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Adjustments for pelican #2

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Adjustments for pelican #2

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fc9c25c
change pfb_to_zip filename
paulmurdoch19 May 3, 2025
441ab05
repo for --analysis flag needs to be dynamic for pelican
paulmurdoch19 May 3, 2025
28b9861
Revert "change pfb_to_zip filename"
paulmurdoch19 May 5, 2025
6b77fc4
add PFBExporter to package's __init__ file
paulmurdoch19 May 5, 2025
62d079d
update check if R is installed to support linux based systems
paulmurdoch19 May 5, 2025
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1 change: 1 addition & 0 deletions pfb_to_zip/__init__.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
from .pfb_to_zip import PFBExporter
19 changes: 11 additions & 8 deletions pfb_to_zip/pfb_to_zip.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,8 +122,7 @@ def initialize(self):
tmp_path = Path(self.analysis_path + "/analysis")
if not tmp_path.exists():
tmp_path.mkdir()

tmp_path = os.path.join("./", "repo")
tmp_path = os.path.join(self.tmp_folder, "repo")
if Path(tmp_path).exists():
rmtree(tmp_path, ignore_errors=False, onerror=None)

Expand Down Expand Up @@ -247,18 +246,22 @@ def setup_and_run_analysis(self, consortium=None):
return

# TODO check R is installed
#check if R is installed
try:
command = 'which RScript'
cmd_output = subprocess.check_output(command, shell=True, text=True).rstrip('\n')
cmd_output = subprocess.check_output('which Rscript', shell=True, text=True).rstrip('\n')
except subprocess.CalledProcessError as grepexc:
print("error code", grepexc.returncode, grepexc.output)
print("R is not installed / not found!")
return
print("Rscript is not installed or found in Path!")
try:
cmd_output = subprocess.check_output('which RScript', shell=True, text=True).rstrip('\n')
except subprocess.CalledProcessError as grepexc:
print("error code", grepexc.returncode, grepexc.output)
print("R is not installed / not found!")
return

current_dir = str(Path( __file__ ).parent.absolute())
# subprocess.call(cmd_output + " --vanilla ./repo/INRG/PCDC_To_INRG_Data_Transformation.R", shell=True)
subprocess.call ([cmd_output, "--vanilla", "./repo/INRG/PCDC_To_INRG_Data_Transformation.R", os.path.join(current_dir, "repo/"), self.analysis_path + "/tsvs/", self.analysis_path + "/analysis/"])

subprocess.call ([cmd_output, "--vanilla", f"{self.tmp_folder}/repo/INRG/PCDC_To_INRG_Data_Transformation.R", os.path.join(self.tmp_folder, "repo/"), self.analysis_path + "/tsvs/", self.analysis_path + "/analysis/"])

# TODO cd to consortia subfolder
# TODO run the script with the input and output parameters
Expand Down