Feat/dss cimprove master rebasing

xfel_calibrate/finalize.py

+from datetime import datetime
 from glob import glob
 from importlib.machinery import SourceFileLoader
 from os import chdir, listdir, makedirs, path, remove, stat
@@ -122,21 +123,23 @@ def prepare_plots(run_path, threshold=1000000):
                        shell=False)
 
 
-def make_timing_summary(run_path, joblist):
+def make_timing_summary(run_path, joblist, request_time, submission_time):
     """
-    Create an rst file with timing summary of executed slurm jobs
+    Create an rst file with timing summary of executed notebooks
 
     :param run_path: Run path of the slurm job
     :param joblist: List of slurm jobs
+    :param request_time: Timestamp of notebook request
+    :param submission_time: Timestamp for slurm jobs being submitted
     """
     print('Prepare timing summary')
     run_path = path.abspath(run_path)
     pars_vals = []
-    pars = 'JobID,Elapsed,Suspended'
+    pars = 'JobID,Start,End,Elapsed,Suspended,State'
     pars_name = pars.split(',')
 
     for job in joblist:
-        out = check_output(['sacct', '-j', job,
+        out = check_output(['sacct', '-T', '-j', job,
                             '--format={}'.format(pars)],
                            shell=False)
         lines = str(out).split('\\n')
@@ -153,17 +156,34 @@ def make_timing_summary(run_path, joblist):
                     ==============
                     
                     .. math::
-                        {% for line in table %}
+                        {% for line in time_table %}
                         {{ line }}
                         {%- endfor %}
+                        
+                    .. math::
+                        {% for line in job_table %}
+                        {{ line }}
+                        {%- endfor %}
+                        
                     ''')
 
+    time_vals = [['Time of Request', request_time],
+                 ['Job submission', submission_time],
+                 ['Report compilation',
+                  datetime.now().strftime('%Y-%m-%dT%H:%M:%S')]]
+
     with open("{}/timing_summary.rst".format(run_path), "w+") as gfile:
 
         if len(pars_vals) > 0:
-            table = tabulate.tabulate(pars_vals, tablefmt='latex',
+            job_table = tabulate.tabulate(pars_vals, tablefmt='latex',
                                       headers=pars_name)
-            gfile.write(dedent(tmpl.render(table=table.split('\n'))))
+
+            time_table = tabulate.tabulate(time_vals, tablefmt='latex',
+                                      headers=['Processing step',
+                                               'Timestamp'])
+
+            gfile.write(dedent(tmpl.render(job_table=job_table.split('\n'),
+                                           time_table=time_table.split('\n'))))
 
 
 def make_report(run_path, tmp_path, out_path, project, author, version,
@@ -240,6 +260,18 @@ def make_report(run_path, tmp_path, out_path, project, author, version,
     move("{}/conf.py.tmp".format(run_path), "{}/conf.py".format(run_path))
 
     direntries = listdir(run_path)
+    lead_rstfiles = ['InputParameters.rst', 'timing_summary.rst']
+
+    # Order rst files based on the known order(lead_rstfiles).
+    for f in direntries:
+        if f in lead_rstfiles:
+            direntries.insert(lead_rstfiles.index(f),
+                              direntries.pop(direntries.index(f)))
+        # Move summary to the top, if it is exists,
+        # after the known leading rst files.
+        if "summary" in f.lower() and f not in lead_rstfiles:
+            direntries.insert(len(lead_rstfiles),
+                              direntries.pop(direntries.index(f)))
     files_to_handle = []
     for entry in direntries:
         if isfile("{}/{}".format(run_path, entry)):
@@ -272,9 +304,21 @@ def make_report(run_path, tmp_path, out_path, project, author, version,
               "can be inspected at: {}".format(run_path))
         return
     print("Moving report to final location: {}".format(out_path))
+    makedirs(out_path, exist_ok=True)
     copy('{}/_build/latex/{}.pdf'.format(run_path, report_name), out_path)
-    print("Removing temporary files at: {}".format(tmp_path))
-    rmtree(tmp_path)
+
+    temp_dirs = glob(f'{tmp_path}/*/')
+    # Remove folders with figures and sphinx files.
+    print(f"Removing directories [{temp_dirs}] in temp folder: {tmp_path}")
+    for dtmp in temp_dirs:
+        rmtree(f'{dtmp}/')
+
+    # Moving temporary files to out-folder after successful execution
+    # This helps in keeping elements needed for re-producibility.
+    print(f"Moving temporary files to final location"
+          f": {out_path}/{os.path.basename(tmp_path)} with name: "
+          f"slurm_out_{report_name}")
+    move(tmp_path, f"{out_path}/slurm_out_{report_name}")
 
 
 def make_titlepage(sphinx_path, project, data_path, version):
@@ -324,7 +368,8 @@ def tex_escape(text):
 
 
 def finalize(joblist, finaljob, run_path, out_path, project, calibration,
-             author, version, report_to, data_path='Unknown'):
+             author, version, report_to, data_path='Unknown',
+             request_time='', submission_time=''):
     print("Waiting on jobs to finish: {}".format(joblist))
     while True:
         found_jobs = set()
@@ -338,7 +383,8 @@ def finalize(joblist, finaljob, run_path, out_path, project, calibration,
         sleep(10)
 
     prepare_plots(run_path)
-    make_timing_summary(run_path, joblist + [str(finaljob)])
+    make_timing_summary(run_path, joblist + [str(finaljob)], request_time,
+                        submission_time)
     sphinx_path = combine_report(run_path, calibration)
     make_titlepage(sphinx_path, project, data_path, version)
     make_report(sphinx_path, run_path, out_path, project, author, version,