Mercurial > repos > greg > validate_temperature_data
changeset 0:4290854f3af5 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 27 Nov 2018 09:47:31 -0500 |
| parents | |
| children | cfe1ce427aa7 |
| files | .shed.yml test-data/30_year_normals.csv test-data/daily_actuals.csv validate_temperature_data.py validate_temperature_data.xml |
| diffstat | 5 files changed, 800 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Nov 27 09:47:31 2018 -0500 @@ -0,0 +1,11 @@ +name: validate_temperature_data +owner: greg +description: | + Contains a tool that validates both 30 year normals and daily temperature data for the insect_phenology_model tool. +homepage_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/entomology/validate_temperature_data +long_description: | + Contains a tool that validates both 30 year normals and daily temperature data for the insect_phenology_model tool +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/entomology/validate_temperature_data +type: unrestricted +categories: + - Entomology
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/30_year_normals.csv Tue Nov 27 09:47:31 2018 -0500 @@ -0,0 +1,367 @@ +stationid,latitude,longitude,elev_m,name,st,mmdd,doy,tmin,tmax +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-01, 001,-6.8,2.8 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-02, 002,-6.8,2.7 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-03, 003,-6.9,2.6 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-04, 004,-7.0,2.6 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-05, 005,-7.1,2.5 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-06, 006,-7.1,2.5 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-07, 007,-7.2,2.4 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-08, 008,-7.2,2.4 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-09, 009,-7.3,2.4 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH LAKE,PA,01-10, 010,-7.3,2.3 +USC00360785,40.3844,-76.0339,106.7,BLUE MARSH 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+ 40.81849,-77.84637,2017-09-08,251,8.86,18.11 + 40.81849,-77.84637,2017-09-09,252,8.44,18.21 + 40.81849,-77.84637,2017-09-10,253,3.93,9.19 + 40.81849,-77.84637,2017-09-11,254,4.98,22.12 + 40.81849,-77.84637,2017-09-12,255,8.70,24.06 + 40.81849,-77.84637,2017-09-13,256,12.75,23.14 + 40.81849,-77.84637,2017-09-14,257,16.60,19.18 + 40.81849,-77.84637,2017-09-15,258,14.89,25.28 + 40.81849,-77.84637,2017-09-16,259,14.73,25.42 + 40.81849,-77.84637,2017-09-17,260,14.85,27.42 + 40.81849,-77.84637,2017-09-18,261,16.12,26.18 + 40.81849,-77.84637,2017-09-19,262,13.36,25.46 + 40.81849,-77.84637,2017-09-20,263,10.90,28.76 + 40.81849,-77.84637,2017-09-21,264,11.68,28.44 + 40.81849,-77.84637,2017-09-22,265,13.10,29.03 + 40.81849,-77.84637,2017-09-23,266,10.11,30.51 + 40.81849,-77.84637,2017-09-24,267,12.33,31.11 + 40.81849,-77.84637,2017-09-25,268,15.03,31.81 + 40.81849,-77.84637,2017-09-26,269,16.01,30.96 + 40.81849,-77.84637,2017-09-27,270,15.03,31.27 + 40.81849,-77.84637,2017-09-28,271,9.61,21.39 + 40.81849,-77.84637,2017-09-29,272,6.03,20.71 + 40.81849,-77.84637,2017-09-30,273,2.85,15.23
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/validate_temperature_data.py Tue Nov 27 09:47:31 2018 -0500 @@ -0,0 +1,162 @@ +#!/usr/bin/env python +import argparse +import datetime +import decimal +import re +import shutil +import sys + +parser = argparse.ArgumentParser() +parser.add_argument('--data_type', dest='data_type', default=None, help='Temperature data type, normals or actuals') +parser.add_argument('--input_actuals', dest='input_actuals', default=None, help='Daily actuals temperature data') +parser.add_argument('--input_normals', dest='input_normals', default=None, help='30 year normals temperature data') +parser.add_argument('--output', dest='output', help='Output dataset'), +args = parser.parse_args() + +ACTUALS_HEADER = "LATITUDE,LONGITUDE,DATE,DOY,TMIN,TMAX" +NORMALS_HEADER = "stationid,latitude,longitude,elev_m,name,st,mmdd,doy,tmin,tmax" + +def add_error_msg(accumulated_msgs, msg): + return "%s\n%s" % (accumulated_msgs, msg) + + +def empty_value(line_no, label, accumulated_msgs): + return add_error_msg(accumulated_msgs, "The required %s value is missing on line %d." % (label, line_no)) + + +def stop_error(msg): + sys.exit(msg) + + +def validate_date_string(line_no, date_string, accumulated_msgs): + try: + datetime.datetime.strptime(date_string, '%Y-%m-%d') + return accumulated_msgs + except ValueError: + return add_error_msg(accumulated_msgs, "Line %d contains an incorrect date format (%s must be YYYY-MM-DD)." % (line_no, date_string)) + + +def validate_decimal(line_no, decimal_string, accumulated_msgs, label): + try: + decimal.Decimal(decimal_string) + return accumulated_msgs + except Exception: + return add_error_msg(accumulated_msgs, "Line %d contains an incorrect %s decimal value (%s)." % (line_no, label, decimal_string)) + + +def validate_integer(line_no, integer_string, accumulated_msgs, label): + if integer_string.isdigit(): + return accumulated_msgs + return add_error_msg(accumulated_msgs, "Line %d contains an incorrect %s integer value (%s)." % (line_no, label, decimal_string)) + + +def validate_mmdd(line_no, mmdd, accumulated_msgs): + try: + datetime.datetime.strptime(date_string, '%m-%d') + return accumulated_msgs + except ValueError: + return add_error_msg(accumulated_msgs, "Line %d contains an incorrect date format (%s must be mm-dd)." % (line_no, date_string)) + + +accumulated_msgs = "" +# Parse the input file, skipping the header, and validating +# that each data line consists of 31 comma-separated items. +if args.data_type == "normals": + input_file = args.input_normals + header = NORMALS_HEADER + last_doy = 0 + num_normals_rows = 0 +else: + input_file = args.input_actuals + header = ACTUALS_HEADER +with open(input_file, "r") as ih: + for i, line in enumerate(ih): + line = line.rstrip("\r\n") + if i == 0: + if line != header: + accumulated_msgs = add_error_msg(accumulated_msgs, "The header is invalid, must be %s" % header) + items = line.split(",") + if args.data_type == "normals": + if i > 367: + accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 367 lines (must be 1 header line and 366 data lines).") + stop_error(accumulated_msgs) + if len(items) != 10: + accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 10)." % (i, len(items))) + stop_error(accumulated_msgs) + stationid = items[0] + if len(station_id) == 0: + accumulated_msgs = empty_value(i, "stationid", accumulated_msgs) + latitude = items[1] + accumulated_msgs = validate_decimal(i, latitude, accumulated_msgs, "latitude") + longitude = items[2] + accumulated_msgs = validate_decimal(i, longitude, accumulated_msgs, "longitude") + elev_m = items[3] + accumulated_msgs = validate_decimal(i, elev_m, accumulated_msgs, "elev_m") + name = items[4] + if len(name) == 0: + accumulated_msgs = empty_value(i, "name", accumulated_msgs) + st = items[5] + if len(st) == 0: + accumulated_msgs = empty_value(i, "st", accumulated_msgs) + mmdd = items[6] + accumulated_msgs = validate_mmdd(i, mmdd, accumulated_msgs) + doy = items[7] + accumulated_msgs = validate_integer(i, doy, accumulated_msgs, "doy") + # Make sure the DOY values are consecutive. + try: + if int(doy) != (last_doy + 1): + accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains a DOY (%s) that is not conexcutive." % (i, doy)) + stop_error(accumulated_msgs) + else: + last_doy += 1 + except Exception: + # The error for an invalid integer was captured above. + pass + tmin = items[8] + accumulated_msgs = validate_decimal(i, tmin, accumulated_msgs, "tmin") + tmax = items[9] + accumulated_msgs = validate_decimal(i, tmax, accumulated_msgs, "tmax") + num_normals_rows += 1 + else: + if i > 367: + accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 367 lines (must be 1 header line and no more than 366 data lines).") + stop_error(accumulated_msgs) + if len(items) != 6: + accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 6)." % (i, len(items))) + stop_error(accumulated_msgs) + latitude = items[0] + accumulated_msgs = validate_decimal(i, latitude, accumulated_msgs, "LATITUDE") + longitude = items[1] + accumulated_msgs = validate_decimal(i, longitude, accumulated_msgs, "LONGITUDE") + date_string = items[2] + accumulated_msgs = validate_date_string(line_no, date_string, accumulated_msgs) + doy = items[3] + accumulated_msgs = validate_integer(i, doy, accumulated_msgs, "doy") + # Make sure the DOY values are consecutive. + if i==0: + try: + last_doy = int(doy) + except Exception: + # The error for an invalid integer was captured above. + pass + else: + try: + if int(doy) != (last_doy + 1): + accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains a DOY (%s) that is not conexcutive." % (i, doy)) + stop_error(accumulated_msgs) + else: + last_doy += 1 + except Exception: + # The error for an invalid integer was captured above. + pass + tmin = items[8] + accumulated_msgs = validate_decimal(i, tmin, accumulated_msgs, "tmin") + tmax = items[9] + accumulated_msgs = validate_decimal(i, tmax, accumulated_msgs, "tmax") + if args.data_type == "normals" and num_normals_rows != 367: + accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains %d rows, (must be 367)." % num_normals_rows)) + +if len(accumulated_msgs) > 0: + stop_error(accumulated_msgs) + +shutil.copyfile(input_file, args.output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/validate_temperature_data.xml Tue Nov 27 09:47:31 2018 -0500 @@ -0,0 +1,76 @@ +<tool id="validate_temperature_data" name="Validate temperature data" version="1.0.0"> + <description>for insect phenology model</description> + <command detect_errors="exit_code"><![CDATA[ +#set temperature_data_type = $temperature_data_type_cond.temperature_data_type +python '$__tool_directory__/validate_temperature_data.py' +--data_type $temperature_data_type +#if str($temperature_data_type) == "normals": + --input_normals '$temperature_data_type_cond.input_normals' +#else: + --input_actuals '$temperature_data_type_cond.input_actuals' +#end if +--output '$output']]></command> + <inputs> + <conditional name="temperature_data_type_cond"> + <param name="temperature_data_type" type="select" label="Validate 30 year normals or daily actuals temperature data?"> + <option value="normals" selected="true">30 year normals</option> + <option value="actuals">daily actuals</option> + </param> + <when value="normals"> + <param name="input_normals" type="data" format="csv" label="30 year normals CSV file"> + <validator type="expression" message="30 year normals temperature data must have 10 columns and 366 rows">value is not None and value.metadata.columns==10 and value.metadata.data_lines==366</validator> + </param> + </when> + <when value="actuals"> + <param name="input_actuals" type="data" format="csv" label="Daily actuals CSV file"> + <validator type="expression" message="Daily actuals temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="csv"/> + </outputs> + <tests> + <test> + <param name="input" value="30_year_normals.csv" ftype="csv"/> + <output name="output" file="30_year_normals.csv" ftype="csv"/> + </test> + <test> + <param name="input" value="daily_actuals.csv" ftype="csv"/> + <output name="output" file="daily_actuals.csv" ftype="csv"/> + </test> + </tests> + <help> +**What it does** + +Validates either a 30 year normals temeprature dataset or a daily actuals temperature dataset which are used +as input to the insect phenology model tool. The tool will output the input file if it is valid. + +----- + +**30 year normals columns** + + * stationid + * latitude + * longitude + * elev_m + * name + * st + * mmdd + * doy + * tmin + * tmax + +**Daily actuals columns** + + * LATITUDE + * LONGITUDE + * DATE + * DOY + * TMIN + * TMAX + </help> + <citations> + </citations> +</tool>