fairscape-cli 1.2.1__tar.gz → 1.2.2__tar.gz

{fairscape_cli-1.2.1/src/fairscape_cli.egg-info → fairscape_cli-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fairscape-cli
-Version: 1.2.1
+Version: 1.2.2
 Summary: A utility for packaging objects and validating metadata for FAIRSCAPE
 Author-email: Max Levinson <mal8ch@virginia.edu>, Justin Niestroy <jniestroy@gmail.com>, Sadnan Al Manir <sadnanalmanir@gmail.com>, Tim Clark <twc8q@virginia.edu>
 License: Copyright 2023 THE RECTOR AND VISITORS OF THE UNIVERSITY OF VIRGINIA

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fairscape-cli"
-version = "1.2.1"
+version = "1.2.2"
 description = "A utility for packaging objects and validating metadata for FAIRSCAPE"
 readme = "README.md"
 requires-python = ">=3.8"

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/commands/build_commands.py

@@ -29,6 +29,7 @@ from fairscape_cli.models import (
 )
 
 from fairscape_models.rocrate import ROCrateV1_2, ROCrateMetadataElem
+from fairscape_cli.utils.serialization import prune_none
 from fairscape_models.conversion.converter import ROCToTargetConverter
 from fairscape_models.conversion.mapping.croissant import MAPPING_CONFIGURATION as CROISSANT_MAPPING
 
@@ -535,7 +536,7 @@ def generate_evidence_graph(
             
             # Write the updated metadata back to the file
             with open(metadata_file, 'w') as f:
-                json.dump(metadata, f, indent=2)
+                json.dump(prune_none(metadata), f, indent=2)
                 
             click.echo(f"Added hasEvidenceGraph reference to {ark_id} in RO-Crate metadata")
         except Exception as e:
@@ -774,4 +775,4 @@ def validate_merkle_command(ctx, rocrate_path: pathlib.Path, release: bool):
             elif s != c:
                 click.echo(f"    CHANGED: {url}")
 
-        ctx.exit(1)
+        ctx.exit(1)

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/data_fetcher/GenomicData.py

@@ -103,6 +103,7 @@ from fairscape_cli.data_fetcher.cell_line_api import get_cell_line_entity
 from fairscape_cli.data_fetcher.bioproject_fetcher import fetch_bioproject_data
 
 from fairscape_cli.models.rocrate import GenerateROCrate, AppendCrate
+from fairscape_cli.utils.serialization import prune_none
 from fairscape_cli.models.dataset import GenerateDataset
 from fairscape_cli.models.experiment import GenerateExperiment
 from fairscape_cli.models.instrument import GenerateInstrument
@@ -342,7 +343,7 @@ class GenomicData(BaseModel):
                              root_dataset_node["hasPart"].append({"@id": entity_id})
 
                 f.seek(0)
-                json.dump(crate_json, f, indent=2)
+                json.dump(prune_none(crate_json), f, indent=2)
                 f.truncate()
 
 
@@ -360,7 +361,7 @@ class GenomicData(BaseModel):
 
             if updated:
                 f.seek(0)
-                json.dump(crate_json_final, f, indent=2)
+                json.dump(prune_none(crate_json_final), f, indent=2)
                 f.truncate()
 
 
@@ -500,4 +501,3 @@ class GenomicData(BaseModel):
             experiments=Experiments(items=internal_experiments),
             outputs=Outputs(items=outputs_list)
         )
-

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/datasheet_builder/rocrate/datasheet_generator.py

@@ -159,6 +159,8 @@ class DatasheetGenerator:
         distribution = distribution_converter.convert()
         
         subcrate_items = self._process_all_subcrates()
+        if not subcrate_items:
+            subcrate_items = self._build_single_crate_composition()
         composition = CompositionSection(items=subcrate_items) if subcrate_items else None
         
         return FairscapeDatasheet(
@@ -226,6 +228,42 @@ class DatasheetGenerator:
         
         return subcrate_items
     
+    def _build_single_crate_composition(self) -> List[SubCrateItem]:
+        """When no subcrates exist, treat the main crate itself as a single subcrate."""
+        try:
+            converter = ROCToTargetConverter(
+                source_crate=self.main_crate,
+                mapping_configuration=SUBCRATE_MAPPING_CONFIGURATION,
+                global_index=self.global_metadata_index
+            )
+            subcrate_item = converter.convert()
+            subcrate_item.published = self.published
+            subcrate_item.preview_url = ""
+
+            if not subcrate_item.size and self.base_dir.exists():
+                try:
+                    dir_size = get_directory_size(str(self.base_dir))
+                    subcrate_item.size = format_size(dir_size)
+                except Exception:
+                    subcrate_item.size = "Unknown"
+
+            main_root = self.main_crate.metadataGraph[1].model_dump()
+            if not subcrate_item.doi:
+                subcrate_item.doi = main_root.get('identifier')
+            if not subcrate_item.related_publications:
+                pubs = main_root.get('associatedPublication', [])
+                if pubs:
+                    subcrate_item.related_publications = pubs if isinstance(pubs, list) else [pubs]
+
+            self._enhance_subcrate_item(subcrate_item, self.main_crate)
+
+            return [subcrate_item]
+        except Exception as e:
+            print(f"Error building single crate composition: {e}")
+            import traceback
+            traceback.print_exc()
+            return []
+
     def _enhance_subcrate_item(self, subcrate_item: SubCrateItem, subcrate: ROCrateV1_2):
         """Add statistical summary info to subcrate item if present."""
         root_dict = subcrate.metadataGraph[1].model_dump() if len(subcrate.metadataGraph) > 1 else {}

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/datasheet_builder/rocrate/summary_generator.py

@@ -11,6 +11,7 @@ from jinja2 import Environment
 from fairscape_models.rocrate import ROCrateV1_2
 from fairscape_models.conversion.mapping.AIReady import score_rocrate
 from fairscape_models.conversion.models.AIReady import AIReadyScore
+from fairscape_cli.utils.serialization import model_dump_pruned
 
 
 @dataclass
@@ -89,7 +90,7 @@ class SummarySectionGenerator:
             formats = []
         formats = [f for f in formats if f and f != "unknown"]
 
-        return SummaryData(
+        summary = SummaryData(
             name=root_data.get("name", "Unnamed Dataset"),
             description=root_data.get("description", ""),
             total_size_formatted=size_str,
@@ -100,6 +101,36 @@ class SummarySectionGenerator:
             formats=formats
         )
 
+        # Fallback: compute from graph if evi:* fields are absent (single crate case)
+        if summary.total_entities == 0:
+            formats_set = set()
+            for item in crate.metadataGraph:
+                if item.guid == "ro-crate-metadata.json":
+                    continue
+                item_dict = item.model_dump(by_alias=True)
+                item_type = item_dict.get("@type", "")
+                type_str = " ".join(item_type) if isinstance(item_type, list) else str(item_type)
+
+                if "ROCrate" in type_str or "CreativeWork" in type_str:
+                    continue
+
+                summary.total_entities += 1
+
+                if "Dataset" in type_str:
+                    summary.dataset_count += 1
+                    fmt = item_dict.get("fileFormat")
+                    if fmt and fmt != "unknown":
+                        formats_set.add(fmt)
+                elif "Software" in type_str or "SoftwareSourceCode" in type_str:
+                    summary.software_count += 1
+                elif "Computation" in type_str:
+                    summary.computation_count += 1
+
+            if not summary.formats and formats_set:
+                summary.formats = sorted(formats_set)
+
+        return summary
+
     @staticmethod
     def _format_size(size_bytes: int) -> str:
         """Format bytes to human-readable size."""
@@ -160,7 +191,7 @@ class SummarySectionGenerator:
 
     def save_aiready_score(self, raw_score: AIReadyScore, output_path: Path) -> None:
         """Save the AI-Ready score to a JSON file."""
-        score_dict = raw_score.model_dump()
+        score_dict = model_dump_pruned(raw_score)
         with open(output_path, 'w') as f:
             json.dump(score_dict, f, indent=2)
 
@@ -183,8 +214,10 @@ class SummarySectionGenerator:
             self.save_aiready_score(raw_score, aiready_json_path)
 
         desc = summary.description
+        description_truncated = False
         if len(desc) > 500:
-            desc = desc[:500].rsplit(" ", 1)[0] + "..."
+            desc = desc[:500].rsplit(" ", 1)[0]
+            description_truncated = True
 
         formats_str = ", ".join(sorted(summary.formats)[:10])
         if len(summary.formats) > 10:
@@ -192,6 +225,7 @@ class SummarySectionGenerator:
 
         context = {
             'description': desc,
+            'description_truncated': description_truncated,
             'total_size': summary.total_size_formatted,
             'total_entities': f"{summary.total_entities:,}" if summary.total_entities else "N/A",
             'formats': formats_str,

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/datasheet_builder/templates/base.html

@@ -18,18 +18,18 @@
       .container {
         max-width: 1100px;
         margin: 0 auto;
-        padding: 20px;
+        padding: 12px;
         background-color: white;
         box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
         /* Added for smooth transition */
         transition: margin-left 0.3s ease-in-out;
       }
       header {
-        margin-bottom: 20px;
+        margin-bottom: 10px;
         border-bottom: 2px solid #2c3e50;
-        padding-bottom: 15px;
+        padding-bottom: 8px;
         background-color: #f8f9fa;
-        padding: 20px;
+        padding: 12px;
         border-radius: 5px;
       }
       h1 {
@@ -40,35 +40,35 @@
       h2 {
         font-size: 20px;
         color: #2c3e50;
-        margin-top: 25px;
-        margin-bottom: 15px;
+        margin-top: 12px;
+        margin-bottom: 8px;
         border-bottom: 1px solid #ddd;
-        padding-bottom: 8px;
+        padding-bottom: 4px;
       }
       h3 {
         font-size: 18px;
         color: #2c3e50;
-        margin-top: 20px;
-        margin-bottom: 10px;
+        margin-top: 10px;
+        margin-bottom: 6px;
       }
       h4 {
         font-size: 16px;
         color: #2c3e50;
-        margin-top: 15px;
-        margin-bottom: 10px;
+        margin-top: 8px;
+        margin-bottom: 6px;
       }
       .summary-section {
         background-color: #f8f9fa;
-        padding: 20px;
+        padding: 12px;
         border-radius: 4px;
-        margin-bottom: 30px;
+        margin-bottom: 15px;
         box-shadow: 0 1px 3px rgba(0, 0, 0, 0.12);
       }
       .summary-row {
         display: flex;
-        margin-bottom: 12px;
+        margin-bottom: 6px;
         border-bottom: 1px solid #eee;
-        padding-bottom: 8px;
+        padding-bottom: 4px;
       }
       .summary-label {
         width: 230px;
@@ -79,24 +79,24 @@
         flex: 1;
       }
       .section-header {
-        margin: 25px 0 15px 0;
-        padding-bottom: 8px;
+        margin: 12px 0 8px 0;
+        padding-bottom: 4px;
         border-bottom: 1px solid #ddd;
         color: #2c3e50;
       }
       .composition-summary {
         display: flex;
         flex-wrap: wrap;
-        gap: 20px;
-        margin-bottom: 20px;
+        gap: 10px;
+        margin-bottom: 10px;
       }
       .composition-item {
         background-color: #f8f9fa;
         border-radius: 4px;
-        padding: 15px;
+        padding: 10px;
         text-align: center;
         box-shadow: 0 1px 3px rgba(0, 0, 0, 0.12);
-        width: calc(20% - 20px);
+        width: calc(20% - 10px);
         min-width: 120px;
       }
       .composition-count {
@@ -110,20 +110,20 @@
         color: #555;
       }
       .subcrates-container {
-        margin-top: 30px;
+        margin-top: 15px;
       }
       .subcrate-summary {
         background-color: #f8f9fa;
         border-radius: 4px;
-        padding: 20px;
-        margin-bottom: 20px;
+        padding: 12px;
+        margin-bottom: 10px;
         box-shadow: 0 1px 3px rgba(0, 0, 0, 0.12);
       }
       .subcrate-metadata {
-        margin-bottom: 15px;
+        margin-bottom: 8px;
       }
       .metadata-item {
-        margin-bottom: 6px;
+        margin-bottom: 3px;
       }
       .metadata-label {
         font-weight: bold;
@@ -133,24 +133,24 @@
       .section-summary {
         background-color: white;
         border-radius: 4px;
-        padding: 15px;
-        margin-top: 15px;
-        margin-bottom: 15px;
+        padding: 10px;
+        margin-top: 8px;
+        margin-bottom: 8px;
         border: 1px solid #eaeaea;
       }
       .summary-grid {
         display: grid;
         grid-template-columns: repeat(auto-fill, minmax(250px, 1fr));
-        gap: 15px;
+        gap: 10px;
       }
       .summary-item {
-        margin-bottom: 15px;
+        margin-bottom: 8px;
       }
       details {
-        margin-top: 15px;
+        margin-top: 8px;
         border: 1px solid #eaeaea;
         border-radius: 4px;
-        padding: 10px;
+        padding: 8px;
       }
       summary {
         font-weight: bold;
@@ -175,7 +175,7 @@
         color: #2c3e50;
       }
       .view-full-link {
-        margin-top: 15px;
+        margin-top: 8px;
         text-align: right;
       }
       .view-full-link a {
@@ -194,15 +194,15 @@
       .use-cases-section {
         background-color: #f8f9fa;
         border-radius: 4px;
-        padding: 20px;
-        margin-bottom: 30px;
+        padding: 12px;
+        margin-bottom: 15px;
         box-shadow: 0 1px 3px rgba(0, 0, 0, 0.12);
       }
       .distribution-item,
       .use-cases-item {
-        margin-bottom: 12px;
+        margin-bottom: 6px;
         border-bottom: 1px solid #eee;
-        padding-bottom: 8px;
+        padding-bottom: 4px;
       }
       .distribution-label,
       .use-cases-label {
@@ -226,16 +226,16 @@
       }
       .subcrate-title {
         border-bottom: 2px solid #2c3e50;
-        padding-bottom: 10px;
-        margin-bottom: 15px;
+        padding-bottom: 6px;
+        margin-bottom: 8px;
         color: #2c3e50;
       }
       .composition-grid {
         display: grid;
         grid-template-columns: repeat(auto-fill, minmax(300px, 1fr));
-        gap: 15px;
-        margin-top: 15px;
-        margin-bottom: 15px;
+        gap: 8px;
+        margin-top: 8px;
+        margin-bottom: 8px;
       }
       .composition-card {
         border: 1px solid #eaeaea;
@@ -259,12 +259,12 @@
         color: #2c3e50;
       }
       .card-content {
-        padding: 15px;
+        padding: 8px 10px;
       }
       .card-stats {
         display: flex;
         flex-direction: column;
-        gap: 10px;
+        gap: 6px;
       }
       .stat-item {
         display: flex;
@@ -292,9 +292,9 @@
       .compact-grid {
         display: grid;
         grid-template-columns: repeat(2, 1fr);
-        gap: 10px;
-        margin-top: 10px;
-        margin-bottom: 10px;
+        gap: 6px;
+        margin-top: 6px;
+        margin-bottom: 6px;
       }
 
       .summary-card {
@@ -312,7 +312,7 @@
 
       .indent {
         margin-left: 12px;
-        margin-bottom: 8px;
+        margin-bottom: 4px;
       }
 
       .small {
@@ -330,13 +330,13 @@
       }
 
       .subcrate-composition h4 {
-        margin-top: 12px;
-        margin-bottom: 8px;
+        margin-top: 8px;
+        margin-bottom: 4px;
       }
 
       footer {
-        margin-top: 30px;
-        padding: 20px;
+        margin-top: 15px;
+        padding: 12px;
         background-color: #f8f9fa;
         border-top: 1px solid #ddd;
         border-radius: 5px;
@@ -354,15 +354,15 @@
         text-decoration: underline;
       }
       .regulatory-section {
-        margin-top: 20px;
-        margin-bottom: 20px;
+        margin-top: 10px;
+        margin-bottom: 10px;
         padding: 0;
       }
 
       .regulatory-section h3 {
         font-size: 18px;
         color: #2c3e50;
-        margin-bottom: 15px;
+        margin-bottom: 8px;
         border-bottom: none;
         padding-bottom: 0;
       }
@@ -370,12 +370,12 @@
       .regulatory-grid {
         display: grid;
         grid-template-columns: repeat(2, 1fr);
-        gap: 15px;
+        gap: 8px;
       }
 
       .regulatory-item {
         background-color: #f8f9fa;
-        padding: 12px 15px;
+        padding: 8px 10px;
         border-radius: 4px;
         border: none;
       }
@@ -388,9 +388,9 @@
 
       .irb-detail {
         background-color: #f8f9fa;
-        padding: 12px 15px;
+        padding: 8px 10px;
         border-radius: 4px;
-        margin-top: 15px;
+        margin-top: 8px;
       }
 
       .irb-org {
@@ -425,9 +425,9 @@
 
       .regulatory-exemptions {
         background-color: #f8f9fa;
-        padding: 12px 15px;
+        padding: 8px 10px;
         border-radius: 4px;
-        margin-top: 15px;
+        margin-top: 8px;
       }
 
       .regulatory-exemptions p {
@@ -504,9 +504,9 @@
       /* START: Executive Summary and AI-Readiness Score styles */
       .executive-summary-section {
         background-color: #e9ecef;
-        padding: 20px;
+        padding: 12px;
         border-radius: 5px;
-        margin-bottom: 20px;
+        margin-bottom: 10px;
         border: 1px solid #ced4da;
       }
 
@@ -521,18 +521,18 @@
       .summary-description {
         font-size: 13px;
         color: #495057;
-        margin-bottom: 15px;
+        margin-bottom: 8px;
       }
 
       .exec-summary-grid {
         display: grid;
         grid-template-columns: 1fr 1fr;
-        gap: 15px;
+        gap: 10px;
       }
 
       .exec-summary-item {
         background-color: #f8f9fa;
-        padding: 12px 15px;
+        padding: 8px 10px;
         border-radius: 4px;
         border: 1px solid #e9ecef;
       }
@@ -541,15 +541,15 @@
         font-weight: bold;
         color: #2c3e50;
         display: block;
-        margin-bottom: 10px;
-        padding-bottom: 6px;
+        margin-bottom: 6px;
+        padding-bottom: 4px;
         border-bottom: 1px solid #dee2e6;
         font-size: 13px;
       }
 
       .exec-summary-item .stat-item {
         display: block;
-        margin-bottom: 6px;
+        margin-bottom: 4px;
         font-size: 12px;
       }
 

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/datasheet_builder/templates/sections/subcrates.html

@@ -297,9 +297,11 @@
         </div>
       </div>
     </div>
+    {% if subcrate.preview_url %}
     <div class="view-full-link">
       <a href="{{ subcrate.preview_url }}">View Full Dataset Details</a>
     </div>
+    {% endif %}
   </div>
   {% endfor %} {% else %}
   <p>No subcrates found.</p>

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/datasheet_builder/templates/sections/summary.html

@@ -1,7 +1,7 @@
 <div id="datasheet-summary" class="executive-summary-section">
     <h2>Datasheet Summary</h2>
     {% if description %}
-    <p class="summary-description">{{ description }}</p>
+    <p class="summary-description">{{ description }}{% if description_truncated %}... <a href="#description" style="color: #2c3e50; font-size: 12px;">[read full description]</a>{% endif %}</p>
     {% endif %}
 
     <div class="exec-summary-grid">

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/entailments/find_outputs.py

@@ -1,6 +1,7 @@
 import pathlib
 import json
 from typing import List, Dict, Tuple, Set, Any
+from fairscape_cli.utils.serialization import prune_none
 
 def extract_datasets_from_graph(graph: List[Dict]) -> List[Tuple[str, bool]]:
     """
@@ -169,7 +170,7 @@ def add_inputs_outputs_to_rocrate(rocrate_path: pathlib.Path) -> Tuple[bool, str
         metadata["@graph"] = graph
         
         with open(metadata_path, 'w') as f:
-            json.dump(metadata, f, indent=2)
+            json.dump(prune_none(metadata), f, indent=2)
         
         input_count = len(inputs)
         output_count = len(outputs)
@@ -179,4 +180,4 @@ def add_inputs_outputs_to_rocrate(rocrate_path: pathlib.Path) -> Tuple[bool, str
     except json.JSONDecodeError as e:
         return False, f"Error parsing JSON: {e}"
     except Exception as e:
-        return False, f"Unexpected error: {e}"
+        return False, f"Unexpected error: {e}"

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/entailments/inverse.py

@@ -1,5 +1,6 @@
 import pathlib
 import json
+from fairscape_cli.utils.serialization import prune_none
 from typing import List, Tuple, Dict, Any
 from rdflib import Graph, URIRef
 from rdflib.namespace import OWL
@@ -192,7 +193,7 @@ def augment_rocrate_with_inverses(
     if modified_count > 0:
         try:
             with open(metadata_file_path, 'w') as f:
-                json.dump(json_data, f, indent=2, ensure_ascii=False)
+                json.dump(prune_none(json_data), f, indent=2, ensure_ascii=False)
             print(f"RO-Crate '{metadata_file_path}' augmented with inverse properties. {modified_count} modifications made.")
         except Exception as e:
             print(f"Error saving augmented RO-Crate JSON to {metadata_file_path}: {e}")
@@ -200,4 +201,4 @@ def augment_rocrate_with_inverses(
     else:
         print(f"No inverse properties needed to be added or RO-Crate '{metadata_file_path}' is already consistent.")
 
-    return True
+    return True

{fairscape_cli-1.2.1 → fairscape_cli-1.2.2}/src/fairscape_cli/models/bagit.py

@@ -10,6 +10,7 @@ from pydantic import (
 from typing import (
     Optional
 )
+from fairscape_cli.utils.serialization import model_dump_pruned
 
 
 class BagIt(BaseModel):
@@ -94,7 +95,7 @@ class BagIt(BaseModel):
         bagit_info_path = self.bagit_path / 'bag-info.txt'
         
         with bagit_info_path.open(mode="w") as bag_info_file:                        
-            for key, value in self.model_dump(by_alias=True).items():                              
+            for key, value in model_dump_pruned(self, by_alias=True).items():
                 if key != 'bagit_path' and key != 'rocrate_path':                    
                     bag_info_file.write('%s: %s\n' % (key, value))