NIDM-Results 1.1.0 release

nidm/nidm-results/scripts/create_results_specification.py

@@ -186,21 +186,31 @@ def main(nidm_original_version):
     owlspec._header_footer(component="nidm-results", version=nidm_version)
 
     if not nidm_version == "dev":
-        if nidm_version == "020":
+        if nidm_version == "110":
+            # Previous version
+            owlspec.text = owlspec.text.replace(
+                "nidm-results_020.html", "nidm-results_100.html")
+        elif nidm_version == "020":
             # Previous version
             owlspec.text = owlspec.text.replace(
                 "nidm-results_020.html", "nidm-results_010.html")
-        owlspec.text = owlspec.text.replace(
-            "(under development)", nidm_original_version)
-        owlspec.text = owlspec.text.replace(
-            "nidm-results_dev.html",
-            "nidm-results_" + nidm_version + ".html", 1)
-        owlspec.text = owlspec.text.replace(
-            "img/", "img/nidm-results_" + nidm_version + "/")
+        owlspec.text = dev_to_release(owlspec.text, nidm_original_version)
 
     owlspec.write_specification(component="nidm-results", version=nidm_version)
 
 
+def dev_to_release(text, full_version):
+    version = full_version.replace(".", "")
+    text = text.replace(
+        "(under development)", full_version)
+    text = text.replace(
+        "nidm-results_dev.html",
+        "nidm-results_" + version + ".html", 1)
+    text = text.replace(
+        "img/", "img/nidm-results_" + version + "/")
+    return text
+
+
 def _replace_term_by(renaming, components, used_by, generated_by,
                      derived_from):
     for original_term, renamed_term in renaming:

nidm/nidm-results/scripts/release_nidm_results.py

@@ -16,10 +16,12 @@
 import sys
 import shutil
 import urllib2
+from create_results_specification import main as create_spec
 
 RELPATH = os.path.dirname(os.path.abspath(__file__))
 NIDMRESULTSPATH = os.path.dirname(RELPATH)
 NIDMPATH = os.path.join(NIDMRESULTSPATH, os.pardir)
+SPECSPATH = os.path.join(NIDMPATH, os.pardir, "doc", "content", "specs")
 
 # Append parent script directory to path
 sys.path.append(os.path.join(NIDMRESULTSPATH, os.pardir, os.pardir, "scripts"))
@@ -99,15 +101,8 @@ def create_release(self):
                 owl_txt = owl_txt + "\n\n##### Imports from %s #####" % (name)
                 owl_txt = owl_txt + im_txt
 
-                # Replace address of examples
-                owl_txt = owl_txt.replace(
-                    "https://raw.githubusercontent.com/incf-nidash/nidm/\
-master/",
-                    "https://raw.githubusercontent.com/incf-nidash/nidm/\
-NIDM-Results_"+self.nidm_original_version+"/")
-
         # Remove AFNI-related terms (not ready for release yet)
-        if int(self.nidm_version) <= 100:
+        if int(self.nidm_version) <= 110:
             owl_txt = owl_txt.replace(
                 "@prefix afni: <http://purl.org/nidash/afni#> .\n", "")
             # Remove terms: nidm:'Legendre Polynomial Order', afni:'BLOCK',
@@ -121,7 +116,28 @@ def create_release(self):
                 owl_txt = owl_txt.replace(m.group(), "")
 
         with open(release_owl_file, 'w') as fp:
-            owl_txt = fp.write(owl_txt)
+            fp.write(owl_txt)
+
+        # Create specification (before the address of examples are updated to
+        # avoid issue with examples pointing to tag not pushed yet)
+        create_spec(self.nidm_original_version)
+        if self.nidm_version == "100":
+            image_dir_prev = os.path.join(
+                SPECSPATH, "img", "nidm-results_100")
+        image_dir = os.path.join(
+            SPECSPATH, "img", "nidm-results_"+self.nidm_version)
+        if not os.path.isdir(image_dir):
+            shutil.copytree(image_dir_prev, image_dir)
+
+        # Replace address of examples
+        owl_txt = owl_txt.replace(
+            "https://raw.githubusercontent.com/incf-nidash/nidm/\
+master/",
+            "https://raw.githubusercontent.com/incf-nidash/nidm/\
+NIDM-Results_"+self.nidm_original_version+"/")
+
+        with open(release_owl_file, 'w') as fp:
+            fp.write(owl_txt)
 
 if __name__ == '__main__':
     if len(sys.argv) > 1:

nidm/nidm-results/spm/example004/README.md

@@ -1,9 +1,9 @@
 
-Prov store: https://provenance.ecs.soton.ac.uk/store/documents/77761/
+Prov store: https://provenance.ecs.soton.ac.uk/store/documents/82084/
 
-Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/77761.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/77761.ttl),
-Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/77761.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/77761.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/77761.png)
+Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/82084.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/82084.ttl),
+Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/82084.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/82084.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/82084.png)
 
-![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/77761.png)
+![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/82084.png)
 
 

nidm/nidm-results/spm/example004/spm_inference_activities.provn

@@ -11,7 +11,6 @@ prefix nidm_ConjunctionInference <http://purl.org/nidash/nidm#NIDM_0000011>
 prefix xsd <http://www.w3.org/2001/XMLSchema>
 prefix obo <http://purl.obolibrary.org/obo/>
 prefix spm <http://purl.org/nidash/spm#>
-prefix nidm_partialConjunctionDegree <http://purl.org/nidash/nidm#NIDM_0000095>
 prefix dctype <http://purl.org/dc/dcmitype/>
 prefix crypto <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#>
 prefix dct <http://purl.org/dc/terms/>
@@ -20,9 +19,10 @@ prefix nidm_OneTailedTest <http://purl.org/nidash/nidm#NIDM_0000060>
 prefix neurolex <http://neurolex.org/wiki/>
 prefix nidm_Inference <http://purl.org/nidash/nidm#NIDM_0000049>
 prefix nidm_hasAlternativeHypothesis <http://purl.org/nidash/nidm#NIDM_0000097>
+prefix spm_partialConjunctionDegree <http://purl.org/nidash/spm#SPM_0000015>
 prefix dc <http://purl.org/dc/elements/1.1/>
 activity(niiri:inference_id_1,-,-,[prov:type = 'nidm:NIDM_0000049', prov:label = "Inference", nidm:NIDM_0000097 = 'nidm:NIDM_0000060'])
-activity(niiri:conjunction_id_2,-,-,[prov:type = 'spm:SPM_0000005', prov:label = "k-Conjunction Inference", nidm:NIDM_0000097 = 'nidm:NIDM_0000060', nidm:NIDM_0000095 = "1" %% xsd:int])
+activity(niiri:conjunction_id_2,-,-,[prov:type = 'spm:SPM_0000005', prov:label = "k-Conjunction Inference", nidm:NIDM_0000097 = 'nidm:NIDM_0000060', spm:SPM_0000015 = "1" %% xsd:int])
 activity(niiri:conjunction_id_1,-,-,[prov:type = 'nidm:NIDM_0000011', prov:label = "Conjunction Inference", nidm:NIDM_0000097 = 'nidm:NIDM_0000060'])
 used(niiri:inference_id_1,niiri:statistic_map_id,-)
 used(niiri:inference_id_1,niiri:height_threshold_id,-)

nidm/nidm-results/spm/example004/spm_inference_activities.ttl

@@ -19,8 +19,8 @@
 @prefix nidm_hasAlternativeHypothesis: <http://purl.org/nidash/nidm#NIDM_0000097> .
 @prefix nidm_OneTailedTest: <http://purl.org/nidash/nidm#NIDM_0000060> .
 @prefix nidm_Inference: <http://purl.org/nidash/nidm#NIDM_0000049> .
-@prefix nidm_partialConjunctionDegree: <http://purl.org/nidash/nidm#NIDM_0000095> .
 @prefix spm_PartialConjunctionInference: <http://purl.org/nidash/spm#SPM_0000005> .
+@prefix spm_partialConjunctionDegree: <http://purl.org/nidash/spm#SPM_0000015> .
 
 
 niiri:conjunction_id_1 a prov:Activity , nidm_ConjunctionInference: ;
@@ -38,7 +38,7 @@ niiri:inference_id_1 a prov:Activity , nidm_Inference: ;
 niiri:conjunction_id_2 a prov:Activity , spm_PartialConjunctionInference: ;
 	rdfs:label "k-Conjunction Inference" ;
 	nidm_hasAlternativeHypothesis: nidm_OneTailedTest: ;
-	nidm_partialConjunctionDegree: "1"^^xsd:int ;
+	spm_partialConjunctionDegree: "1"^^xsd:int ;
     prov:used niiri:statistic_map_id_1, niiri:statistic_map_id_2, niiri:height_threshold_id, niiri:extent_threshold_id, niiri:display_map_id, niiri:peak_definition_criteria_id, niiri:cluster_definition_criteria_id, niiri:mask_id_1 ;
     prov:wasAssociatedWith niiri:software_id .