New schema

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fairscape-cli"
-version = "1.2.8"
+version = "1.2.9"
 description = "A utility for packaging objects and validating metadata for FAIRSCAPE"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -39,9 +39,8 @@ dependencies = [
         "prettytable>=3.9.0",
         "jsonschema>=4.20.0",
         "sqids>=0.4.1",
-        "fairscape-models[schema-infer]>=1.2.0",
+        "fairscape-models[schema-tabular]>=1.2.2",
         "pyyaml",
-        "h5py",
         "frictionless>=5.0,<6.0",
         "beautifulsoup4",
         "pandas",
@@ -101,3 +100,8 @@ test = [
 shacl = [
     "pyshacl>=0.27"
 ]
+# Optional per-format schema inference/validation.
+schema-hdf5 = ["fairscape-models[schema-hdf5]"]
+schema-signal = ["fairscape-models[schema-signal]"]
+schema-image = ["fairscape-models[schema-image]"]
+schema-all = ["fairscape-models[schema-infer]"]

src/fairscape_cli/commands/schema_commands.py

@@ -5,12 +5,11 @@
     ValidationError
 )
 
-from fairscape_models.schema import Schema
-
 from fairscape_cli.config import DEFAULT_CONTEXT, DEFAULT_SCHEMA_TYPE
 from fairscape_cli.models import ReadROCrateMetadata, AppendCrate
 
 from fairscape_cli.models.schema import (
+    TabularSchema,
     infer_schema,
     validate_schema,
     load_schema,
@@ -52,7 +51,7 @@ def create_tabular_schema(
     """Initialize a Tabular Schema.
     """
     try:
-        schema_model = Schema.model_validate({
+        schema_model = TabularSchema.model_validate({
             "@id": guid or generate_schema_guid(name),
             "@context": DEFAULT_CONTEXT,
             "@type": DEFAULT_SCHEMA_TYPE,
@@ -289,7 +288,8 @@ def validate(ctx, schema, data):
 def infer_schema_rocrate(ctx, name, description, guid, input_file, rocrate_path, schema_file):
     """Infer a schema from a file and optionally append it to an RO-Crate.
 
-    INPUT_FILE: File to infer schema from (CSV, TSV, Parquet, or HDF5)
+    INPUT_FILE: File to infer schema from. Supported: CSV, TSV, Parquet
+    (tabular); HDF5 (.h5/.hdf5); WFDB header (.hea); DICOM (.dcm).
     SCHEMA_FILE: Path to save the schema file
     """
     try:
@@ -322,6 +322,12 @@ def infer_schema_rocrate(ctx, name, description, guid, input_file, rocrate_path,
     except ValueError as e:
         click.echo(f"Error with file type: {str(e)}")
         ctx.exit(code=1)
+    except ImportError as e:
+        click.echo(
+            f"Missing optional dependency for this file type ({str(e)}). "
+            "Install with: pip install 'fairscape-models[schema-infer]'"
+        )
+        ctx.exit(code=1)
     except Exception as e:
         click.echo(f"Error inferring schema: {str(e)}")
         ctx.exit(code=1)

src/fairscape_cli/datasheet_builder/rocrate/datasheet_generator.py

@@ -30,6 +30,7 @@
     SUBCRATE_MAPPING_CONFIGURATION,
     PREVIEW_MAPPING_CONFIGURATION
 )
+from fairscape_models.conversion.mapping.subcrate_utils import enrich_preview_computations
 
 from fairscape_cli.utils.rocrate_helpers import get_root_entity
 
@@ -394,6 +395,7 @@ def process_subcrates(self):
                 )
 
                 preview = converter.convert()
+                enrich_preview_computations(preview, subcrate, self.global_metadata_index)
 
                 preview_html = self.preview_generator.generate(preview, self.published)
 

src/fairscape_cli/datasheet_builder/rocrate/section_generators.py

@@ -226,6 +226,7 @@ def _prepare_subcrate_context(self, item: SubCrateItem, published: bool) -> Dict
                 'computations_count': details.computations_count,
                 'schemas_count': details.schemas_count,
                 'other_count': details.other_count,
+                'datasets_with_provenance_count': details.datasets_with_provenance_count,
 
                 # Format and access summaries - convert to dict for template
                 'file_formats': dict(details.file_formats) if details.file_formats else {},
@@ -327,7 +328,8 @@ def _prepare_items(self, items: List) -> List[Dict[str, Any]]:
                 'content_status': item.content_status or "Not specified",
                 'experimentType': getattr(item, 'experimentType', None) or "N/A",
                 'manufacturer': getattr(item, 'manufacturer', None) or "N/A",
-                'schema_properties': getattr(item, 'schema_properties', None)
+                'schema_properties': getattr(item, 'schema_properties', None),
+                'computation_details': getattr(item, 'computation_details', None)
             }
             prepared.append(item_context)
         return prepared

src/fairscape_cli/datasheet_builder/templates/evidence_graph/evidence_graph.html.j2

@@ -104,6 +104,94 @@
             line-height: 1.3;
             box-sizing: border-box;
         }
+        .node-info-button {
+            position: absolute;
+            top: 0;
+            right: 0;
+            width: 22px;
+            height: 22px;
+            color: #333;
+            border: none;
+            font-size: 12px;
+            font-weight: bold;
+            display: flex;
+            align-items: center;
+            justify-content: center;
+            cursor: pointer;
+            z-index: 10;
+            padding: 0;
+            margin: 0;
+            border-bottom-left-radius: 4px;
+            opacity: 0.8;
+            transition: opacity 0.2s ease;
+        }
+        .node-info-button:hover {
+            opacity: 1;
+        }
+        .node-info-popover {
+            position: fixed;
+            max-height: 70vh;
+            overflow-y: auto;
+            background: #fff;
+            border: 1px solid #ccc;
+            border-radius: 4px;
+            box-shadow: 0 4px 12px rgba(0,0,0,0.15);
+            padding: 10px 12px;
+            font-size: 13px;
+            color: #333;
+            text-align: left;
+            z-index: 50;
+            box-sizing: border-box;
+            cursor: default;
+            user-select: text;
+        }
+        .node-info-popover h4 {
+            margin: 0 22px 8px 0;
+            font-size: 1.1em;
+            color: #000;
+            border-bottom: 1px solid #eee;
+            padding-bottom: 4px;
+            word-break: break-word;
+        }
+        .node-info-popover .popover-section {
+            margin-bottom: 8px;
+            padding-bottom: 8px;
+        }
+        .node-info-popover .popover-section:not(:last-child) {
+            border-bottom: 1px dotted #eee;
+        }
+        .node-info-popover .prop-item {
+            display: flex;
+            margin: 4px 0;
+            line-height: 1.4;
+        }
+        .node-info-popover .prop-key {
+            font-weight: bold;
+            min-width: 100px;
+            flex-shrink: 0;
+            margin-right: 8px;
+            color: #555;
+        }
+        .node-info-popover .prop-value {
+            word-break: break-word;
+        }
+        .node-info-popover .popover-close {
+            position: absolute;
+            top: 6px;
+            right: 6px;
+            width: 20px;
+            height: 20px;
+            border: none;
+            background: transparent;
+            font-size: 16px;
+            line-height: 1;
+            color: #888;
+            cursor: pointer;
+            padding: 0;
+        }
+        .node-info-popover .popover-close:hover {
+            color: #333;
+        }
         .svg-layer {
             position: absolute;
             top: 0;

src/fairscape_cli/datasheet_builder/templates/evidence_graph/evidence_graph.js

@@ -530,9 +530,33 @@ const evidenceGraphData = window.__EVIDENCE_GRAPH_DATA__;
         }
     }
 
+    function formatPropertyValue(value) {
+        if (value === null || value === undefined) return "";
+        if (Array.isArray(value)) {
+            return value.map(formatPropertyValue).filter(Boolean).join(", ");
+        }
+        if (typeof value === "object") {
+            return value["@id"] || value.name || JSON.stringify(value);
+        }
+        return String(value);
+    }
+
+    // Properties from the entity's source data worth showing in the info
+    // popover, beyond the ones the popover displays explicitly.
+    function getDisplayableProperties(sourceData) {
+        const EXCLUDED = new Set(["@id", "@type", "@context", "name", "label", "description", "count"]);
+        const props = {};
+        Object.entries(sourceData || {}).forEach(([key, value]) => {
+            if (key.startsWith("_") || EXCLUDED.has(key)) return;
+            const formatted = formatPropertyValue(value);
+            if (formatted) props[key] = formatted;
+        });
+        return props;
+    }
+
     const { createElement, useState, useCallback, useEffect, useRef, memo } = React;
 
-    const EvidenceNode = memo(({ nodeData, onClick }) => {
+    const EvidenceNode = memo(({ nodeData, onClick, onInfoClick }) => {
         const { id, type, label, displayName, description, expandable, x, y, width, height } = nodeData;
         const nodeColor = getNodeColor(type);
         // DatasetGroup (graph-condensation node) and DatasetCollection (synthetic UI grouping
@@ -548,6 +572,14 @@ const evidenceGraphData = window.__EVIDENCE_GRAPH_DATA__;
             }
         }, [id, expandable, onClick]);
 
+        const handleInfoClick = useCallback((event) => {
+            // Keep the 'i' click from triggering node expansion.
+            event.stopPropagation();
+            if (onInfoClick) {
+                onInfoClick(id, event.currentTarget.getBoundingClientRect());
+            }
+        }, [id, onInfoClick]);
+
         const style = {
             left: `${x}px`,
             top: `${y}px`,
@@ -567,11 +599,62 @@ const evidenceGraphData = window.__EVIDENCE_GRAPH_DATA__;
                 createElement('div', { key: 'header', className: 'node-header', style: { backgroundColor: nodeColor } }, displayType),
                 createElement('div', { key: 'content', className: 'node-content' },
                      createElement('div', { style: { width: '100%', textAlign: 'center' } }, displayName)
-                )
+                ),
+                createElement('button', {
+                    key: 'info',
+                    className: 'node-info-button',
+                    style: { backgroundColor: nodeColor },
+                    onClick: handleInfoClick,
+                    onMouseDown: (e) => e.stopPropagation(),
+                    'aria-label': `Details for ${displayName || label || id}`
+                }, 'i')
             ])
         );
     });
 
+    // Details panel opened by a node's 'i' button — the standalone equivalent
+    // of the web client's Tippy tooltip on EvidenceNode.
+    const NodeInfoPopover = ({ node, anchorRect, onClose }) => {
+        const { id, type, label, displayName, description } = node;
+        const sourceData = node._sourceData || {};
+        const otherProps = getDisplayableProperties(sourceData);
+
+        const PANEL_WIDTH = 360;
+        let left = anchorRect.right + 8;
+        if (left + PANEL_WIDTH > window.innerWidth - 10) {
+            left = Math.max(10, anchorRect.left - PANEL_WIDTH - 8);
+        }
+        const top = Math.max(10, Math.min(anchorRect.top, window.innerHeight - 200));
+
+        const propRow = (key, value) => createElement('div', { key: key, className: 'prop-item' }, [
+            createElement('span', { key: 'k', className: 'prop-key' }, `${key}:`),
+            createElement('span', { key: 'v', className: 'prop-value' }, value)
+        ]);
+
+        const metaRows = [
+            propRow('@id', id),
+            propRow('@type', type),
+        ];
+        if (description) metaRows.push(propRow('description', description));
+        if (type === 'DatasetCollection' && sourceData.count !== undefined) {
+            metaRows.push(propRow('Items', String(sourceData.count)));
+        }
+
+        return createElement('div', {
+            className: 'node-info-popover',
+            style: { left: `${left}px`, top: `${top}px`, width: `${PANEL_WIDTH}px` },
+            onMouseDown: (e) => e.stopPropagation(),
+            onClick: (e) => e.stopPropagation()
+        }, [
+            createElement('button', { key: 'close', className: 'popover-close', onClick: onClose, 'aria-label': 'Close details' }, '×'),
+            createElement('h4', { key: 'title' }, label || displayName || 'Node Details'),
+            createElement('div', { key: 'meta', className: 'popover-section' }, metaRows),
+            Object.keys(otherProps).length > 0 && createElement('div', { key: 'props', className: 'popover-section' },
+                Object.entries(otherProps).map(([key, value]) => propRow(key, value))
+            )
+        ]);
+    };
+
     const Edge = memo(({ edgeData, sourceNode, targetNode }) => {
         if (!sourceNode || !targetNode || sourceNode.x === undefined || targetNode.x === undefined) {
              return null;
@@ -659,6 +742,7 @@ const evidenceGraphData = window.__EVIDENCE_GRAPH_DATA__;
         const [translate, setTranslate] = useState({ x: 0, y: 0 });
         const [isDragging, setIsDragging] = useState(false);
         const [startDragPos, setStartDragPos] = useState({ x: 0, y: 0 });
+        const [infoPopover, setInfoPopover] = useState(null); // { nodeId, anchorRect }
         const rootRef = useRef(null);
 
 
@@ -709,7 +793,15 @@ const evidenceGraphData = window.__EVIDENCE_GRAPH_DATA__;
         }, [graphData, applyLayout]);
 
 
+        const handleInfoClick = useCallback((nodeId, anchorRect) => {
+            // Toggle: clicking the same node's 'i' again closes the popover.
+            setInfoPopover(current =>
+                current && current.nodeId === nodeId ? null : { nodeId, anchorRect }
+            );
+        }, []);
+
         const handleNodeClick = useCallback((nodeId) => {
+            setInfoPopover(null);
             const clickedNodeIndex = nodes.findIndex(n => n.id === nodeId);
             if (clickedNodeIndex === -1) return;
 
@@ -775,9 +867,10 @@ const evidenceGraphData = window.__EVIDENCE_GRAPH_DATA__;
 
         const handleMouseDown = useCallback((event) => {
             if (event.button !== 0) return;
-             if (event.target.closest('.controls-container') || event.target.closest('.node-wrapper')) {
+             if (event.target.closest('.controls-container') || event.target.closest('.node-wrapper') || event.target.closest('.node-info-popover')) {
                  return;
              }
+            setInfoPopover(null);
             setIsDragging(true);
             setStartDragPos({ x: event.clientX - translate.x, y: event.clientY - translate.y });
             if(rootRef.current) rootRef.current.classList.add('dragging');
@@ -864,12 +957,25 @@ const evidenceGraphData = window.__EVIDENCE_GRAPH_DATA__;
                                 nodes.map(node => createElement(EvidenceNode, {
                                     key: node.id,
                                     nodeData: node,
-                                    onClick: handleNodeClick
+                                    onClick: handleNodeClick,
+                                    onInfoClick: handleInfoClick
                                 }))
                             )
                         ]
                     )
                 ),
+                 (() => {
+                     if (!infoPopover) return null;
+                     const infoNode = nodeMap.get(infoPopover.nodeId);
+                     if (!infoNode) return null;
+                     return createElement(NodeInfoPopover, {
+                         key: 'info-popover',
+                         node: infoNode,
+                         anchorRect: infoPopover.anchorRect,
+                         onClose: () => setInfoPopover(null)
+                     });
+                 })(),
+
                  isLoading && createElement('div', { key: 'loading', className: 'loading-overlay' }, 'Loading...'),
 
                  createElement('div', {key: 'controls', className: 'controls-container'}, [