diff --git a/src/bioflowinsighterror.py b/src/bioflowinsighterror.py
index e5936faef440367150d3f0710e970a0e00afe3ab..3a2f3d4f32dfc7af01cdf3b26d6647e0e2ea57e3 100644
--- a/src/bioflowinsighterror.py
+++ b/src/bioflowinsighterror.py
@@ -53,6 +53,7 @@ class BioFlowInsightError(Exception):
#* [7] -> Tuple with emit (ch1, ch2) = emit.out
#* [9] -> Tuple with call (ch1, ch2) = wf()
#* [11] -> Failed to extract the operation or call at the line x. Try rewriting it in a simplified version.
+#* [13] -> Multiple scripts with the same name were defined in the source code -> don't know which one to extract then when calling 'get_external_scripts_code'
diff --git a/src/outils.py b/src/outils.py
index a8082d4d9b5930b4fe905f173ebaba4fdb9fee76..4021381674f0ad62b6b92ffbc8d857846d617fc7 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -846,4 +846,49 @@ def check_if_element_in_tab_rocrate(tab, id):
for ele in tab:
if(ele["@id"]==id):
return True
- return False
\ No newline at end of file
+ return False
+
+
+#Function that parses python script and extracts the packages which are imported
+def get_python_packages(script):
+ packages = []
+ #Examples that i need to consider:
+ # from fibo import *
+ # from sound.effects.echo import echofilter
+ # import fibo
+ # import fibo, sys
+ # import sound.effects.echo
+ # import numpy as np
+
+ #STEP1
+ patterns_from = [r"fr(om)\s+(\w+)\s+import.+",
+ r"from\s+((\w+)(\.\w+)+)\s+import.+",]
+ #First step is to extract the packages which are imported from the from and then removing them from the string
+ froms = []
+ for pattern in patterns_from:
+ for match in re.finditer(pattern, script):
+ packages.append(match.group(2))
+ froms.append(match.group(0))
+ for f in froms:
+ script = script.replace(f, "")
+
+ #STEP2
+ #Remove the rest of the 'simple' imports
+ def remove_commas(text):
+ tab = text.split(',')
+ words = []
+ for t in tab:
+ words.append(t.strip())
+ return words
+ for match in re.finditer(r"import\s+(\w+(\s*\,\s*\w+)+|(\w+))", script):
+ packages+= remove_commas(match.group(1))
+
+ return packages
+
+
+#Function that parses R script and extracts the libraries which are loaded
+def get_R_libraries(script):
+ libraries = []
+ for match in re.finditer(r"library\s*\(\s*(\w+)\s*\)", script):
+ libraries.append(match.group(1))
+ return libraries
\ No newline at end of file
diff --git a/src/process.py b/src/process.py
index 78f39e444f36c579bf939e81abaa4da4936f3002..eb9a691c3b86eaa9ec2c2ac331324e858c4e988f 100644
--- a/src/process.py
+++ b/src/process.py
@@ -3,7 +3,7 @@ import glob
from .code_ import Code
from .nextflow_building_blocks import Nextflow_Building_Blocks
-from .outils import remove_jumps_inbetween_parentheses, remove_jumps_inbetween_curlies, sort_and_filter, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate
+from .outils import remove_jumps_inbetween_parentheses, remove_jumps_inbetween_curlies, sort_and_filter, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate, get_python_packages, get_R_libraries
from .bioflowinsighterror import BioFlowInsightError
from . import constant
@@ -67,20 +67,65 @@ class Process(Nextflow_Building_Blocks):
#print(workflow_directory)
#import os
#print(os.getcwd(), self.origin.get_address(), self.get_workflow_address())
+ scripts = []
for call in calls:
#Check first if the file is in the bin
file = glob.glob(f'{self.get_workflow_address()}/bin/**/{call}', recursive=True)
if(len(file)>1):
- print(file)
- print("More than one file found!")
+ raise BioFlowInsightError(f"More than one script named '{call}' in the workflow source code bin, don't know which one to use when using the process '{self.get_name()}'", num = 13, origin=self)
#If not we search again
- if(len(file)==0):
+ elif(len(file)==0):
file = glob.glob(f'{self.get_workflow_address()}/**/{call}', recursive=True)
if(len(file)>1):
- print(file)
- print("More than one file found!")
+ raise BioFlowInsightError(f"More than one script named '{call}' in the workflow source code, don't know which one to use when using the process '{self.get_name()}'", num = 13, origin=self)
+ for f in file:
+ with open(f, 'r') as s:
+ scripts.append(s.read())
+
+ return scripts
+
+
+ def get_python_packages_imported_internal_script(self):
+ packages = []
+ packages+= get_python_packages(self.get_script_code())
+ return packages
+
+ def get_python_packages_imported_external_scripts(self):
+ packages = []
+ for s in self.get_external_scripts_code():
+ packages+= get_python_packages(s)
+ return packages
+
+ #This methods checks the script and the external script calls for python packages imports
+ def get_python_packages_imported(self):
+ packages = []
+ packages+= self.get_python_packages_imported_internal_script()
+ packages+= self.get_python_packages_imported_external_scripts()
+ return packages
+
+
+ def get_R_libraries_loaded_internal_script(self):
+ libraries = []
+ libraries+= get_R_libraries(self.get_script_code())
+ return libraries
+
+ def get_R_libraries_loaded_external_scripts(self):
+ libraries = []
+ for s in self.get_external_scripts_code():
+ libraries+= get_R_libraries(s)
+ return libraries
+
+ #This methods checks the script and the external script calls for python packages imports
+ def get_R_libraries_loaded(self):
+ libraries = []
+ libraries+= self.get_R_libraries_loaded_internal_script()
+ libraries+= self.get_R_libraries_loaded_external_scripts()
+ return libraries
+
+ #TODO -> do the same with Ruby/PErl scripts
+