Merge feature/standardise-term-links-reports: standardise VFB term links to /reports permalinks (v1.15.0)

Robbie1977 · Robbie1977 · commit ac5ada2d3a06 · 2026-06-04T06:51:13.000+01:00
diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 
 here = path.abspath(path.dirname(__file__))
 
-__version__ = "1.14.12"
+__version__ = "1.15.0"
 
 # Get the long description from the README file
 with open(path.join(here, 'README.md')) as f:
diff --git a/src/test/term_info_queries_test.py b/src/test/term_info_queries_test.py
@@ -487,13 +487,13 @@ def test_term_info_serialization_template(self):
         self.assertTrue("filemeta" in serialized)
         self.assertEqual(3, len(serialized["filemeta"]))
         self.assertEqual({'obj': {'local': '/MeshFiles(OBJ)/my_id_(my_name).obj',
-                                  'url': 'https://v2.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume_man.obj'}},
+                                  'url': 'https://virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume_man.obj'}},
                          serialized["filemeta"][0])
         self.assertEqual({'wlz': {'local': '/Slices(WOOLZ)/my_id_(my_name).wlz',
-                                  'url': 'https://v2.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume.wlz'}},
+                                  'url': 'https://virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume.wlz'}},
                          serialized["filemeta"][1])
         self.assertEqual({'nrrd': {'local': '/SignalFiles(NRRD)/my_id_(my_name).nrrd',
-                                   'url': 'https://v2.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume.nrrd'}},
+                                   'url': 'https://virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume.nrrd'}},
                          serialized["filemeta"][2])
         self.assertTrue("template" in serialized)
         self.assertEqual("[JRC2018UnisexVNC](VFB_00200000)", serialized["template"])
diff --git a/src/vfbquery/term_info_queries.py b/src/vfbquery/term_info_queries.py
@@ -1069,12 +1069,14 @@ def get_secure_data_url(data_url: str) -> str:
 
 def get_secure_data_v2_url(data_url: str) -> str:
     """
-    Generates a secure data v2 url from the given url
+    Generates a secure, canonical data url from the given url: forces https and
+    rewrites the www data host to the environment-independent virtualflybrain.org
+    host, consistent with VFB term permalinks.
     :param data_url: data url to secure
-    :return: secured v2 url
+    :return: secured data url
     """
     return data_url.replace("http://", "https://").replace("https://www.virtualflybrain.org/data/",
-                                                           "https://v2.virtualflybrain.org/data/")
+                                                           "https://virtualflybrain.org/data/")
 
 
 def serialize_term_info_to_json(vfb_term: VfbTerminfo, show_types=False) -> str:
diff --git a/src/vfbquery/vfb_queries.py b/src/vfbquery/vfb_queries.py
@@ -64,6 +64,29 @@ def get_dict_cursor():
 # Replace VfbConnect with SimpleVFBConnect
 vc = SimpleVFBConnect()
 
+# ---------------------------------------------------------------------------
+# Canonical VFB term link
+# ---------------------------------------------------------------------------
+# Public, environment-independent permalink base for a VFB term. This resolves
+# to the term's report page outside the app and is recognised as an internal
+# link by the v2 query-results table (MarkdownLinkComponent parses the
+# short_form out of the `/reports/<id>` path). Never hard-code an app URL such
+# as https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=<id> into
+# query output -- that pins results to one deployment. Build every VFB term
+# link from here (or via the helpers below) so the form is defined in one place.
+VFB_REPORT_BASE = "https://virtualflybrain.org/reports/"
+
+
+def vfb_report_url(short_form: str) -> str:
+    """Public permalink for a VFB term id, e.g. .../reports/VFB_00101567."""
+    return f"{VFB_REPORT_BASE}{short_form}"
+
+
+def vfb_term_link(label: str, short_form: str) -> str:
+    """Markdown link for a VFB term: [label](https://virtualflybrain.org/reports/<id>)."""
+    return f"[{label}]({vfb_report_url(short_form)})"
+
+
 def initialize_vfb_connect():
     """
     Initialize VFB_connect by triggering the lazy load of the vfb and nc properties.
@@ -4777,7 +4800,7 @@ def get_similar_morphology(neuron_short_form: str, return_dataframe=True, limit:
         }}) END AS types, primary, channel_image, nblast
         RETURN
             primary.short_form AS id,
-            '[' + primary.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + primary.short_form + ')' AS name,
+            '[' + primary.label + ']({VFB_REPORT_BASE}' + primary.short_form + ')' AS name,
             apoc.text.join(coalesce(primary.uniqueFacets, []), '|') AS tags,
             nblast.NBLAST_score[0] AS score,
             types,
@@ -4835,7 +4858,7 @@ def get_similar_morphology_part_of(neuron_short_form: str, return_dataframe=True
         WITH primary, nblast, channel, ri, templ, technique
         OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ IS NULL THEN [] ELSE collect({{short_form: typ.short_form, label: coalesce(typ.label, ''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')}}) END AS types, primary, nblast, channel, ri, templ, technique
         RETURN primary.short_form AS id,
-               '[' + primary.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + primary.short_form + ')' AS name,
+               '[' + primary.label + ']({VFB_REPORT_BASE}' + primary.short_form + ')' AS name,
                apoc.text.join(coalesce(primary.uniqueFacets, []), '|') AS tags,
                nblast.NBLAST_score[0] AS score,
                types,
@@ -4866,7 +4889,7 @@ def get_similar_morphology_part_of_exp(expression_short_form: str, return_datafr
         WITH primary, nblast, channel, ri, templ, technique
         OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ IS NULL THEN [] ELSE collect({{short_form: typ.short_form, label: coalesce(typ.label, ''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')}}) END AS types, primary, nblast, channel, ri, templ, technique
         RETURN primary.short_form AS id,
-               '[' + primary.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + primary.short_form + ')' AS name,
+               '[' + primary.label + ']({VFB_REPORT_BASE}' + primary.short_form + ')' AS name,
                apoc.text.join(coalesce(primary.uniqueFacets, []), '|') AS tags,
                nblast.NBLAST_score[0] AS score,
                types,
@@ -4897,7 +4920,7 @@ def get_similar_morphology_nb(neuron_short_form: str, return_dataframe=True, lim
         WITH primary, nblast, channel, ri, templ, technique
         OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ IS NULL THEN [] ELSE collect({{short_form: typ.short_form, label: coalesce(typ.label, ''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')}}) END AS types, primary, nblast, channel, ri, templ, technique
         RETURN primary.short_form AS id,
-               '[' + primary.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + primary.short_form + ')' AS name,
+               '[' + primary.label + ']({VFB_REPORT_BASE}' + primary.short_form + ')' AS name,
                apoc.text.join(coalesce(primary.uniqueFacets, []), '|') AS tags,
                nblast.neuronbridge_score[0] AS score,
                types,
@@ -4943,7 +4966,7 @@ def get_similar_morphology_nb_exp(expression_short_form: str, return_dataframe=T
             RETURN ri, templ, technique
         }}
         RETURN primary.short_form AS id,
-               '[' + primary.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + primary.short_form + ')' AS name,
+               '[' + primary.label + ']({VFB_REPORT_BASE}' + primary.short_form + ')' AS name,
                apoc.text.join(coalesce(primary.uniqueFacets, []), '|') AS tags,
                nblast.neuronbridge_score[0] AS score,
                type,
@@ -4989,7 +5012,7 @@ def get_painted_domains(template_short_form: str, return_dataframe=True, limit:
     total_count = get_dict_cursor()(count_results)[0]['count'] if count_results else 0
     
     main_query = f"""MATCH (n:Template {{short_form:'{template_short_form}'}})<-[:depicts]-(:Template)<-[r:in_register_with]-(dc:Individual)-[:depicts]->(di:Individual)-[:INSTANCEOF]->(d:Class) WHERE EXISTS(r.index)
-        RETURN DISTINCT di.short_form AS id, '[' + di.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + di.short_form + ')' AS name, coalesce(di.description[0], d.description[0]) AS description, COLLECT(DISTINCT d.label) AS type, replace(r.folder[0],'http:','https:') + '/thumbnailT.png' AS thumbnail"""
+        RETURN DISTINCT di.short_form AS id, '[' + di.label + ']({VFB_REPORT_BASE}' + di.short_form + ')' AS name, coalesce(di.description[0], d.description[0]) AS description, COLLECT(DISTINCT d.label) AS type, replace(r.folder[0],'http:','https:') + '/thumbnailT.png' AS thumbnail"""
     if limit != -1: main_query += f" LIMIT {limit}"
     
     results = vc.nc.commit_list([main_query])
@@ -5143,16 +5166,15 @@ def get_template_roi_tree(template_short_form: str, return_dataframe=False):
     def _node_summary_md(class_id, class_label, painted_list, parent_label):
         parts = [
             f"**{class_label or class_id}** "
-            f"([{class_id}](http://virtualflybrain.org/reports/{class_id}))",
+            f"({vfb_term_link(class_id, class_id)})",
             "",
         ]
         if parent_label:
             parts.append(f"Part of: *{parent_label}*.")
             parts.append("")
         if painted_list:
             ind_lines = [
-                f"[{p.get('individual_label') or p.get('individual_id')}]"
-                f"(http://virtualflybrain.org/reports/{p.get('individual_id')})"
+                vfb_term_link(p.get('individual_label') or p.get('individual_id'), p.get('individual_id'))
                 for p in painted_list if p.get('individual_id')
             ]
             if ind_lines:
@@ -5190,7 +5212,7 @@ def _build(node_id, ancestors, parent_label):
     summary_md = (
         f"## ROI tree for **{template_label}**\n\n"
         f"Anatomy root: "
-        f"[{root_label or root_id}](http://virtualflybrain.org/reports/{root_id}) "
+        f"{vfb_term_link(root_label or root_id, root_id)} "
         f"({root_id}).\n\n"
         f"{painted_class_count} painted region"
         f"{'s' if painted_class_count != 1 else ''} "
@@ -5260,7 +5282,7 @@ def get_dataset_images(dataset_short_form: str, return_dataframe=True, limit: in
         OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class)
         OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class)
         RETURN primary.short_form AS id,
-               '[' + primary.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + primary.short_form + ')' AS name,
+               '[' + primary.label + ']({VFB_REPORT_BASE}' + primary.short_form + ')' AS name,
                apoc.text.join(coalesce(primary.uniqueFacets, []), '|') AS tags,
                typ.label AS type,
                REPLACE(apoc.text.format("[%s](%s)",[COALESCE(template.symbol[0],template.label),template.short_form]), '[null](null)', '') AS template,
@@ -5286,7 +5308,7 @@ def get_all_aligned_images(template_short_form: str, return_dataframe=True, limi
         OPTIONAL MATCH (di)-[:INSTANCEOF]->(typ:Class)
         OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class)
         RETURN DISTINCT di.short_form AS id,
-               '[' + di.label + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + di.short_form + ')' AS name,
+               '[' + di.label + ']({VFB_REPORT_BASE}' + di.short_form + ')' AS name,
                apoc.text.join(coalesce(di.uniqueFacets, []), '|') AS tags,
                typ.label AS type,
                REPLACE(apoc.text.format("[%s](%s)",[COALESCE(templ.symbol[0],templ.label),templ.short_form]), '[null](null)', '') AS template,
@@ -5358,7 +5380,7 @@ def _dataset_return_clause(ds_var: str = "ds") -> str:
     return f"""
         RETURN
             {ds_var}.short_form AS id,
-            '[' + coalesce({ds_var}.label, {ds_var}.short_form) + '](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=' + {ds_var}.short_form + ')' AS name,
+            '[' + coalesce({ds_var}.label, {ds_var}.short_form) + ']({VFB_REPORT_BASE}' + {ds_var}.short_form + ')' AS name,
             pubs,
             apoc.text.join(coalesce({ds_var}.uniqueFacets, []), '|') AS tags,
             license,
@@ -6288,7 +6310,7 @@ def build(node_id, depth):
     # Render display text and HTML
     # ------------------------------------------------------------------
 
-    VFB_BASE = 'https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id='
+    VFB_BASE = VFB_REPORT_BASE
     DEFAULT_MAX_SIBLINGS = 10  # truncate large sibling groups in text display
 
     def _text_tree(node, prefix='', is_last=True, is_root=True, max_siblings=DEFAULT_MAX_SIBLINGS):
