From 269ca16c12eecc729261dd34248e344831de9728 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Fri, 23 Aug 2024 10:48:54 +0200
Subject: [PATCH] add citations to output + added modifications to Ro-Crate
---
README.md | 4 ++--
src/nextflow_file.py | 4 ++--
src/process.py | 6 +++---
src/ro_crate.py | 9 ++++++---
src/subworkflow.py | 4 ++--
src/workflow.py | 7 +++++++
6 files changed, 22 insertions(+), 12 deletions(-)
diff --git a/README.md b/README.md
index 42dbd76..92f97da 100644
--- a/README.md
+++ b/README.md
@@ -122,10 +122,10 @@ The structure of this folder is organised as such :
│  ├── specification_wo_orphan_operations_wo_labels.dot
│  ├── specification_wo_orphan_operations_wo_labels.mmd
│  └── specification_wo_orphan_operations_wo_labels.png
-└── ro-crate-metadata-rnaseq-nf.json
+└── ro-crate-metadata.json
```
-* The `ro-crate-metadata-rnaseq-nf.json` describes the workflow following an extended Workflow [RO-Crate](https://www.researchobject.org/ro-crate/) profile. The description of this extended profile can be found [here](https://gitlab.liris.cnrs.fr/sharefair/posters/swat4hcls-2024).
+* The `ro-crate-metadata.json` describes the workflow following an extended Workflow [RO-Crate](https://www.researchobject.org/ro-crate/) profile. The description of this extended profile can be found [here](https://gitlab.liris.cnrs.fr/sharefair/posters/swat4hcls-2024).
* the `debug` folder contains different intermediary files which are ussefull for debugging
* the `graphs` folder contains the different graphs which are generated. For each of the 3 graphs described above, **BioFlow-Insight** generates :
* A `json` file which describes the graph using **BioFlow-Insight** specific format
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 4a43c44..c6588d6 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -706,7 +706,7 @@ class Nextflow_File(Nextflow_Building_Blocks):
# self.graph.get_metadata_graph_wo_operations()
def add_main_DSL1_2_rocrate(self, dico, file_dico, file_name):
- main_key = f"{file_name}/main"
+ main_key = f"{file_name}#main"
file_dico["hasPart"].append(main_key)
dico_main = {}
dico_main["@id"] = main_key
@@ -719,7 +719,7 @@ class Nextflow_File(Nextflow_Building_Blocks):
dico_main["output"] = []
dico_main["isPartOf"] = [{"@id": file_name}]
dico_main["hasPart"] = []
- self.add_processes_2_rocrate(dico, dico_main, main_key)
+ self.add_processes_2_rocrate(dico, dico_main, main_key.split("#")[0])
dico["@graph"].append(dico_main)
def add_processes_2_rocrate(self, dico, file_dico, file_name):
diff --git a/src/process.py b/src/process.py
index e5b25ac..c825e4c 100644
--- a/src/process.py
+++ b/src/process.py
@@ -434,7 +434,7 @@ class Process(Nextflow_Building_Blocks):
dico_process = {}
dico_process["@id"] = process_key
dico_process["name"] = "Process"
- dico_process["@type"] = ["SoftwareSourceCode", "Script"]
+ dico_process["@type"] = ["SoftwareSourceCode"]
#ADD INPUTS
dico_process["input"] = []
for input in self.get_inputs():
@@ -444,7 +444,7 @@ class Process(Nextflow_Building_Blocks):
name_input = input.get_code()
dico_input = get_dico_from_tab_from_id(dico, name_input)
if(dico_input==None):
- dico_input = {"@id":name_input, "@type": "FormalParameter"}
+ dico_input = {"@id":f"#{name_input}", "@name": name_input, "@type": "FormalParameter"}
dico["@graph"].append(dico_input)
dico_process["input"].append({"@id":dico_input["@id"]})
#ADD OUTPUTS
@@ -456,7 +456,7 @@ class Process(Nextflow_Building_Blocks):
name_output = output.get_code()
dico_output = get_dico_from_tab_from_id(dico, name_output)
if(dico_output==None):
- dico_output = {"@id":name_output, "@type": "FormalParameter"}
+ dico_output = {"@id":f"#{name_output}", "@name": name_output, "@type": "FormalParameter"}
dico["@graph"].append(dico_output)
dico_process["output"].append({"@id":dico_output["@id"]})
#ADD isPartOf
diff --git a/src/ro_crate.py b/src/ro_crate.py
index 793a680..804ba34 100644
--- a/src/ro_crate.py
+++ b/src/ro_crate.py
@@ -47,9 +47,11 @@ class RO_Crate:
tab_authors = []
for author in authors:
try:
- tab_authors.append({"@id":author["@id"], "email":author["email"]})
+ #tab_authors.append({"@id":author["@id"], "email":author["email"]})
+ tab_authors.append({"@id":f'#{"_".join(author["@id"].split())}', "@name":author["@id"],"email":author["email"]})
except:
- tab_authors.append({"@id":author["@id"]})
+ #tab_authors.append({"@id":author["@id"]})
+ tab_authors.append({"@id":f'#{"_".join(author["@id"].split())}', "@name":author["@id"]})
root["author"] = tab_authors
root["maintainer"] = tab_authors #Right now i'm assuming that all the authors are maintainers
files = self.get_files()
@@ -163,5 +165,6 @@ class RO_Crate:
name = name.replace('github.com/', '')
name = re.sub(r"^[ .]|[/<>:\"\\|?*]+|[ .]$", "-", name)
- with open(f"{self.workflow.get_output_dir()}/ro-crate-metadata-{name}.json", 'w') as output_file :
+ #with open(f"{self.workflow.get_output_dir()}/ro-crate-metadata-{name}.json", 'w') as output_file :
+ with open(f"{self.workflow.get_output_dir()}/ro-crate-metadata.json", 'w') as output_file :
json.dump(self.dico, output_file, indent=2)
\ No newline at end of file
diff --git a/src/subworkflow.py b/src/subworkflow.py
index 363a7db..d468e06 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -256,7 +256,7 @@ class Subworkflow(Main_DSL2):
name_input = input.get_code()
dico_input = get_dico_from_tab_from_id(dico, name_input)
if(dico_input==None):
- dico_input = {"@id":name_input, "@type": "FormalParameter"}
+ dico_input = {"@id":f"#{name_input}", "@name": name_input, "@type": "FormalParameter"}
dico["@graph"].append(dico_input)
dico_sub["input"].append({"@id":dico_input["@id"]})
#ADD OUTPUTS
@@ -268,7 +268,7 @@ class Subworkflow(Main_DSL2):
name_output = output.get_code()
dico_output = get_dico_from_tab_from_id(dico, name_output)
if(dico_output==None):
- dico_output = {"@id":name_output, "@type": "FormalParameter"}
+ dico_output = {"@id":f"#{name_output}", "@name": name_output, "@type": "FormalParameter"}
dico["@graph"].append(dico_output)
dico_sub["output"].append({"@id":dico_output["@id"]})
diff --git a/src/workflow.py b/src/workflow.py
index 925193d..96b6b5e 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -71,6 +71,7 @@ class Workflow:
self.workflow_directory = '/'.join(file.split('/')[:-1])
self.output_dir = Path(output_dir)
self.rocrate = None
+ self.display_info = display_info
self.name = name
self.datePublished = datePublished
self.description = description
@@ -505,6 +506,12 @@ class Workflow:
self.nextflow_file.initialise()
if(create_rocrate):
self.initialise_rocrate()
+
+ if(self.display_info):
+ citation = """To cite BioFlow-Insight, please use the following publication:
+George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen-Boulakia, BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization, NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae092, https://doi.org/10.1093/nargab/lqae092"""
+ print()
+ print(citation)
def generate_all_graphs(self, render_graphs = True):
"""Method that generates all graphs representing the workflow
--
GitLab