Merge pull request #72 from simleo/sw_req

Convert SoftwareRequirement

cwl/grepucase/greptool.cwl

@@ -1,6 +1,13 @@
 class: CommandLineTool
 cwlVersion: v1.0
 
+hints:
+  SoftwareRequirement:
+    packages:
+      grep:
+        specs: ["https://www.gnu.org/software/grep/"]
+        version: ["3.8"]
+
 baseCommand: ["bash", "-c"]
 
 inputs:

src/runcrate/convert.py

@@ -396,13 +396,31 @@ def add_tool(self, crate, workflow, cwl_tool):
                     ramMin = req.ramMin
                     if ramMin:
                         properties["memoryRequirements"] = f"{int(ramMin)} MiB"
+        deps = []
         if hasattr(cwl_tool, "hints") and cwl_tool.hints:
             for req in cwl_tool.hints:
                 if hasattr(req, "class_") and req.class_ == "ResourceRequirement":
                     ramMin = req.ramMin
                     if ramMin:
                         properties["memoryRequirements"] = f"{int(ramMin)} MiB"
+                if hasattr(req, "class_") and req.class_ == "SoftwareRequirement":
+                    for p in req.packages:
+                        if hasattr(p, "specs") and p.specs:
+                            dep_id = p.specs[0]
+                            dep_properties = {
+                                "@type": "SoftwareApplication",
+                                "name": p.package
+                            }
+                            if p.version:
+                                dep_properties["softwareVersion"] = p.version
+                            deps.append(
+                                crate.add(ContextEntity(crate, dep_id, properties=dep_properties))
+                            )
         tool = crate.add(ContextEntity(crate, tool_id, properties=properties))
+        if deps:
+            tool["softwareRequirements"] = deps
+        if len(deps) == 1:
+            tool["mainEntity"] = deps[0]
         tool["input"] = self.add_params(crate, cwl_tool.inputs)
         tool["output"] = self.add_params(crate, cwl_tool.outputs)
         workflow.append_to("hasPart", tool)

tests/data/grepucase-run-1/bag-info.txt

@@ -1,6 +1,6 @@
-Bag-Software-Agent: cwltool 3.1.20230213100550
+Bag-Software-Agent: cwltool 3.1.20231020140205
 BagIt-Profile-Identifier: https://w3id.org/ro/bagit/profile
-Bagging-Date: 2023-02-17
+Bagging-Date: 2023-11-22
 External-Description: Research Object of CWL workflow run
-External-Identifier: arcp://uuid,422fecc5-1e57-45bc-a653-1513a7a6fe70/
+External-Identifier: arcp://uuid,03322031-8508-4afe-94a8-0198cc6b81f0/
 Payload-Oxum: 151.7

tests/data/grepucase-run-1/manifest-sha1.txt

@@ -1,7 +1,7 @@
-8d84ef91f0aba379f5edc3836b4b5f6727920f22  data/8d/8d84ef91f0aba379f5edc3836b4b5f6727920f22
 d60dd58346cf7e533252f35399cd510b1b1467f7  data/d6/d60dd58346cf7e533252f35399cd510b1b1467f7
+8d84ef91f0aba379f5edc3836b4b5f6727920f22  data/8d/8d84ef91f0aba379f5edc3836b4b5f6727920f22
 1078cf414b2625a240b16392085d66580bb66f4d  data/10/1078cf414b2625a240b16392085d66580bb66f4d
-8545949f96b96cb721485066bafad9b768bc4e52  data/85/8545949f96b96cb721485066bafad9b768bc4e52
 5aa9aa3b336778cf2a7db648fc530892c3b3dabb  data/5a/5aa9aa3b336778cf2a7db648fc530892c3b3dabb
-3ccdc7533084b641e6c941cc6dbb091d2e5f8a41  data/3c/3ccdc7533084b641e6c941cc6dbb091d2e5f8a41
+8545949f96b96cb721485066bafad9b768bc4e52  data/85/8545949f96b96cb721485066bafad9b768bc4e52
 ec0270052a78321508502ed915815c4daf75fe46  data/ec/ec0270052a78321508502ed915815c4daf75fe46
+3ccdc7533084b641e6c941cc6dbb091d2e5f8a41  data/3c/3ccdc7533084b641e6c941cc6dbb091d2e5f8a41

tests/data/grepucase-run-1/metadata/directory-107dd13d-3630-4e81-bd71-026b638facbc.ttl

@@ -0,0 +1,26 @@
+@prefix id: <urn:uuid:> .
+@prefix ore: <http://www.openarchives.org/ore/terms/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix ro: <http://purl.org/wf4ever/ro#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+id:be8d4460-90f6-43c5-8287-ceab31972de2 a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "bar.out"^^xsd:string ;
+    ore:proxyFor id:a9ab8653-e354-4b7c-9bf8-0ae63766739b ;
+    ore:proxyIn id:107dd13d-3630-4e81-bd71-026b638facbc .
+
+id:f2ecfe9a-f8cc-4a93-be80-f432fe07c9fc a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "foo.out"^^xsd:string ;
+    ore:proxyFor id:79a136c8-0972-4775-a580-7bbcc534560e ;
+    ore:proxyIn id:107dd13d-3630-4e81-bd71-026b638facbc .
+
+id:107dd13d-3630-4e81-bd71-026b638facbc a ro:Folder,
+        ore:Aggregation,
+        prov:Entity ;
+    ore:aggregates id:be8d4460-90f6-43c5-8287-ceab31972de2,
+        id:f2ecfe9a-f8cc-4a93-be80-f432fe07c9fc .
+

tests/data/grepucase-run-1/metadata/directory-4ed2e115-3819-4223-b391-50c40fa8e7df.ttl

@@ -0,0 +1,26 @@
+@prefix id: <urn:uuid:> .
+@prefix ore: <http://www.openarchives.org/ore/terms/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix ro: <http://purl.org/wf4ever/ro#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+id:2075729e-b057-4fdc-9c86-09311d9c0ecc a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "foo.out"^^xsd:string ;
+    ore:proxyFor id:ddf09a83-68c1-43e9-b94f-014037afe00c ;
+    ore:proxyIn id:4ed2e115-3819-4223-b391-50c40fa8e7df .
+
+id:7470117c-b551-42be-8b7a-8185375db7e7 a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "bar.out"^^xsd:string ;
+    ore:proxyFor id:6e4a760b-51e7-472a-b732-fd31c1acf858 ;
+    ore:proxyIn id:4ed2e115-3819-4223-b391-50c40fa8e7df .
+
+id:4ed2e115-3819-4223-b391-50c40fa8e7df a ro:Folder,
+        ore:Aggregation,
+        prov:Entity ;
+    ore:aggregates id:2075729e-b057-4fdc-9c86-09311d9c0ecc,
+        id:7470117c-b551-42be-8b7a-8185375db7e7 .
+

tests/data/grepucase-run-1/metadata/directory-66dbb40f-d6d1-42db-8220-8b51ad4dd5ba.ttl

@@ -0,0 +1,26 @@
+@prefix id: <urn:uuid:> .
+@prefix ore: <http://www.openarchives.org/ore/terms/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix ro: <http://purl.org/wf4ever/ro#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+id:95b7c437-983d-496b-9f5d-76920586668e a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "foo"^^xsd:string ;
+    ore:proxyFor id:fb8bdb45-b85e-4fa3-b385-26bb40577340 ;
+    ore:proxyIn id:66dbb40f-d6d1-42db-8220-8b51ad4dd5ba .
+
+id:caf7defd-a8f4-4bb7-9961-02ff95d40c76 a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "bar"^^xsd:string ;
+    ore:proxyFor id:92d8ca48-5172-458e-901e-5763cf093663 ;
+    ore:proxyIn id:66dbb40f-d6d1-42db-8220-8b51ad4dd5ba .
+
+id:66dbb40f-d6d1-42db-8220-8b51ad4dd5ba a ro:Folder,
+        ore:Aggregation,
+        prov:Entity ;
+    ore:aggregates id:95b7c437-983d-496b-9f5d-76920586668e,
+        id:caf7defd-a8f4-4bb7-9961-02ff95d40c76 .
+

tests/data/grepucase-run-1/metadata/directory-bea1dc23-0537-4874-82ce-454f48c08d0a.ttl → tests/data/grepucase-run-1/metadata/directory-79a136c8-0972-4775-a580-7bbcc534560e.ttl

@@ -4,15 +4,15 @@
 @prefix ro: <http://purl.org/wf4ever/ro#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
-id:7329bf41-05c0-4881-8bd3-1203a530f736 a ro:FolderEntry,
-        ore:Proxy,
+id:79a136c8-0972-4775-a580-7bbcc534560e a ro:Folder,
+        ore:Aggregation,
         prov:Entity ;
-    ro:entryName "foo.out.out"^^xsd:string ;
-    ore:proxyFor id:cb12bf67-5541-4f8c-b897-47a87e11a242 ;
-    ore:proxyIn id:bea1dc23-0537-4874-82ce-454f48c08d0a .
+    ore:aggregates id:d72a309c-26f9-422c-a812-74127256c8a2 .
 
-id:bea1dc23-0537-4874-82ce-454f48c08d0a a ro:Folder,
-        ore:Aggregation,
+id:d72a309c-26f9-422c-a812-74127256c8a2 a ro:FolderEntry,
+        ore:Proxy,
         prov:Entity ;
-    ore:aggregates id:7329bf41-05c0-4881-8bd3-1203a530f736 .
+    ro:entryName "foo.out.out"^^xsd:string ;
+    ore:proxyFor id:b604cd9a-7a66-4bf2-83fc-b61b515b06bb ;
+    ore:proxyIn id:79a136c8-0972-4775-a580-7bbcc534560e .
 

tests/data/grepucase-run-1/metadata/directory-99571210-dcea-4991-bc3d-64b28f87a0d7.ttl

@@ -0,0 +1,26 @@
+@prefix id: <urn:uuid:> .
+@prefix ore: <http://www.openarchives.org/ore/terms/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix ro: <http://purl.org/wf4ever/ro#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+id:4e117ee5-4bcb-41be-a18a-98163d76839f a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "foo"^^xsd:string ;
+    ore:proxyFor id:cb8da8f0-ac68-4ee4-96be-e7251eee8743 ;
+    ore:proxyIn id:99571210-dcea-4991-bc3d-64b28f87a0d7 .
+
+id:e4231925-b712-419b-89c9-feb7468faf0d a ro:FolderEntry,
+        ore:Proxy,
+        prov:Entity ;
+    ro:entryName "bar"^^xsd:string ;
+    ore:proxyFor id:608f6a9a-4d1f-4255-9424-328b4f68a291 ;
+    ore:proxyIn id:99571210-dcea-4991-bc3d-64b28f87a0d7 .
+
+id:99571210-dcea-4991-bc3d-64b28f87a0d7 a ro:Folder,
+        ore:Aggregation,
+        prov:Entity ;
+    ore:aggregates id:4e117ee5-4bcb-41be-a18a-98163d76839f,
+        id:e4231925-b712-419b-89c9-feb7468faf0d .
+

tests/data/grepucase-run-1/metadata/directory-8cb9abec-9ecf-4e54-86b5-7f08a073ce60.ttl → tests/data/grepucase-run-1/metadata/directory-a9ab8653-e354-4b7c-9bf8-0ae63766739b.ttl

@@ -4,15 +4,15 @@
 @prefix ro: <http://purl.org/wf4ever/ro#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
-id:899d951e-0ef0-42a7-a460-3cf4c3b3aff5 a ro:FolderEntry,
+id:0928d1de-6468-4558-8787-f8fef8fc3384 a ro:FolderEntry,
         ore:Proxy,
         prov:Entity ;
     ro:entryName "bar.out.out"^^xsd:string ;
-    ore:proxyFor id:2c6ae84c-c98c-4173-aa24-44b9bb21d372 ;
-    ore:proxyIn id:8cb9abec-9ecf-4e54-86b5-7f08a073ce60 .
+    ore:proxyFor id:124c0ca7-05d4-4867-9770-7dde9ed93a52 ;
+    ore:proxyIn id:a9ab8653-e354-4b7c-9bf8-0ae63766739b .
 
-id:8cb9abec-9ecf-4e54-86b5-7f08a073ce60 a ro:Folder,
+id:a9ab8653-e354-4b7c-9bf8-0ae63766739b a ro:Folder,
         ore:Aggregation,
         prov:Entity ;
-    ore:aggregates id:899d951e-0ef0-42a7-a460-3cf4c3b3aff5 .
+    ore:aggregates id:0928d1de-6468-4558-8787-f8fef8fc3384 .
 

tests/data/grepucase-run-1/metadata/logs/engine.fdbae933-9344-4455-8592-efa0f72862ac.txt

@@ -0,0 +1,28 @@
+[2023-11-22T14:00:34,368.000000Z] [cwltool] /home/simleo/git/runcrate/venv/bin/cwltool --provenance ro grepucase.cwl grepucase-job.yml
+[2023-11-22T14:00:34,370.000000Z] Resolved 'grepucase.cwl' to 'file:///home/simleo/git/runcrate/cwl/grepucase/grepucase.cwl'
+[2023-11-22T14:00:34,662.000000Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepucase/grepucase_in/foo
+[2023-11-22T14:00:34,663.000000Z] [provenance] Adding to RO file:///home/simleo/git/runcrate/cwl/grepucase/grepucase_in/bar
+[2023-11-22T14:00:34,674.000000Z] [workflow ] start
+[2023-11-22T14:00:34,674.000000Z] [workflow ] starting step grep
+[2023-11-22T14:00:34,674.000000Z] [step grep] start
+[2023-11-22T14:00:34,676.000000Z] [job grep] /tmp/vkckwf2j$ bash \
+    -c \
+    'mkdir -p grep_out
+find /tmp/c3z_ayvp/stgbd555114-f2e4-41d0-88aa-b579666d7084/grepucase_in/ -type f | while read f; do
+  grep lazy ${f} > grep_out/`basename ${f}`.out
+done'
+[2023-11-22T14:00:34,693.000000Z] [job grep] completed success
+[2023-11-22T14:00:34,693.000000Z] [step grep] completed success
+[2023-11-22T14:00:34,693.000000Z] [workflow ] starting step ucase
+[2023-11-22T14:00:34,693.000000Z] [step ucase] start
+[2023-11-22T14:00:34,695.000000Z] [job ucase] /tmp/nozkr02w$ bash \
+    -c \
+    'mkdir -p ucase_out
+find /tmp/4vfdgmw2/stg829c996f-6110-4091-90e8-9075cabe7301/grep_out/ -type f | while read f; do
+  mkdir ucase_out/`basename ${f}`
+  awk '"'"'{print toupper($0)}'"'"' < ${f} > ucase_out/`basename ${f}`/`basename ${f}`.out
+done'
+[2023-11-22T14:00:34,717.000000Z] [job ucase] completed success
+[2023-11-22T14:00:34,718.000000Z] [step ucase] completed success
+[2023-11-22T14:00:34,718.000000Z] [workflow ] completed success
+[2023-11-22T14:00:34,768.000000Z] Final process status is success