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simplify assertion for stable files in a folder #7462

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simplify assertion for stable files in a folder #7462

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48d87a4
simplify assertion for stable files in a folder
maxulysse Feb 10, 2025
9fa91e6
recursive is different
maxulysse Feb 10, 2025
a1a941c
Update modules/nf-core/catpack/prepare/tests/main.nf.test
maxulysse Feb 11, 2025
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23 changes: 12 additions & 11 deletions modules/nf-core/catpack/prepare/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ nextflow_process {
tag "catpack"
tag "catpack/prepare"

test("metagenome -sarscov2 - fasta") {
test("metagenome - sarscov2 - fasta") {

when {
process {
Expand All @@ -24,24 +24,27 @@ nextflow_process {
}

then {
def stablefiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && !["database.dmnd", "database.log", "database.fastaid2LCAtaxid", "database.taxids_with_multiple_offspring"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
def unstablefiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (["database.dmnd", "database.log", "database.fastaid2LCAtaxid", "database.taxids_with_multiple_offspring"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
def allFiles = file(process.out.db.get(0).get(1)).listFiles().sort()
// Filter out all files that have unstable content (ie: timestamp, non-deterministic or any other variable content)
def unstableNames = ["database.dmnd", "database.fastaid2LCAtaxid", "database.log", "database.taxids_with_multiple_offspring"]
// Filter out the unstable files
def stableFiles = allFiles.grep { file -> !unstableNames.contains(file.name) }
// Collect the stable file names
def stableNames = allFiles.grep { file -> unstableNames.contains(file.name) }.collect { file -> file.name }

assertAll(
{ assert process.success },
{ assert snapshot(
stablefiles.sort(),
unstablefiles.sort(),
stableFiles,
stableNames,
process.out.taxonomy,
process.out.versions
).match() }
)
}

}

test("metagenome -sarscov2 - fasta - stub") {
test("metagenome - sarscov2 - fasta - stub") {

options "-stub"

Expand All @@ -62,7 +65,5 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

}
12 changes: 6 additions & 6 deletions modules/nf-core/catpack/prepare/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"metagenome -sarscov2 - fasta": {
"metagenome - sarscov2 - fasta": {
"content": [
[

Expand Down Expand Up @@ -28,9 +28,9 @@
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-25T16:19:17.838393903"
"timestamp": "2025-02-10T17:04:51.995020979"
},
"metagenome -sarscov2 - fasta - stub": {
"metagenome - sarscov2 - fasta - stub": {
"content": [
{
"0": [
Expand Down Expand Up @@ -88,9 +88,9 @@
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-19T07:53:12.595910196"
"timestamp": "2025-02-10T16:13:53.612506113"
}
}
50 changes: 34 additions & 16 deletions modules/nf-core/krakenuniq/build/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -46,24 +46,33 @@ nextflow_process {
}

then {
def stablefiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && !["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
def unstablefiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
def allFiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory()) {allFiles.add(file)} }

def allFolders = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ folder -> if (folder.isDirectory()) {allFolders.add(folder)} }

// Defile all files that have unstable content (ie: timestamp, non-deterministic or any other variable content)
def unstableNames = ["database-build.log", "database.report.tsv", "names.dmp", "nodes.dmp", "taxdump.tar.gz", "timestamp"]
// Filter out the unstable files
def stableFiles = allFiles.grep { file -> !unstableNames.contains(file.name) }.sort()
// Collect the stable file names
def stableNames = allFiles.grep { file -> unstableNames.contains(file.name) }.collect { file -> file.name }
stableNames = (stableNames + allFolders.collect { file -> file.name }).sort()

assertAll(
{ assert process.success },
{ assert snapshot(
stablefiles.sort(),
unstablefiles.sort(),
stableFiles,
stableNames,
process.out.versions
).match()
}
)
}

}

test("sarscov2 - fasta - nocleanup") {
test("sarscov2 - fasta - nocleanup") {

when {
process {
Expand All @@ -87,21 +96,30 @@ test("sarscov2 - fasta - nocleanup") {
}

then {
def stablefiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && !["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
def unstablefiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
def allFiles = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory()) {allFiles.add(file)} }

def allFolders = []
file(process.out.db.get(0).get(1)).eachFileRecurse{ folder -> if (folder.isDirectory()) {allFolders.add(folder)} }

// Defile all files that have unstable content (ie: timestamp, non-deterministic or any other variable content)
def unstableNames = ["database-build.log", "database.report.tsv", "names.dmp", "nodes.dmp", "taxdump.tar.gz", "timestamp"]
// Filter out the unstable files
def stableFiles = allFiles.grep { file -> !unstableNames.contains(file.name) }.sort()
// Collect the stable file names
def stableNames = allFiles.grep { file -> unstableNames.contains(file.name) }.collect { file -> file.name }
stableNames = (stableNames + allFolders.collect { file -> file.name }).sort()

assertAll(
{ assert process.success },
{ assert snapshot(
stablefiles.sort(),
unstablefiles.sort(),
stableFiles,
stableNames,
process.out.versions
).match()
}
)
}

}

test("sarscov2 - fasta - stub") {
Expand All @@ -120,7 +138,7 @@ test("sarscov2 - fasta - nocleanup") {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
)
}
}
}
21 changes: 12 additions & 9 deletions modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -60,45 +60,48 @@
"library-files.txt:md5,8a9817d2de8465eb436aa3aa8696a717",
"genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
"seqid2taxid.map:md5,fe738f2333d57dde0db32239c04a93b8",
"taxDB:md5,37ea954363803b13c2c9f6ae36fc81c7"
"taxDB:md5,f9969245ac82fa42682289f5b0b6c67a"
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ok, so I'm concerned that taxDB is actually not stable

],
[
"database-build.log",
"database.report.tsv",
"library",
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I rescued library as a folder name

"names.dmp",
"nodes.dmp",
"taxdump.tar.gz",
"taxonomy",
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and taxonomy

"timestamp"
],
[
"versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-17T08:29:04.791324194"
"timestamp": "2025-02-10T18:41:57.14608044"
},
"sarscov2 - fasta": {
"content": [
[
"database.idx:md5,f5298aa4215c956d2f737b5988721a24",
"database.kdb:md5,46542be19979e867075f9e455a314e00",
"database0.kdb:md5,46542be19979e867075f9e455a314e00",
"taxDB:md5,37ea954363803b13c2c9f6ae36fc81c7"
"taxDB:md5,f9969245ac82fa42682289f5b0b6c67a"
],
[

"library",
"taxonomy"
],
[
"versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-17T08:28:18.051752599"
"timestamp": "2025-02-10T18:44:37.662290616"
}
}
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