Starting to add Ro-crate support

src/constant.py

@@ -21,6 +21,27 @@ LIST_OPERATORS = ["distinct", "filter", "first", "last", "randomSample", "take",
                           "close","dump","ifEmpty","print","println","set","view",
                           "empty", "of", "fromPath", "fromList", "subscribe", "value", "from"]#This last line is added by me:)
 
+TOOLS = [
+    "samtools",
+    "bcftools",
+    "fastqc",
+    "bedtools",
+    "multiqc",
+    "gatk",
+    "bwa",
+    "minimap2",
+    "tabix",
+    "vcf",
+    "wget",
+    "bgzip",
+    "hmmsearch",
+    "pigz",
+    "picard",
+    "star",
+    "iqtree",
+    "idxstats",
+]
+
 
 #==========================
 #         PATTERNS
@@ -122,3 +143,5 @@ SUBWORKFLOW_HEADER = r'workflow +(\w+|\'[\w ]+\'|\"[\w ]+\") *{'
 WORKFLOW_HEADER = r"workflow\s*\{"
 WORKFLOW_HEADER_2 = r'[^\w](workflow\s*{)'
 
+
+

src/process.py

@@ -19,6 +19,7 @@ class Process(Nextflow_Building_Blocks):
         self.output_code = ""
         self.when_code = ""
         self.script_code = ""
+        self.tools = []
         self.initialise()
         self.initialised = True
 
@@ -71,6 +72,12 @@ class Process(Nextflow_Building_Blocks):
     def get_nb_outputs(self):
         return len(self.outputs)
     
+    def extract_tools(self):
+        script = self.script_code.lower()
+        for tool in constant.TOOLS:
+            if tool in script:
+                self.tools.append(tool)
+    
 
     def initialise_parts(self):
         code = self.get_code()
@@ -126,6 +133,7 @@ class Process(Nextflow_Building_Blocks):
                 self.when_code = temp_code
             elif(variables_index[i]=='script'):
                 self.script_code = temp_code
+                self.extract_tools()
             else:
                 raise Exception("This shoudn't happen!")
 

src/ro_crate.py

+
+
+class RO_Crate:
+    def __init__(self, workflow):
+        self.nextflow_file = workflow
+        self.directroy = '/'.join(workflow.get_file_address().split('/')[:-1])
+        self.dico = {}
+
+    def initialise_dico(self):
+        None
+
+    def initialise(self):
+        self.initialise_dico()
+        print("i'm initialised")
\ No newline at end of file

src/workflow.py

+
+from .nextflow_file import Nextflow_File
+from .ro_crate import RO_Crate
+
+
+class Workflow:
+    def __init__(self, file, duplicate=False, display_info=True):
+        self.nextflow_file = Nextflow_File(file, duplicate = duplicate, display_info = display_info)
+        self.rocrate = None
+
+
+    def get_file_address(self):
+        return self.nextflow_file.get_file_address()
+
+    def initialise_rocrate(self):
+        self.rocrate = RO_Crate(self)
+        self.rocrate.initialise()
+
+
+    def initialise(self):
+        self.nextflow_file.initialise()
+        self.initialise_rocrate()
+
+    def generate_all_graphs(self, render_graphs = True):
+        self.nextflow_file.generate_all_graphs(render_graphs = render_graphs)