From bcd1bcbe39d71372603243af28a269400ba1eb05 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 19 Feb 2024 15:34:12 +0100
Subject: [PATCH] Update Ro-Crate Profile
---
src/ro_crate.py | 7 ++++---
src/workflow.py | 4 ++--
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/src/ro_crate.py b/src/ro_crate.py
index 3b180dd..6330b41 100644
--- a/src/ro_crate.py
+++ b/src/ro_crate.py
@@ -39,8 +39,8 @@ class RO_Crate:
root["name"] = self.workflow.get_name()
root["datePublished"] = self.workflow.get_datePublished()
root["description"] = self.workflow.get_description()
- root["mainEntity"] = {"@id": self.workflow.get_main_file(),
- "@type":["File", "SoftwareSourceCode"]} #We do not consider a File as a "ComputationalWorkflow" since multiple (sub)workflows can be defined in a same file
+ root["mainEntity"] = {"@id": self.workflow.get_main_file()}
+ #, "@type":["File", "SoftwareSourceCode"]} #We do not consider a File as a "ComputationalWorkflow" since multiple (sub)workflows can be defined in a same file
root["license"] = {"@id":self.workflow.get_license()}
authors = self.workflow.get_authors()
tab_authors = []
@@ -77,7 +77,7 @@ class RO_Crate:
current_directory = os.getcwd()
os.chdir("/".join(self.workflow.nextflow_file.get_file_address().split("/")[:-1]))
try:
- os.system(f"git log {'--reverse'*reverse} {file} > temp_{id(self)}.txt >/dev/null 2>&1")
+ os.system(f"git log {'--reverse'*reverse} {file} > temp_{id(self)}.txt")
with open(f'temp_{id(self)}.txt') as f:
info = f.read()
os.system(f"rm temp_{id(self)}.txt")
@@ -153,6 +153,7 @@ class RO_Crate:
for file in self.files:
self.initialise_file(file)
self.fill_from_workflow()
+ self.dico.pop("temp_directory")
with open(f"{self.workflow.get_output_dir()}/ro-crate-metadata-{self.workflow.get_name()}.json", 'w') as output_file :
json.dump(self.dico, output_file, indent=2)
\ No newline at end of file
diff --git a/src/workflow.py b/src/workflow.py
index cd29a6a..b29ea75 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -37,7 +37,7 @@ class Workflow:
current_directory = os.getcwd()
os.chdir("/".join(self.nextflow_file.get_file_address().split("/")[:-1]))
try:
- os.system(f"git log --reverse > temp_{id(self)}.txt >/dev/null 2>&1")
+ os.system(f"git log --reverse > temp_{id(self)}.txt")
with open(f'temp_{id(self)}.txt') as f:
self.log = f.read()
os.system(f"rm temp_{id(self)}.txt")
@@ -52,7 +52,7 @@ class Workflow:
current_directory = os.getcwd()
os.chdir("/".join(self.nextflow_file.get_file_address().split("/")[:-1]))
try:
- os.system(f"git ls-remote --get-url origin > temp_address_{id(self)}.txt >/dev/null 2>&1")
+ os.system(f"git ls-remote --get-url origin > temp_address_{id(self)}.txt")
with open(f'temp_address_{id(self)}.txt') as f:
self.address = f.read()
os.system(f"rm temp_address_{id(self)}.txt")
--
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