- {exportBlocked?'Source update needed':Number.isFinite(eligible)?number(eligible):'Loading…'}
{exportBlocked?
This retained dataset includes sources excluded from queries. Open Data stores and propagate the proposed changes before exporting.
:eligible===0?
{policy==='approved_only'&&counts.included>0?'No included epochs are marked reviewed. Choose “Included epochs” to export without a review requirement, or mark review status during inspection.':tagFilterLabel(filters)?'No epochs match this tag filter. Clear or change the filter to export matching epochs.':'No epochs are included in this query. Change the query scope or include the epochs you want to export.'}
:
{policy==='include_unreviewed'?'All included epochs are eligible; review is not required.':'Only included epochs marked reviewed are eligible.'} The server rechecks membership before saving. Each export remains a separate saved revision.
}
{error}
}{result&&}Previous exports
);
const exportFooter=(
Logged in project activity
);
return
{treeLayout.save.status==='saving'?'Saving tree…':treeLayout.save.status==='error'?'Tree not saved':treeLayout.save.version>0?'Tree saved':''}{Object.keys(filters).length?`${Object.keys(filters).length} active filters`:'All matching cells'}
-
{treeLayout.save.status==='error'&&
Tree layout could not be saved: {treeLayout.save.error}
}
{protocol.reload();treeLayout.reload();}}>{data&&<>{exportOpen&&setExportOpen(false)} footer={exportFooter}>{exportPanel}}{tab==='inspect'?setTab('overview')} onImport={onImport} onStores={onStores} onExport={()=>setExportOpen(true)}/>:PROTOCOL WORKSPACE
{humanize(data.definition?.name)}
{data.binding?`Working dataset version ${data.binding.version}. Use Search predicate to compare and apply new source data.`:"A saved query into the project catalog. Inspection decisions stay linked to each epoch."}
{initialRecipe&&
Reused saved query; matching the current catalog. Previous export unchanged.
}{diff&&
{diff.message || (diff.baseline_created?'Saved a comparison baseline.':`Query refreshed: ${typeof diff.diff?.added==='number'?diff.diff.added:diff.diff?.added?.length||0} added · ${typeof diff.diff?.changed==='number'?diff.diff.changed:diff.diff?.changed?.length||0} changed · ${typeof diff.diff?.removed==='number'?diff.diff.removed:diff.diff?.removed?.length||0} no longer matching`)}<>{diff.candidate_revision_uuid&&} }{error&&tab!=='export'&&
{error}
}
Loading dataset summary…Filter results{Object.keys(filters).length>0&&}Group labels are original metadata, not inferred drug phases.
<>{suggestionsError&&New-data suggestions could not load.
}{suggestion&&}Cells in this protocol
}}