Installing AOD creator scripts in AOD folder + fixes (#87)

- Fix name of directory
- Improve logging of errors
- Removing disallineament for the primary vertexing

Author: njacazio

examples/CMakeLists.txt

@@ -30,6 +30,8 @@ file(GLOB AOD
   aod/*.C
   aod/*.h
   aod/*.root
+  scripts/common.py
+  scripts/createO2tables.py
   )
 
 install(FILES    ${PYTHIA8}       DESTINATION examples/pythia8)

examples/aod/createO2tables.C

@@ -75,7 +75,7 @@ int createO2tables(const char* inputFile = "delphes.root",
   TDatabasePDG::Instance()->AddAntiParticle("anti-helium3", -1000020030);
 
   if (do_vertexing) {
-    o2::base::GeometryManager::loadGeometry();
+    o2::base::GeometryManager::loadGeometry("./", false);
     o2::base::Propagator::initFieldFromGRP("o2sim_grp.root");
   }
 
@@ -502,8 +502,8 @@ int createO2tables(const char* inputFile = "delphes.root",
 
   Printf("Writing tables for %i events", eventextra.fStart[kEvents] + 1);
   TString out_dir = outputFile;
-  out_dir.ReplaceAll(".root", "");
-  out_dir.ReplaceAll("AODRun5.", "");
+  const TObjArray* out_tag = out_dir.Tokenize(".");
+  out_dir = out_tag->GetEntries() > 1 ? out_tag->At(1)->GetName() : "";
   if (!out_dir.IsDec()) {
     out_dir = "DF_0";
   } else {

examples/scripts/common.py

@@ -82,7 +82,7 @@ def run_in_parallel(processes, job_runner, job_arguments, job_message):
                                bar_format='{l_bar}{bar:10}{r_bar}{bar:-10b}'))
 
 
-def run_cmd(cmd, comment="", check_status=True):
+def run_cmd(cmd, comment="", check_status=True, log_file=None):
     """
     Function to run a command in bash, allows to check the status of the command and to log the command output
     """
@@ -96,6 +96,10 @@ def run_cmd(cmd, comment="", check_status=True):
             content = content.strip()
             for i in content.strip().split("\n"):
                 verbose_msg("++", i)
+            if log_file is not None:
+                with open(log_file) as f_log:
+                    for i in content.strip().split("\n"):
+                        f_log.write(i + "\n")
         if "Encountered error" in content:
             warning_msg("Error encountered runtime error in", cmd)
         if check_status:

examples/scripts/createO2tables.py

@@ -18,8 +18,10 @@ def process_run(run_number):
     processing_time = time.time()
     verbose_msg("> starting run", run_number)
     run_cmd(f"bash runner{run_number}.sh")
-    if not os.path.isfile(f"AODRun5.{run_number}.root"):
-        msg(f"++ something went wrong for run {run_number}, no output table found. Please check: 'AODRun5.{run_number}.log'",
+    aod_name = f"AODRun5.{run_number}.root"
+    if not os.path.isfile(aod_name):
+        msg(f"++ something went wrong for run {run_number}, no output AOD file {aod_name} found.",
+            f"Please check: 'AODRun5.{run_number}.log'",
             color=bcolors.FAIL)
     verbose_msg("< complete run", run_number)
     processing_time = time.time() - processing_time
@@ -345,9 +347,9 @@ def copy_and_link(file_name):
                             check_status=True)
             # Check that there were no O2 errors
             write_to_runner(
-                f"if grep -q \"\[ERROR\]\" {aod_log_file}; then echo \": got some errors in '{aod_log_file}'\" && exit 1; fi")
+                f"if grep -q \"\[ERROR\]\" {aod_log_file}; then echo \": got some errors in '{aod_log_file}'\" && echo \"Found some ERROR in this log\" >> {aod_log_file}; fi")
             write_to_runner(
-                f"if grep -q \"\[FATAL\]\" {aod_log_file}; then echo \": got some fatals in '{aod_log_file}'\" && exit 1; fi")
+                f"if grep -q \"\[FATAL\]\" {aod_log_file}; then echo \": got some fatals in '{aod_log_file}'\" && echo \"Found some FATAL in this log\" >> {aod_log_file} && exit 1; fi")
             # Rename the temporary AODs to standard AODs
             write_to_runner(f"mv tmp_{aod_file} {aod_file}", check_status=True)
             if not clean_delphes_files: