Update RO-Crate -> complet version

src/nextflow_file.py

@@ -679,7 +679,7 @@ class Nextflow_File(Nextflow_Building_Blocks):
     def add_subworkflows_2_rocrate(self, dico, file_dico, file_name):
         for sub in self.subworkflows:
             sub_key = sub.get_rocrate_key(dico)
-            file_dico["hasPart"].append(sub_key)
+            file_dico["hasPart"].append({"@id":sub_key})
             sub.add_2_rocrate(dico, file_name)
 
     def add_2_rocrate(self, dico):

src/ro_crate.py

 import json
 import glob
 import os
+import re
+
+from . import constant
 
 class RO_Crate:
     def __init__(self, workflow):
@@ -42,7 +45,7 @@ class RO_Crate:
         authors = self.workflow.get_authors()
         tab_authors = []
         for author in authors:
-            tab_authors.append({"@id":author["@id"], "name":author["name"]})
+            tab_authors.append({"@id":author["@id"], "email":author["email"]})
         root["author"] = tab_authors
         root["maintainer"] = tab_authors #Right now i'm assuming that all the authors are maintainers
         files = self.get_files()
@@ -69,23 +72,53 @@ class RO_Crate:
         file_stats = os.stat(file)
         return file_stats.st_size/1e3
     
-    #TODO
+    def fill_log_file(self, file, reverse = True):
+        info = ""
+        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")
+            with open(f'temp_{id(self)}.txt') as f:
+                info = f.read()
+            os.system(f"rm temp_{id(self)}.txt")
+        except:
+            None
+        os.chdir(current_directory)
+        return info
+
     def get_dateCreated(self, file):
-        return "TODO"
+        info = self.fill_log_file(file, reverse = True)
+        for match in re.finditer(r"Date: +\w+ +(\w+) +(\d+) +\d+:\d+:\d+ +(\d+)", info):
+            month = constant.month_mapping[match.group(1)]
+            day = match.group(2)
+            year = match.group(3)
+            return f"{year}-{month}-{day}"
+        return None
     
-    #TODO
+ 
     def get_dateModified(self, file):
-        return "TODO"
+        info = self.fill_log_file(file, reverse = False)
+        for match in re.finditer(r"Date: +\w+ +(\w+) +(\d+) +\d+:\d+:\d+ +(\d+)", info):
+            month = constant.month_mapping[match.group(1)]
+            day = match.group(2)
+            year = match.group(3)
+            return f"{year}-{month}-{day}"
+        return None
     
-    #TODO
+
     def get_url(self, file):
-        return "TODO"
+        if(self.workflow.dico!={}):
+            return f"https://github.com/{self.workflow.get_address()}/blob/main/{file}"
+        return None
     
-    #TODO
+
     def get_creators(self, file):
-        return [{"@id": "George"}]
-    
-    #TODO
+        info = self.fill_log_file(file, reverse = True)
+        for match in re.finditer(r"Author: ([ \w-]+) <([^>]+)>", info):
+            return [{"@id": match.group(1)}]
+        return None
+
+
     def get_types(self, file):
         types = ["File"]
         if(file[-3:]==".nf"):
@@ -101,10 +134,10 @@ class RO_Crate:
         dico["@type"] = self.get_types(file)
         dico["programmingLanguage"] = {"@id":self.get_programming_language(file)}
         dico["contentSize"] = self.get_contentSize(file)
-        dico["dateCreated"] = self.get_dateCreated(file)
-        dico["dateModified"] = self.get_dateModified(file)
-        dico["url"] = self.get_url(file)
-        creators = self.get_creators(file)
+        dico["dateCreated"] = self.get_dateCreated(key)
+        dico["dateModified"] = self.get_dateModified(key)
+        dico["url"] = self.get_url(key)
+        creators = self.get_creators(key)
         dico["creator"] = []
         for creator in creators:
             dico["creator"].append({"@id": creator["@id"]})

src/workflow.py

@@ -5,6 +5,7 @@ from . import constant
 
 import os
 import re
+import json
 
 
 class Workflow:
@@ -25,17 +26,52 @@ class Workflow:
         self.keywords = keywords
         self.producer = producer
         self.publisher = publisher
-        self.log = None
+        self.log = ""
         self.fill_log()
-
+        self.address = ""
+        self.set_address()
+        self.dico = {}
+        self.get_dico()
     
     def fill_log(self):
         current_directory = os.getcwd()
         os.chdir("/".join(self.nextflow_file.get_file_address().split("/")[:-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")
+        try:
+            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")
+        except:
+            None
+        os.chdir(current_directory)
+
+    def get_address(self):
+        return self.address
+
+    def set_address(self):
+        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")
+            with open(f'temp_address_{id(self)}.txt') as f:
+                self.address = f.read()
+            os.system(f"rm temp_address_{id(self)}.txt")
+        except:
+            None
+        os.chdir(current_directory)
+        for match in re.finditer(r"https:\/\/github\.com\/([^\.]+)\.git", self.address):
+            self.address = match.group(1)
+
+    def get_dico(self):
+        current_directory = os.getcwd()
+        os.chdir("/".join(self.nextflow_file.get_file_address().split("/")[:-1]))
+        try:
+            _ = os.system(f"wget -qO - https://api.github.com/repos/{self.address} > temp_dico_{id(self)}.json")
+            with open(f'temp_dico_{id(self)}.json') as json_file:
+                self.dico = json.load(json_file)
+            os.system(f"rm temp_dico_{id(self)}.json")
+        except:
+            None
         os.chdir(current_directory)
     
 
@@ -47,6 +83,7 @@ class Workflow:
             return self.name
 
     #Format yyyy-mm-dd
+    #Here i return the first commit date
     def get_datePublished(self):
         if(self.datePublished==None):
             for match in re.finditer(r"Date: +\w+ +(\w+) +(\d+) +\d+:\d+:\d+ +(\d+)",self.log):
@@ -58,18 +95,32 @@ class Workflow:
             return self.datePublished
         
 
-    
-    #TODO
     def get_description(self):
-        return "TODO"
+        if(self.description==None):
+            try:
+                res = self.dico["description"]
+            except:
+                res = None
+            return res
+        else:
+            return self.description
+        
     
 
     def get_main_file(self):
         return self.nextflow_file.get_file_address().split("/")[-1]
-    
-    #TODO
+
+
     def get_license(self):
-        return "TODO"
+        if(self.license==None):
+            try:
+                res = self.dico["license"]["key"]
+            except:
+                res = None
+            return res
+        else:
+            return self.license
+        
     
     #TODO
     def get_creativeWorkStatus(self):
@@ -78,32 +129,51 @@ class Workflow:
     #TODO
     def get_version(self):
         return "TODO"
-    
-    #TODO -> this doesn't workf perfectly
+
+
     def get_authors(self):
         if(self.authors==None):
             authors = {}
-            for match in re.finditer(r"Author: (\w+ +\w+) <([^>]+)>",self.log):
+            for match in re.finditer(r"Author: ([ \w-]+) <([^>]+)>",self.log):
                 authors[match.group(2)] = match.group(1)
             tab = []
             for author in authors:
-                tab.append({"@id":author, "name":authors[author]})
+                #tab.append({"@id":author, "name":authors[author]})
+                tab.append({"@id":authors[author], "email":author})
             return tab
         else:
             return self.authors
     
-    #TODO
+
     #Need to follow this format : "rna-seq, nextflow, bioinformatics, reproducibility, workflow, reproducible-research, bioinformatics-pipeline"
     def get_keywords(self):
-        return "TODO"
+        if(self.keywords==None):
+            try:
+                res = ", ".join(self.dico["topics"])
+            except:
+                res = None
+            return res
+        else:
+            return self.keywords
+
     
-    #TODO
+
     def get_producer(self):
-        return "TODO"
+        if(self.producer==None):
+            try:
+                res = {"@id": self.dico["owner"]["login"]}
+            except:
+                res = None
+            return res
+        else:
+            return self.producer
     
-    #TODO
+
     def get_publisher(self):
-        return "TODO"
+        if(self.dico!={}):
+            return "https://github.com/"
+        else:
+            return None
     
     def get_output_dir(self):
         return self.nextflow_file.get_output_dir()