update ro-crate

src/constant.py

@@ -144,4 +144,19 @@ WORKFLOW_HEADER = r"workflow\s*\{"
 WORKFLOW_HEADER_2 = r'[^\w](workflow\s*{)'
 
 
-
+#         MONTHS
+#--------------------------
+month_mapping = {
+    'Jan': '01',
+    'Feb': '02',
+    'Mar': '03',
+    'Apr': '04',
+    'May': '05',
+    'Jun': '06',
+    'Jul': '07',
+    'Aug': '08',
+    'Sep': '09',
+    'Oct': '10',
+    'Nov': '11',
+    'Dec': '12'
+}
\ No newline at end of file

src/ro_crate.py

@@ -42,7 +42,7 @@ class RO_Crate:
         authors = self.workflow.get_authors()
         tab_authors = []
         for author in authors:
-            tab_authors.append({"@id":author["@id"]})
+            tab_authors.append({"@id":author["@id"], "name":author["name"]})
         root["author"] = tab_authors
         root["maintainer"] = tab_authors #Right now i'm assuming that all the authors are maintainers
         files = self.get_files()

src/subworkflow.py

@@ -285,7 +285,6 @@ class Subworkflow(Main_DSL2):
                 else:
                     for o in exe.get_origins():
                         if(o.get_type()=="Call"):
-                            print("works")
                             called+=o.get_elements_called()
 
             for c in called:

src/workflow.py

 
 from .nextflow_file import Nextflow_File
 from .ro_crate import RO_Crate
+from . import constant
+
+import os
+import re
 
 
 class Workflow:
-    def __init__(self, file, duplicate=False, display_info=True):
+    def __init__(self, file, duplicate=False, display_info=True, 
+                 name = None, datePublished=None, description=None,
+                 license = None, creativeWorkStatus = None, authors = None, 
+                 version = None, keywords = None, producer = None,
+                 publisher = None):
         self.nextflow_file = Nextflow_File(file, duplicate = duplicate, display_info = display_info)
         self.rocrate = None
+        self.name = name
+        self.datePublished = datePublished
+        self.description = description
+        self.license = license
+        self.creativeWorkStatus = creativeWorkStatus
+        self.authors = authors
+        self.version = version
+        self.keywords = keywords
+        self.producer = producer
+        self.publisher = publisher
+        self.log = None
+        self.fill_log()
 
-    #TODO
-    def get_name(self):
-        return "TODO"
     
-    #TODO
+    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")
+        os.chdir(current_directory)
+    
+
+
+    def get_name(self):
+        if(self.name==None):
+            return self.nextflow_file.get_file_address().split("/")[-2]
+        else:
+            return self.name
+
+    #Format yyyy-mm-dd
     def get_datePublished(self):
-        return "TODO"
+        if(self.datePublished==None):
+            for match in re.finditer(r"Date: +\w+ +(\w+) +(\d+) +\d+:\d+:\d+ +(\d+)",self.log):
+                month = constant.month_mapping[match.group(1)]
+                day = match.group(2)
+                year = match.group(3)
+                return f"{year}-{month}-{day}"
+        else:
+            return self.datePublished
+        
+
     
     #TODO
     def get_description(self):
         return "TODO"
     
-    #TODO
+
     def get_main_file(self):
-        return "TODO"
+        return self.nextflow_file.get_file_address().split("/")[-1]
     
     #TODO
     def get_license(self):
         return "TODO"
     
-    #TODO
-    def get_main_license(self):
-        return "TODO"
-    
     #TODO
     def get_creativeWorkStatus(self):
         return "TODO"
@@ -40,9 +79,18 @@ class Workflow:
     def get_version(self):
         return "TODO"
     
-    #TODO
+    #TODO -> this doesn't workf perfectly
     def get_authors(self):
-        return [{"@id": "George"}]
+        if(self.authors==None):
+            authors = {}
+            for match in re.finditer(r"Author: (\w+ +\w+) <([^>]+)>",self.log):
+                authors[match.group(2)] = match.group(1)
+            tab = []
+            for author in authors:
+                tab.append({"@id":author, "name":authors[author]})
+            return tab
+        else:
+            return self.authors
     
     #TODO
     #Need to follow this format : "rna-seq, nextflow, bioinformatics, reproducibility, workflow, reproducible-research, bioinformatics-pipeline"