Fix output format settings

Closes #8
cthoyt · Sep 12, 2023 · afac5c8 · afac5c8
1 parent 4817bcf
commit afac5c8
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Showing 9 changed files with 71 additions and 70 deletions.
diff --git a/selventa_knowledge/__init__.py b/selventa_knowledge/__init__.py
@@ -35,6 +35,7 @@
     from_path_kwargs=dict(
         citation_clearing=False,
     ),
+    formats=("pickle", "nodelink.json.gz")
 )
 
 get_graph = repository.get_graph

diff --git a/selventa_knowledge/large_corpus.bel.nodelink.json.gz b/selventa_knowledge/large_corpus.bel.nodelink.json.gz
diff --git a/selventa_knowledge/large_corpus.bel.pickle b/selventa_knowledge/large_corpus.bel.pickle
diff --git a/selventa_knowledge/large_corpus.bel.summary.json b/selventa_knowledge/large_corpus.bel.summary.json
@@ -1,14 +1,14 @@
 {
   "Name": "BEL Framework Large Corpus Document",
   "Version": "20170611",
-  "Author": "Selventa",
+  "Authors": "Selventa",
   "Number of Nodes": 27967,
   "Number of Namespaces": 15,
   "Number of Edges": 80053,
   "Number of Annotations": 8,
   "Number of Citations": 16187,
-  "Number of Authors": 57243,
-  "Network Density": "1.02E-04",
+  "Number of Authors": 57245,
   "Number of Components": 47,
-  "Number of Warnings": 987
+  "Number of Warnings": 987,
+  "Network Density": "1.02E-04"
 }
diff --git a/selventa_knowledge/large_corpus.bel.warnings.tsv b/selventa_knowledge/large_corpus.bel.warnings.tsv
diff --git a/selventa_knowledge/small_corpus.bel.nodelink.json.gz b/selventa_knowledge/small_corpus.bel.nodelink.json.gz
diff --git a/selventa_knowledge/small_corpus.bel.pickle b/selventa_knowledge/small_corpus.bel.pickle
diff --git a/selventa_knowledge/small_corpus.bel.summary.json b/selventa_knowledge/small_corpus.bel.summary.json
@@ -1,14 +1,14 @@
 {
   "Name": "BEL Framework Small Corpus Document",
   "Version": "20150611",
-  "Author": "Selventa",
+  "Authors": "Selventa",
   "Number of Nodes": 1301,
   "Number of Namespaces": 15,
   "Number of Edges": 2671,
   "Number of Annotations": 8,
   "Number of Citations": 57,
   "Number of Authors": 350,
-  "Network Density": "1.58E-03",
   "Number of Components": 20,
-  "Number of Warnings": 102
+  "Number of Warnings": 102,
+  "Network Density": "1.58E-03"
 }
diff --git a/selventa_knowledge/small_corpus.bel.warnings.tsv b/selventa_knowledge/small_corpus.bel.warnings.tsv
@@ -9,7 +9,7 @@ Line Number	Position	Line	Error	Message
 1228	69	tloc(p(HGNC:CYCS),MESHCS:Mitochondria,MESHCS:Cytoplasm) increases bp(GOBP:necrosis)	MissingNamespaceNameWarning	"""necrosis"" is not in the GOBP namespace"
 1315	83	"bp(GOBP:""positive regulation of mitochondrial membrane permeability"") increases bp(GOBP:necrosis)"	MissingNamespaceNameWarning	"""necrosis"" is not in the GOBP namespace"
 1341	4	SET Cell = Hepatocytes	IllegalAnnotationValueWarning	"""Hepatocytes"" is not defined in the Cell annotation"
-1359	32	"path(SDIS:Steatosis) association bp(SDIS:""Lipid Droplet"")"	InvalidFunctionSemantic	"BiologicalProcess SDIS:""Lipid Droplet"" should be encoded as one of: Abundance, Gene, Protein, RNA, Complex, miRNA"
+1359	32	"path(SDIS:Steatosis) association bp(SDIS:""Lipid Droplet"")"	InvalidFunctionSemantic	"BiologicalProcess SDIS:""Lipid Droplet"" should be encoded as one of: Abundance, Protein, Complex, RNA, Gene, miRNA"
 1368	4	"SET Cell = ""Kupffer Cells"""	IllegalAnnotationValueWarning	"""Kupffer Cells"" is not defined in the Cell annotation"
 1373	23	p(HGNC:TGFB1) increases bp(SDIS:fibrosis)	InvalidFunctionSemantic	BiologicalProcess SDIS:fibrosis should be encoded as one of: Pathology
 1472	4	"SET CellLine = ""HT-1080"""	IllegalAnnotationValueWarning	"""HT-1080"" is not defined in the CellLine annotation"