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Fix and simplify online archiving #2687

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merged 11 commits into from
Jun 21, 2024
Merged

Fix and simplify online archiving #2687

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345b5c9
Fix and simplify online archiving #2673
DavidHuber-NOAA Jun 13, 2024
6b2e82c
Fix search/replace var names, remove unused wxflow classes
DavidHuber-NOAA Jun 17, 2024
339238e
Merge remote-tracking branch 'origin/develop' into fix/archive
DavidHuber-NOAA Jun 17, 2024
9a1d251
Ignore bufr2ioda_insitu links
DavidHuber-NOAA Jun 17, 2024
21ccd39
Moved mkdir section to the end with copy
DavidHuber-NOAA Jun 18, 2024
79c333c
Explicitly check for True to prevent 'undefined' false positives
DavidHuber-NOAA Jun 18, 2024
3329fe7
Merge remote-tracking branch 'origin/develop' into fix/archive
DavidHuber-NOAA Jun 18, 2024
3239e86
Merge remote-tracking branch 'origin/develop' into fix/archive
DavidHuber-NOAA Jun 20, 2024
fd7875c
Add missing ')'s and '{'s.
DavidHuber-NOAA Jun 20, 2024
2d8402f
Add gdas product logs explicitly, rework tabbing in jinja template
DavidHuber-NOAA Jun 20, 2024
5600924
Reenable METplus jobs by default
DavidHuber-NOAA Jun 20, 2024
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -176,6 +176,8 @@ ush/fv3gfs_make_grid.sh
ush/fv3gfs_make_orog.sh
ush/gen_bufr2ioda_json.py
ush/gen_bufr2ioda_yaml.py
ush/bufr2ioda_insitu_profile*.py
ush/bufr2ioda_insitu_surface*.py
ush/global_chgres.sh
ush/global_chgres_driver.sh
ush/global_cycle.sh
Expand Down
250 changes: 141 additions & 109 deletions parm/archive/arcdir.yaml.j2
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Expand Up @@ -4,121 +4,153 @@
{% set head = RUN + ".t" + cycle_HH + "z." %}

# Select data to store in the ARCDIR and VFYARC from deterministic runs
Base: &base # GDAS, GFS, ENKFGDAS, or ENKFGFS
common:
mkdir:
- "{{ ARCDIR }}"

# Common files to be added to both the gfs and gdas keys below
Deterministic: &deterministic
cyclone:
copy:
# Cyclone forecasts, produced for both gdas and gfs cycles
## Only created if tracking is on and there were systems to track
{% if path_exists(COMIN_ATMOS_TRACK ~ "/atcfunix." ~ RUN ~ "." ~ cycle_YMDH) %}
- ["{{ COMIN_ATMOS_TRACK }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}"]
- ["{{ COMIN_ATMOS_TRACK }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}"]
{% endif %}

# Cyclone tracking data
{% for basin in ["epac", "natl"] %}
{% if path_exists(COMIN_ATMOS_TRACK + "/" + basin) %}
- ["{{ COMIN_ATMOS_TRACK }}/{{ basin }}", "{{ ARCDIR }}/{{ basin }}"]
{% endif %}
{% endfor %}
# This file set will contain all source-destination pairs to send to the FileHandler for copying
{% set file_set = [] %}

# Declare the VFYARC where Fit2Obs data will be sent
{% set VFYARC = ROTDIR ~ "/vrfyarch" %}

# Deterministic files
{% if "enkf" not in RUN %}
# Common files to be added to both the gfs and gdas keys below
{% set det_files = [] %}
# Cyclone forecasts, produced for both gdas and gfs cycles
## Only created if tracking is on and there were systems to track
{% if path_exists(COMIN_ATMOS_TRACK ~ "/atcfunix." ~ RUN ~ "." ~ cycle_YMDH) %}
{% do det_files.append([COMIN_ATMOS_TRACK ~ "/atcfunix." ~ RUN ~ "." ~ cycle_YMDH,
ARCDIR ~"/atcfunix." ~ RUN ~ "." ~ cycle_YMDH ]) %}
{% do det_files.append([COMIN_ATMOS_TRACK ~ "/atcfunixp." ~ RUN ~ "." ~ cycle_YMDH,
ARCDIR ~ "/atcfunixp." ~ RUN ~ "." ~ cycle_YMDH]) %}
{% endif %}

{% if MODE == "cycled" %}
analysis:
copy:
# Analysis data (if we are running in cycled mode)
- ["{{ COMIN_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.anl", "{{ ARCDIR }}/pgbanl.{{ RUN }}.{{ cycle_YMDH }}.grib2"]

{% if DO_JEDIATMVAR %}
- ["{{ COMIN_ATMOS_ANALYSIS }}/{{ head }}atmstat", "{{ ARCDIR }}/atmstat.{{ RUN }}.{{ cycle_YMDH }}"]
{% else %}
- ["{{ COMIN_ATMOS_ANALYSIS }}/{{ head }}gsistat", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}"]
{% endif %}

{% if DO_JEDISNOWDA %}
- ["{{ COMIN_SNOW_ANALYSIS }}/{{ head }}snowstat.tgz", "{{ ARCDIR }}/snowstat.{{ RUN }}.{{ cycle_YMDH }}.tgz"]
{% endif %}

{% if AERO_ANL_CDUMP == RUN or AERO_ANL_CDUMP == "both" %}
- ["{{ COMIN_CHEM_ANALYSIS }}/{{ head }}aerostat", "{{ ARCDIR }}/aerostat.{{ RUN }}.{{ cycle_YMDH }}"]
{% endif %}

{% if DO_PREP_OBS_AERO %}
- ["{{ COMIN_OBS }}/{{ head }}aeroobs", "{{ ARCDIR }}/aeroobs.{{ RUN }}.{{ cycle_YMDH }}"]
- ["{{ COMIN_OBS }}/{{ head }}aerorawobs", "{{ ARCDIR }}/aerorawobs.{{ RUN }}.{{ cycle_YMDH }}"]
{% endif %}
# Cyclone tracking data
{% for basin in ["epac", "natl"] %}
{% if path_exists(COMIN_ATMOS_TRACK + "/" + basin) %}
{% do det_files.append([COMIN_ATMOS_TRACK ~ "/" ~ basin,
ARCDIR ~ "/" ~ basin ]) %}
{% endif %}
{% endfor %}

# Deterministic analysis files (generated for cycled experiments)
{% set det_anl_files = [] %}
# Analysis data (if we are running in cycled mode)
{% do det_anl_files.append([COMIN_ATMOS_GRIB_1p00 ~ "/" ~ head ~ "pgrb2.1p00.anl",
ARCDIR ~ "/pgbanl." ~ RUN ~ "." ~ cycle_YMDH ~ ".grib2"]) %}

{% if DO_JEDIATMVAR == True %}
{% do det_anl_files.append([COMIN_ATMOS_ANALYSIS ~ "/" ~ head ~ "atmstat",
ARCDIR ~ "/atmstat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
{% else %}
{% do det_anl_files.append([COMIN_ATMOS_ANALYSIS ~ "/" ~ head ~ "gsistat",
ARCDIR ~ "/gsistat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
{% endif %}

{% if DO_JEDISNOWDA == True %}
{% do det_anl_files.append([COMIN_SNOW_ANALYSIS ~ "/" ~ head ~ "snowstat.tgz",
ARCDIR ~ "/snowstat." ~ RUN ~ "." ~ cycle_YMDH ~ ".tgz"]) %}
{% endif %}

{% if RUN == "gfs" %}
gfs: # GFS specific
<<: *base
<<: *deterministic

gfs:
copy:
{% for fhr in range(0, FHMAX_GFS + 1, FHOUT_GFS) %}
- ["{{ COMIN_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
{% endfor %}

# Cyclone genesis data (only present if there are storms)
{% if path_exists(COMIN_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH) %}
- ["{{ COMIN_ATMOS_GENESIS }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}"]
- ["{{ COMIN_ATMOS_GENESIS }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}"]
{% endif %}

{% if path_exists(COMIN_ATMOS_GENESIS ~ "/trak.gfso.atcfunix." ~ cycle_YMDH) %}
- ["{{ COMIN_ATMOS_GENESIS }}/trak.gfso.atcfunix.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.{{ cycle_YMDH }}"]
- ["{{ COMIN_ATMOS_GENESIS }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}"]
{% endif %}

{% if DO_FIT2OBS %}
fit2obs:

mkdir:
{% set VFYARC = ROTDIR + "/vrfyarch" %}
- "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}"

copy:
{% for fhr in range(0, FHMAX_FITS + 1, 6) %}
{% set sfcfile = "/" + head + "sfcf" + '%03d'|format(fhr) + ".nc" %}
{% set sigfile = "/" + head + "atmf" + '%03d'|format(fhr) + ".nc" %}
- ["{{COMIN_ATMOS_HISTORY}}/{{ sfcfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sfcfile }}"]
- ["{{COMIN_ATMOS_HISTORY}}/{{ sigfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sigfile }}"]
{% endfor %}
{% if AERO_ANL_CDUMP == RUN or AERO_ANL_CDUMP == "both" %}
{% do det_anl_files.append([COMIN_CHEM_ANALYSIS ~ "/" ~ head ~ "aerostat",
ARCDIR ~ "/aerostat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
{% endif %}

{% if DO_PREP_OBS_AERO == True %}
{% do det_anl_files.append([COMIN_OBS ~ "/" ~ head ~ "aeroobs",
ARCDIR ~ "/aeroobs." ~ RUN ~ "." ~ cycle_YMDH]
{% do det_anl_files.append([COMIN_OBS ~ "/" ~ head ~ "aeroawobs",
ARCDIR ~ "/aeroawobs." ~ RUN ~ "." ~ cycle_YMDH]
{% endif %}
{% endif %}

{% if RUN == "gdas" %}
gdas: # GDAS specific
<<: *base
<<: *deterministic
gdas:
copy:
{% for fhr in range(0, FHMAX + 1, FHOUT) %}
- ["{{ COMIN_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
{% endfor %}
{% endif %}
# GFS-specific files
{% set gfs_files = [] %}
{% for fhr in range(0, FHMAX_GFS + 1, FHOUT_GFS) %}
{% do gfs_files.append([COMIN_ATMOS_GRIB_1p00 ~ "/" ~ head ~ "pgrb2.1p00.f" ~ '%03d'|format(fhr),
ARCDIR ~ "/pgbf" ~ '%02d'|format(fhr) ~ "." ~ RUN ~ "." ~ cycle_YMDH ~ ".grib2"]) %}
{% endfor %}

# Cyclone genesis data (only present if there are storms)
{% if path_exists(COMIN_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH) %}
{% do gfs_files.append([COMIN_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH,
ARCDIR ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH ]) %}
{% do gfs_files.append([COMIN_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen.altg." ~ cycle_YMDH,
ARCDIR ~ "/storms.gfso.atcf_gen.altg." ~ cycle_YMDH ]) %}
{% endif %}

{% if path_exists(COMIN_ATMOS_GENESIS ~ "/trak.gfso.atcfunix." ~ cycle_YMDH) %}
{% do gfs_files.append([COMIN_ATMOS_GENESIS ~ "/trak.gfso.atcfunix." ~ cycle_YMDH,
ARCDIR ~ "/trak.gfso.atcfunix." ~ cycle_YMDH ]) %}
{% do gfs_files.append([COMIN_ATMOS_GENESIS ~ "/trak.gfso.atcfunix.altg." ~ cycle_YMDH,
ARCDIR ~ "/trak.gfso.atcfunix.altg." ~ cycle_YMDH ]) %}
{% endif %}

# GFS Fit2Obs data
{% set fit2obs_files = [] %}
{% for fhr in range(0, FHMAX_FITS + 1, 6) %}
{% set sfcfile = "/" + head + "sfcf" + '%03d'|format(fhr) + ".nc" %}
{% set sigfile = "/" + head + "atmf" + '%03d'|format(fhr) + ".nc" %}
{% do fit2obs_files.append([COMIN_ATMOS_HISTORY ~ "/" ~ sfcfile,
VFYARC ~ "/" ~ RUN ~ "." ~ cycle_YMD ~ "/" ~ cycle_HH ~ "/" ~ sfcfile ]) %}
{% do fit2obs_files.append([COMIN_ATMOS_HISTORY ~ "/" ~ sigfile,
VFYARC ~ "/" ~ RUN ~ "." ~ cycle_YMD ~ "/" ~ cycle_HH ~ "/" ~ sigfile ]) %}
{% endfor %}

# GDAS-specific files
{% set gdas_files = [] %}
{% for fhr in range(0, FHMAX + 1, FHOUT) %}
{% do gdas_files.append([COMIN_ATMOS_GRIB_1p00 ~ "/" ~ head ~ "pgrb2.1p00.f" ~ '%03d'|format(fhr),
ARCDIR ~ "/pgbf" ~ '%02d'|format(fhr) ~ "." ~ RUN ~ "." ~ cycle_YMDH ~ ".grib2"]) %}
{% endfor %}

# Now append the necessary file pairs to file_set
# Common deterministic files
{% set file_set = file_set + det_files %}
{% if MODE == "cycled" %}
{% set file_set = file_set + det_anl_files %}
{% endif %}

# Run-specific deterministic files
{% if RUN == "gfs" %}
{% set file_set = file_set + gfs_files %}
# Fit2Obs files
{% if DO_FIT2OBS == True %}
{% set file_set = file_set + fit2obs_files %}
{% endif %}
{% elif RUN == "gdas" %}
{% set file_set = file_set + gdas_files %}
{% endif %}

{% else %} # End of deterministic files

# Ensemble analysis files
{% set enkf_files = [] %}
{% if DO_JEDIATMENS == True %}
{% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "atmensstat",
ARCDIR ~ "/atmensstat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
{% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "atminc.ensmean.nc",
ARCDIR ~ "/atmensstat." ~ RUN ~ "." ~ cycle_YMDH ~ ".ensmean.nc"]) %}
{% else %}
{% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "enkfstat",
ARCDIR ~ "/enkfstat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
{% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "gsistat.ensmean",
ARCDIR ~ "/gsistat." ~ RUN ~ "." ~ cycle_YMDH ~ ".ensmean"]) %}
{% endif %}

# Construct the final file set
{% set file_set = file_set + enkf_files %}

Ensemble: &ensemble # ENKFGDAS or ENKFGFS
analysis:
copy:
# Copy ensemble analyses
{% if DO_JEDIATMENS %}
- ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atmensstat", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}"]
- ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atminc.ensmean.nc", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}.ensmean.nc"]
{% else %}
- ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}enkfstat", "{{ ARCDIR }}/enkfstat.{{ RUN }}.{{ cycle_YMDH }}"]
- ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}gsistat.ensmean", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}.ensmean"]
{% endif %}

{% if "enkf" in RUN %}
{{ RUN }}:
<<: *base
<<: *ensemble
{% endif %}


# Actually write the yaml
mkdir:
- "{{ ARCDIR }}"

{% if DO_FIT2OBS == True %}
- "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}"
{% endif %}

copy:
{% for source_dest_pair in file_set %}
- {{ source_dest_pair }}
{% endfor %}
24 changes: 8 additions & 16 deletions ush/python/pygfs/task/archive.py
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Expand Up @@ -7,9 +7,9 @@
from logging import getLogger
from typing import Any, Dict, List

from wxflow import (AttrDict, FileHandler, Hsi, Htar, Task, cast_strdict_as_dtypedict,
from wxflow import (AttrDict, FileHandler, Hsi, Htar, Task,
chgrp, get_gid, logit, mkdir_p, parse_j2yaml, rm_p, strftime,
to_YMD, to_YMDH, Template, TemplateConstants)
to_YMDH)

logger = getLogger(__name__.split('.')[-1])

Expand Down Expand Up @@ -348,19 +348,11 @@ def _construct_arcdir_set(arcdir_j2yaml, arch_dict) -> Dict:
files need to be copied to the ARCDIR and the Fit2Obs directory.
"""

# Parse the input jinja yaml template
arcdir_yaml = parse_j2yaml(arcdir_j2yaml,
arch_dict,
allow_missing=True)

# Collect the needed FileHandler dicts and construct arcdir_set
arcdir_set = {}
for key, handler in arcdir_yaml[arch_dict.RUN].items():
# Different RUNs can have different filesets that need to be copied.
# Each fileset is stored as a dictionary. Collect the contents of
# each (which should be 'mkdir' and/or 'copy') to produce singular
# mkdir and copy lists.
arcdir_set.update(handler)
# Get the FileHandler dictionary for creating directories and copying
# to the ARCDIR and VFYARC directories.
arcdir_set = parse_j2yaml(arcdir_j2yaml,
arch_dict,
allow_missing=True)

return arcdir_set

Expand Down Expand Up @@ -421,7 +413,7 @@ def replace_string_from_to_file(filename_in, filename_out, search_str, replace_s
with open(filename_in) as old_file:
lines = old_file.readlines()

out_lines = [line.replace(search, replace) for line in lines]
out_lines = [line.replace(search_str, replace_str) for line in lines]

with open("/tmp/track_file", "w") as new_file:
new_file.writelines(out_lines)
Expand Down
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