Merge pull request #76 from dnlbauer/fix_agent_without_name

Fix failing conversion if author name is not set

Author: simleo

CITATION.cff

@@ -10,6 +10,9 @@ authors:
   - family-names: Crusoe
     given-names: Michael R.
     orcid: https://orcid.org/0000-0002-2961-9670
+  - family-names: Bauer
+    given-names: Daniel
+    orcid: https://orcid.org/0000-0001-9447-460X
 title: "runcrate"
 version: 0.5.0
 doi: 10.5281/zenodo.7762627

src/runcrate/convert.py

@@ -1,5 +1,6 @@
 # Copyright 2022-2024 CRS4.
 # Copyright 2023-2024 Michael R. Crusoe
+# Copyright 2024 Senckenberg Society for Nature Research
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -472,10 +473,12 @@ def add_agent(self, crate, roc_engine_run, engine):
             agent_id = a.identifier.uri
             if not agent_id.startswith("http"):
                 agent_id = "#" + agent_id.rsplit(":", 1)[-1]
-            ro_a = crate.add(ContextEntity(crate, agent_id, properties={
-                "@type": "Person",
-                "name": a.label
-            }))
+            properties = {
+                "@type": "Person"
+            }
+            if isinstance(a.label, str):
+                properties["name"] = a.label
+            ro_a = crate.add(ContextEntity(crate, agent_id, properties=properties))
             roc_engine_run.append_to("agent", ro_a, compact=True)
 
     def add_action(self, crate, activity, parent_instrument=None):

tests/data/revsort-no-agent-name-run-1/bag-info.txt

@@ -0,0 +1,6 @@
+Bag-Software-Agent: cwltool 3.1.20240112164112
+BagIt-Profile-Identifier: https://w3id.org/ro/bagit/profile
+Bagging-Date: 2024-03-26
+External-Description: Research Object of CWL workflow run
+External-Identifier: arcp://uuid,73420c43-a023-4f52-9630-13bcdd9441c2/
+Payload-Oxum: 3333.3

tests/data/revsort-no-agent-name-run-1/bagit.txt

@@ -0,0 +1,2 @@
+BagIt-Version: 0.97
+Tag-File-Character-Encoding: UTF-8

tests/data/revsort-no-agent-name-run-1/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376

@@ -0,0 +1,16 @@
+Call me Ishmael. Some years ago--never mind how long precisely--having
+little or no money in my purse, and nothing particular to interest me on
+shore, I thought I would sail about a little and see the watery part of
+the world. It is a way I have of driving off the spleen and regulating
+the circulation. Whenever I find myself growing grim about the mouth;
+whenever it is a damp, drizzly November in my soul; whenever I find
+myself involuntarily pausing before coffin warehouses, and bringing up
+the rear of every funeral I meet; and especially whenever my hypos get
+such an upper hand of me, that it requires a strong moral principle to
+prevent me from deliberately stepping into the street, and methodically
+knocking people's hats off--then, I account it high time to get to sea
+as soon as I can. This is my substitute for pistol and ball. With a
+philosophical flourish Cato throws himself upon his sword; I quietly
+take to the ship. There is nothing surprising in this. If they but knew
+it, almost all men in their degree, some time or other, cherish very
+nearly the same feelings towards the ocean with me.

tests/data/revsort-no-agent-name-run-1/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f

@@ -0,0 +1,16 @@
+gnivah--ylesicerp gnol woh dnim reven--oga sraey emoS .leamhsI em llaC
+no em tseretni ot ralucitrap gnihton dna ,esrup ym ni yenom on ro elttil
+fo trap yretaw eht ees dna elttil a tuoba lias dluow I thguoht I ,erohs
+gnitaluger dna neelps eht ffo gnivird fo evah I yaw a si tI .dlrow eht
+;htuom eht tuoba mirg gniworg flesym dnif I revenehW .noitalucric eht
+dnif I revenehw ;luos ym ni rebmevoN ylzzird ,pmad a si ti revenehw
+pu gnignirb dna ,sesuoheraw niffoc erofeb gnisuap yliratnulovni flesym
+teg sopyh ym revenehw yllaicepse dna ;teem I larenuf yreve fo raer eht
+ot elpicnirp larom gnorts a seriuqer ti taht ,em fo dnah reppu na hcus
+yllacidohtem dna ,teerts eht otni gnippets yletarebiled morf em tneverp
+aes ot teg ot emit hgih ti tnuocca I ,neht--ffo stah s'elpoep gnikconk
+a htiW .llab dna lotsip rof etutitsbus ym si sihT .nac I sa noos sa
+ylteiuq I ;drows sih nopu flesmih sworht otaC hsiruolf lacihposolihp
+wenk tub yeht fI .siht ni gnisirprus gnihton si erehT .pihs eht ot ekat
+yrev hsirehc ,rehto ro emit emos ,eerged rieht ni nem lla tsomla ,ti
+.em htiw naeco eht sdrawot sgnileef emas eht ylraen

tests/data/revsort-no-agent-name-run-1/data/b9/b9214658cc453331b62c2282b772a5c063dbd284

@@ -0,0 +1,16 @@
+yrev hsirehc ,rehto ro emit emos ,eerged rieht ni nem lla tsomla ,ti
+ylteiuq I ;drows sih nopu flesmih sworht otaC hsiruolf lacihposolihp
+yllacidohtem dna ,teerts eht otni gnippets yletarebiled morf em tneverp
+wenk tub yeht fI .siht ni gnisirprus gnihton si erehT .pihs eht ot ekat
+teg sopyh ym revenehw yllaicepse dna ;teem I larenuf yreve fo raer eht
+pu gnignirb dna ,sesuoheraw niffoc erofeb gnisuap yliratnulovni flesym
+ot elpicnirp larom gnorts a seriuqer ti taht ,em fo dnah reppu na hcus
+no em tseretni ot ralucitrap gnihton dna ,esrup ym ni yenom on ro elttil
+gnivah--ylesicerp gnol woh dnim reven--oga sraey emoS .leamhsI em llaC
+gnitaluger dna neelps eht ffo gnivird fo evah I yaw a si tI .dlrow eht
+fo trap yretaw eht ees dna elttil a tuoba lias dluow I thguoht I ,erohs
+dnif I revenehw ;luos ym ni rebmevoN ylzzird ,pmad a si ti revenehw
+aes ot teg ot emit hgih ti tnuocca I ,neht--ffo stah s'elpoep gnikconk
+a htiW .llab dna lotsip rof etutitsbus ym si sihT .nac I sa noos sa
+;htuom eht tuoba mirg gniworg flesym dnif I revenehW .noitalucric eht
+.em htiw naeco eht sdrawot sgnileef emas eht ylraen

tests/data/revsort-no-agent-name-run-1/manifest-sha1.txt

@@ -0,0 +1,3 @@
+327fc7aedf4f6b69a42a7c8b808dc5a7aff61376  data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
+97fe1b50b4582cebc7d853796ebd62e3e163aa3f  data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f
+b9214658cc453331b62c2282b772a5c063dbd284  data/b9/b9214658cc453331b62c2282b772a5c063dbd284

tests/data/revsort-no-agent-name-run-1/metadata/logs/engine.577e0cfe-9f26-4170-872b-94c1b2578771.txt

@@ -0,0 +1,49 @@
+[2024-03-26T08:34:59,882.000000Z] [cwltool] /home/dbauer/.local/bin/cwltool --provenance testprov revsort.cwl input.yml
+[2024-03-26T08:34:59,883.000000Z] Resolved 'revsort.cwl' to 'file:///home/dbauer/projects/runcrate/tests/data/revsort-run-author/snapshot/revsort.cwl'
+[2024-03-26T08:35:00,191.000000Z] [provenance] Adding to RO file:///home/dbauer/projects/runcrate/tests/data/revsort-run-author/snapshot/hello.txt
+[2024-03-26T08:35:00,192.000000Z] [workflow ] start
+[2024-03-26T08:35:00,192.000000Z] [workflow ] starting step rev
+[2024-03-26T08:35:00,192.000000Z] [step rev] start
+[2024-03-26T08:35:00,204.000000Z] [job rev] /tmp/j235527o$ docker \
+    run \
+    -i \
+    --mount=type=bind,source=/tmp/j235527o,target=/bhhcmi \
+    --mount=type=bind,source=/tmp/ikqpjjr8,target=/tmp \
+    --mount=type=bind,source=/home/dbauer/projects/runcrate/tests/data/revsort-run-author/snapshot/hello.txt,target=/var/lib/cwl/stgc6fb3435-bf77-40bf-a2d7-2ce7ffbd3469/hello.txt,readonly \
+    --workdir=/bhhcmi \
+    --read-only=true \
+    --log-driver=none \
+    --user=1000:1000 \
+    --rm \
+    --cidfile=/tmp/crhqjdrm/20240326093500-204573.cid \
+    --env=TMPDIR=/tmp \
+    --env=HOME=/bhhcmi \
+    debian:8 \
+    rev \
+    /var/lib/cwl/stgc6fb3435-bf77-40bf-a2d7-2ce7ffbd3469/hello.txt > /tmp/j235527o/output.txt
+[2024-03-26T08:35:01,207.000000Z] [job rev] completed success
+[2024-03-26T08:35:01,207.000000Z] [step rev] completed success
+[2024-03-26T08:35:01,207.000000Z] [workflow ] starting step sorted
+[2024-03-26T08:35:01,207.000000Z] [step sorted] start
+[2024-03-26T08:35:01,209.000000Z] [job sorted] /tmp/eo0fu8e3$ docker \
+    run \
+    -i \
+    --mount=type=bind,source=/tmp/eo0fu8e3,target=/bhhcmi \
+    --mount=type=bind,source=/tmp/2bhihxc0,target=/tmp \
+    --mount=type=bind,source=/tmp/j235527o/output.txt,target=/var/lib/cwl/stg35a7c99e-7809-482d-92a1-712ed8215b58/output.txt,readonly \
+    --workdir=/bhhcmi \
+    --read-only=true \
+    --log-driver=none \
+    --user=1000:1000 \
+    --rm \
+    --cidfile=/tmp/0gcyad43/20240326093501-209419.cid \
+    --env=TMPDIR=/tmp \
+    --env=HOME=/bhhcmi \
+    debian:8 \
+    sort \
+    --reverse \
+    /var/lib/cwl/stg35a7c99e-7809-482d-92a1-712ed8215b58/output.txt > /tmp/eo0fu8e3/output.txt
+[2024-03-26T08:35:02,211.000000Z] [job sorted] completed success
+[2024-03-26T08:35:02,211.000000Z] [step sorted] completed success
+[2024-03-26T08:35:02,212.000000Z] [workflow ] completed success
+[2024-03-26T08:35:02,250.000000Z] Final process status is success