diff --git a/src/ro_crate.py b/src/ro_crate.py index 3b180dd288b999320b9e9240785a18497b72e93d..6330b41360c657e60d60190a7bd040b159830ede 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 cd29a6a812b733f6cf37b0465420310016a4a042..b29ea75bb39edab8f5cd7c0265fc5a97df092b6e 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")