check for input/output files appropriately, things look like theyre p…

…assing nicely now

these tests wont pass on the pipeline unforutnately... dependence on cmip6-data-tables
... dependence on a netcdf file that has megabytes assoc with it
... dont want to blow up repo size... can we do an ncgen + cdl for the metadata?

fre/cmor/cmor_mixer.py

@@ -269,7 +269,7 @@ def gfdl_to_pcmdi_var( proj_table_vars, var_lst, dir2cmor, gfdl_var, time_arr,
 
         # copy ps also, if it's there
         nc_ps_file_work = ''
-        nc_ps_file = nc_fls[i].replace(f'.{gfdl_var}.nc', '.ps.nc')        
+        nc_ps_file = nc_fls[i].replace(f'.{gfdl_var}.nc', '.ps.nc')
         if os.path.exists(nc_ps_file):
             print(f"(gfdl_to_pcmdi_var) nc_ps_file = {nc_ps_file}")
             nc_ps_file_work = nc_file_work.replace(f'.{gfdl_var}.nc', '.ps.nc')

fre/cmor/tests/test_cmor_run_subtool.py

@@ -1,6 +1,8 @@
 ''' tests for fre.cmor._cmor_run_subtool '''
 import subprocess
 import datetime
+import pathlib
+from pathlib import Path
 from datetime import date
 
 import fre
@@ -17,9 +19,28 @@
 exp_config = f'{rootdir}/CMOR_input_example.json'
 outdir = f'{rootdir}/outdir'
 
+# determined by cmor_run_subtool
+YYYYMMDD=date.today().strftime('%Y%m%d')
+cmor_creates_dir='CMIP6/CMIP6/ISMIP6/PCMDI/PCMDI-test-1-0/piControl-withism/r3i1p1f1/Omon/sos/gn'
+# why does this have "fre" at the end of it?
+full_outputdir = \
+   f"{outdir}fre/{cmor_creates_dir}/v{YYYYMMDD}"
+full_outputfile=f"{full_outputdir}/sos_Omon_PCMDI-test-1-0_piControl-withism_r3i1p1f1_gn_199307-199807.nc"
+
+# FYI
+filename = 'ocean_monthly_1x1deg.199301-199712.sos.nc' # unneeded, this is mostly for reference
+full_inputfile=f"{indir}/{filename}"
+
+
+
+
 def test_fre_cmor_run(capfd):
     ''' fre cmor run, test-use case '''
 
+    # clean up, lest we fool outselves
+    if Path(full_outputfile).exists():
+        Path(full_outputfile).unlink()
+
     fre.cmor._cmor_run_subtool(
         indir = indir,
         varlist = varlist,
@@ -29,31 +50,23 @@ def test_fre_cmor_run(capfd):
     )
     # success condition tricky... tool doesnt return anything really... ?
     # TODO think about returns and success conditions
-    assert True
+    assert all( [ Path(full_outputfile).exists(),
+                  Path(full_inputfile).exists() ] )
     out, err = capfd.readouterr()
 
-# determined by cmor_run_subtool
-YYYYMMDD=date.today().strftime('%Y%m%d')
-cmor_creates_dir='CMIP6/CMIP6/ISMIP6/PCMDI/PCMDI-test-1-0/piControl-withism/r3i1p1f1/Omon/sos/gn'
-full_outputdir = \
-    f"{outdir}/{cmor_creates_dir}/v{YYYYMMDD}"
-full_outputfile=f"{full_outputdir}/sos_Omon_PCMDI-test-1-0_piControl-withism_r3i1p1f1_gn_199307-199807.nc"
-
-# FYI
-filename = 'ocean_monthly_1x1deg.199301-199712.sos.nc' # unneeded, this is mostly for reference
-full_inputfile=f"{indir}/{filename}"
-
 def test_fre_cmor_run_output_compare(capfd):
     ''' I/O comparison of prev test-use case '''
+    print(f'full_outputfile={full_outputfile}')
+    print(f'full_inputfile={full_inputfile}')
+
     nccmp_cmd= [ "nccmp", "-f", "-m", "-g", "-d",
                  f"{full_inputfile}",
                  f"{full_outputfile}"    ]
     print(f"via subprocess, running {' '.join(nccmp_cmd)}")
-    result = subprocess.run( nccmp_cmd
-                             ,
-                            shell=True
+    result = subprocess.run( ' '.join(nccmp_cmd),
+                             shell=True,
+                             check=False
                           )
     #subprocess.run(["rm", "-rf", f"{outdir}/CMIP6/CMIP6/"])
-    #assert result.returncode == 1
-    assert False
+    assert result.returncode == 1
     out, err = capfd.readouterr()

fre/tests/test_fre_cmor_cli.py

@@ -1,6 +1,10 @@
 #!/usr/bin/env python3
 ''' test "fre cmor" calls '''
 
+import datetime
+from datetime import date
+import pathlib
+from pathlib import Path
 import subprocess
 import netCDF4 as nc
 
@@ -42,39 +46,45 @@ def test_cli_fre_cmor_run_opt_dne():
     result = runner.invoke(fre.fre, args=["cmor", "run", "optionDNE"])
     assert result.exit_code == 2
 
-##def test_cli_fre_cmor_run_case1(capfd):
-def test_cli_fre_cmor_run_case1(capsys):
+def test_cli_fre_cmor_run_case1(capfd):
     ''' fre cmor run, test-use case '''
+
+
     # where are we? we're running pytest from the base directory of this repo
     rootdir = 'fre/tests/test_files'
-    
+
     # explicit inputs to tool
     indir = f'{rootdir}/ocean_sos_var_file'
     varlist = f'{rootdir}/varlist'
     table_config = f'{rootdir}/cmip6-cmor-tables/Tables/CMIP6_Omon.json'
     exp_config = f'{rootdir}/CMOR_input_example.json'
     outdir = f'{rootdir}/outdir'
 
-#    indir = 'fre/tests/test_files'
-#    varlist = 'fre/tests/test_files/varlist'
-#    table_config = 'fre/tests/test_files/cmip6-cmor-tables/Tables/CMIP6_Omon.json'
-#    exp_config = 'fre/tests/test_files/CMOR_input_example.json'
-#    outdir = 'fre/tests/test_files/outdir'
+    # determined by cmor_run_subtool
+    YYYYMMDD=date.today().strftime('%Y%m%d')
+    cmor_creates_dir = \
+        'CMIP6/CMIP6/ISMIP6/PCMDI/PCMDI-test-1-0/piControl-withism/r3i1p1f1/Omon/sos/gn'
+    # why does this have "fre" at the end of it?
+    full_outputdir = \
+        f"{outdir}fre/{cmor_creates_dir}/v{YYYYMMDD}"
+    full_outputfile = \
+        f"{full_outputdir}/sos_Omon_PCMDI-test-1-0_piControl-withism_r3i1p1f1_gn_199307-199807.nc"
+
+    # FYI
+    filename = 'ocean_monthly_1x1deg.199301-199712.sos.nc' # unneeded, this is mostly for reference
+    full_inputfile=f"{indir}/{filename}"
+
+    # clean up, lest we fool outselves
+    if Path(full_outputfile).exists():
+        Path(full_outputfile).unlink()
 
-    #subprocess.run(["mkdir", "-p", outdir+'/tmp'])
     result = runner.invoke(fre.fre, args = ["cmor", "run",
                                             "--indir", indir,
                                             "--varlist", varlist,
                                             "--table_config", table_config,
                                             "--exp_config", exp_config,
                                             "--outdir",  outdir])
-    #assert False
-    #out, err = capfd.readouterr()
-    out, err = capsys.readouterr()
-    #print(out)
-    #print(err)
-
-    assert result.exit_code == 0
-
-    assert False
-
+    assert all ( [ result.exit_code == 0,
+                   Path(full_outputfile).exists(),
+                   Path(full_inputfile).exists() ] )
+    out, err = capfd.readouterr()