tests/testthat/test-wait_on_slurm_job_id.R
In epi-sam/SamsElves: Helper functions for the data science at IHME
test_that(
"wait_on_slurm_job_id dry-run produces expected command string",
{
# NULL filter
expect_message(
cmd_list <- wait_on_slurm_job_id(
job_id = c(58812401, 58659687, 58811515)
, initial_sleep_sec = 0
, cycle_sleep_sec = 0
, filter_by = NULL
, dryrun = TRUE
)
, regexp = "Waiting on batch_idx: 1"
)
expect_equal(
cmd_list$cmd_base,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1 | grep -P '.*'"
)
expect_equal(
cmd_list$cmd_pass,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1 | grep -P '.*' | grep -P 'RUNNING|PENDING'"
)
expect_equal(
cmd_list$cmd_fail,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1 | grep -P '.*' | grep -P 'FAILED'"
)
# Complex filter
expect_message(
cmd_list <- wait_on_slurm_job_id(
job_id = c(58812401, 58659687, 58811515)
, initial_sleep_sec = 0
, cycle_sleep_sec = 0
, filter_by = c('jobidraw', 'jobname', 'user')
, filter_regex = "proj_geospatial"
, dryrun = TRUE
)
, regexp = "Waiting on batch_idx: 1"
)
expect_equal(
cmd_list$cmd_base,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3,4,5 | grep -P '.*' | grep -P '58812401|58659687|58811515' | grep -P proj_geospatial | grep -P ssbyrne"
)
expect_equal(
cmd_list$cmd_pass,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3,4,5 | grep -P '.*' | grep -P '58812401|58659687|58811515' | grep -P proj_geospatial | grep -P ssbyrne | grep -P 'RUNNING|PENDING'"
)
expect_equal(
cmd_list$cmd_fail,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3,4,5 | grep -P '.*' | grep -P '58812401|58659687|58811515' | grep -P proj_geospatial | grep -P ssbyrne | grep -P 'FAILED'"
)
}
)
test_that(
"Validations perform.",
{
expect_message(
expect_warning(
wait_on_slurm_job_id(
job_id = c(58812401, 58659687, 58811515)
, initial_sleep_sec = 0
, cycle_sleep_sec = 0
, filter_by = c('account', 'jobname')
, filter_regex = "proj_geospatial"
, dryrun = TRUE
)
, regexp = "More than one field depends on filter_regex - this may affect results: account, jobname"
)
, regexp = "Waiting on batch_idx: 1"
)
}
)
test_that(
"Batching performs correctly",
{
expect_message(
cmd_list <- wait_on_slurm_job_id(
job_id = seq(1, 600, by = 1)
,initial_sleep_sec = 0
, cycle_sleep_sec = 0
, dryrun = TRUE
, batch_size = 500
)
, regexp = "Warning: You have submitted more than 500 JobIDs. Waiting for all jobs in batch_idx 1 before proceeding to batch_idx 2, etc. \\(grep limitation\\)"
)
expect_equal(
cmd_list$cmd_base,
"sacct -j '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3 | grep -P '.*' | grep -P '1|2|3|4|5|6|7|8|9|10|11|12|13|14|15|16|17|18|19|20|21|22|23|24|25|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|50|51|52|53|54|55|56|57|58|59|60|61|62|63|64|65|66|67|68|69|70|71|72|73|74|75|76|77|78|79|80|81|82|83|84|85|86|87|88|89|90|91|92|93|94|95|96|97|98|99|100|101|102|103|104|105|106|107|108|109|110|111|112|113|114|115|116|117|118|119|120|121|122|123|124|125|126|127|128|129|130|131|132|133|134|135|136|137|138|139|140|141|142|143|144|145|146|147|148|149|150|151|152|153|154|155|156|157|158|159|160|161|162|163|164|165|166|167|168|169|170|171|172|173|174|175|176|177|178|179|180|181|182|183|184|185|186|187|188|189|190|191|192|193|194|195|196|197|198|199|200|201|202|203|204|205|206|207|208|209|210|211|212|213|214|215|216|217|218|219|220|221|222|223|224|225|226|227|228|229|230|231|232|233|234|235|236|237|238|239|240|241|242|243|244|245|246|247|248|249|250|251|252|253|254|255|256|257|258|259|260|261|262|263|264|265|266|267|268|269|270|271|272|273|274|275|276|277|278|279|280|281|282|283|284|285|286|287|288|289|290|291|292|293|294|295|296|297|298|299|300|301|302|303|304|305|306|307|308|309|310|311|312|313|314|315|316|317|318|319|320|321|322|323|324|325|326|327|328|329|330|331|332|333|334|335|336|337|338|339|340|341|342|343|344|345|346|347|348|349|350|351|352|353|354|355|356|357|358|359|360|361|362|363|364|365|366|367|368|369|370|371|372|373|374|375|376|377|378|379|380|381|382|383|384|385|386|387|388|389|390|391|392|393|394|395|396|397|398|399|400|401|402|403|404|405|406|407|408|409|410|411|412|413|414|415|416|417|418|419|420|421|422|423|424|425|426|427|428|429|430|431|432|433|434|435|436|437|438|439|440|441|442|443|444|445|446|447|448|449|450|451|452|453|454|455|456|457|458|459|460|461|462|463|464|465|466|467|468|469|470|471|472|473|474|475|476|477|478|479|480|481|482|483|484|485|486|487|488|489|490|491|492|493|494|495|496|497|498|499|500'"
)
}
)
epi-sam/SamsElves documentation built on June 12, 2025, 7 a.m.
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test_that(
"wait_on_slurm_job_id dry-run produces expected command string",
{
# NULL filter
expect_message(
cmd_list <- wait_on_slurm_job_id(
job_id = c(58812401, 58659687, 58811515)
, initial_sleep_sec = 0
, cycle_sleep_sec = 0
, filter_by = NULL
, dryrun = TRUE
)
, regexp = "Waiting on batch_idx: 1"
)
expect_equal(
cmd_list$cmd_base,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1 | grep -P '.*'"
)
expect_equal(
cmd_list$cmd_pass,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1 | grep -P '.*' | grep -P 'RUNNING|PENDING'"
)
expect_equal(
cmd_list$cmd_fail,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1 | grep -P '.*' | grep -P 'FAILED'"
)
# Complex filter
expect_message(
cmd_list <- wait_on_slurm_job_id(
job_id = c(58812401, 58659687, 58811515)
, initial_sleep_sec = 0
, cycle_sleep_sec = 0
, filter_by = c('jobidraw', 'jobname', 'user')
, filter_regex = "proj_geospatial"
, dryrun = TRUE
)
, regexp = "Waiting on batch_idx: 1"
)
expect_equal(
cmd_list$cmd_base,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3,4,5 | grep -P '.*' | grep -P '58812401|58659687|58811515' | grep -P proj_geospatial | grep -P ssbyrne"
)
expect_equal(
cmd_list$cmd_pass,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3,4,5 | grep -P '.*' | grep -P '58812401|58659687|58811515' | grep -P proj_geospatial | grep -P ssbyrne | grep -P 'RUNNING|PENDING'"
)
expect_equal(
cmd_list$cmd_fail,
"sacct -j '58812401,58659687,58811515' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3,4,5 | grep -P '.*' | grep -P '58812401|58659687|58811515' | grep -P proj_geospatial | grep -P ssbyrne | grep -P 'FAILED'"
)
}
)
test_that(
"Validations perform.",
{
expect_message(
expect_warning(
wait_on_slurm_job_id(
job_id = c(58812401, 58659687, 58811515)
, initial_sleep_sec = 0
, cycle_sleep_sec = 0
, filter_by = c('account', 'jobname')
, filter_regex = "proj_geospatial"
, dryrun = TRUE
)
, regexp = "More than one field depends on filter_regex - this may affect results: account, jobname"
)
, regexp = "Waiting on batch_idx: 1"
)
}
)
test_that(
"Batching performs correctly",
{
expect_message(
cmd_list <- wait_on_slurm_job_id(
job_id = seq(1, 600, by = 1)
,initial_sleep_sec = 0
, cycle_sleep_sec = 0
, dryrun = TRUE
, batch_size = 500
)
, regexp = "Warning: You have submitted more than 500 JobIDs. Waiting for all jobs in batch_idx 1 before proceeding to batch_idx 2, etc. \\(grep limitation\\)"
)
expect_equal(
cmd_list$cmd_base,
"sacct -j '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600' --format=State%16,JobID%20,JobIDRaw%20,User%12,JobName%50,Account%20 | tail -n +3 | grep -vP 'batch|extern' | sed 's/ \\+/ /g; s/^[[:space:]]*//; s/[[:space:]]*$//' | cut -d' ' -f1,3 | grep -P '.*' | grep -P '1|2|3|4|5|6|7|8|9|10|11|12|13|14|15|16|17|18|19|20|21|22|23|24|25|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|50|51|52|53|54|55|56|57|58|59|60|61|62|63|64|65|66|67|68|69|70|71|72|73|74|75|76|77|78|79|80|81|82|83|84|85|86|87|88|89|90|91|92|93|94|95|96|97|98|99|100|101|102|103|104|105|106|107|108|109|110|111|112|113|114|115|116|117|118|119|120|121|122|123|124|125|126|127|128|129|130|131|132|133|134|135|136|137|138|139|140|141|142|143|144|145|146|147|148|149|150|151|152|153|154|155|156|157|158|159|160|161|162|163|164|165|166|167|168|169|170|171|172|173|174|175|176|177|178|179|180|181|182|183|184|185|186|187|188|189|190|191|192|193|194|195|196|197|198|199|200|201|202|203|204|205|206|207|208|209|210|211|212|213|214|215|216|217|218|219|220|221|222|223|224|225|226|227|228|229|230|231|232|233|234|235|236|237|238|239|240|241|242|243|244|245|246|247|248|249|250|251|252|253|254|255|256|257|258|259|260|261|262|263|264|265|266|267|268|269|270|271|272|273|274|275|276|277|278|279|280|281|282|283|284|285|286|287|288|289|290|291|292|293|294|295|296|297|298|299|300|301|302|303|304|305|306|307|308|309|310|311|312|313|314|315|316|317|318|319|320|321|322|323|324|325|326|327|328|329|330|331|332|333|334|335|336|337|338|339|340|341|342|343|344|345|346|347|348|349|350|351|352|353|354|355|356|357|358|359|360|361|362|363|364|365|366|367|368|369|370|371|372|373|374|375|376|377|378|379|380|381|382|383|384|385|386|387|388|389|390|391|392|393|394|395|396|397|398|399|400|401|402|403|404|405|406|407|408|409|410|411|412|413|414|415|416|417|418|419|420|421|422|423|424|425|426|427|428|429|430|431|432|433|434|435|436|437|438|439|440|441|442|443|444|445|446|447|448|449|450|451|452|453|454|455|456|457|458|459|460|461|462|463|464|465|466|467|468|469|470|471|472|473|474|475|476|477|478|479|480|481|482|483|484|485|486|487|488|489|490|491|492|493|494|495|496|497|498|499|500'"
)
}
)
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