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Windows issue fix #14

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Windows issue fix #14

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eb4bfb3
Fix issue with spaces and less than operator
pverkind Jul 8, 2022
d166007
Fix less than issue (Windows)
pverkind Jul 8, 2022
8281e0b
Generalize the replacement commands
pverkind Jul 8, 2022
b35fbc3
placeholder replacement for all relevant fields
pverkind Jul 8, 2022
5511792
wrap replacement in function with try except
pverkind Jul 8, 2022
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30 changes: 28 additions & 2 deletions bin/passim.cmd
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Original file line number Diff line number Diff line change
@@ -1,3 +1,29 @@
@echo off
call %~dp0seriatim --all-pairs ^
--fields "xxhash64(series)^ as^ gid" -f gid^<gid2 %*

:: Replace special characters <, >, |, & in all arguments with a placeholder
:: which will be replaced with the original character in seriatim.py
:: NB: unfortunately, this does not work with the equals sign; use _EQ_, _LTE_ and _GTE_ instead.

:: make sure variables are not expanded before the script is run:
SETLOCAL EnableDelayedExpansion

:: first, set up an empty variable that will contain all modified variables:
set modifiedArgs=

:: loop through all arguments passed to the script (%*)
:: and replace all special characters in them
:: finally, add each argument to the modified arguments list
for %%i in (%*) do (
set arg=%%i
set arg=!arg:^<=_LT_!
set arg=!arg:^>=_GT_!
set arg=!arg:^|=_PIPE_!
set arg=!arg:^&=_AMPERSAND_!
set modifiedArgs=!modifiedArgs! !arg!
echo !arg!
)
::echo MODIFIED ARGS:
::echo %modifiedArgs%

echo %~dp0seriatim.cmd --all-pairs --fields "xxhash64(series) as gid" -f gid_LT_gid2 %modifiedArgs%
call %~dp0seriatim.cmd --all-pairs --fields "xxhash64(series) as gid" -f gid_LT_gid2 %modifiedArgs%
9 changes: 9 additions & 0 deletions passim/seriatim.py
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Original file line number Diff line number Diff line change
Expand Up @@ -545,6 +545,12 @@ def clusterJoin(self, config, corpus):

setattr(DataFrame, 'clusterJoin', clusterJoin)

def replace_placeholders(s):
try:
return s.replace("_LT_", "<").replace("_LTE_", "<=").replace("_GT_", ">").replace("_GTE_", ">=").replace("_PIPE_", "|").replace("_AMPERSAND_", "&")
except:
return s

def main(args):
parser = argparse.ArgumentParser(description='Passim Alignment',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
Expand Down Expand Up @@ -597,6 +603,9 @@ def main(args):
parser.add_argument('outputPath', metavar='<path>', help='output')
config = parser.parse_args(args)

# replace placeholders in the relevant arguments:
config.filterpairs = replace_placeholders(config.filterpairs)
config.link_features = replace_placeholders(config.link_features)
print(config)

spark = SparkSession.builder.appName('Passim Alignment').getOrCreate()
Expand Down