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Merge pull request #37 from platforma-open/julenmendieta/avoidCheckingFastaContent
Julenmendieta/avoidCheckingFastaContent
2 parents 73faf66 + 941be59 commit e2b2b79

10 files changed

Lines changed: 203 additions & 105 deletions

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‎.changeset/tasty-loops-flash.md‎

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---
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"@platforma-open/milaboratories.immune-assay-data.check-content-empty": patch
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"@platforma-open/milaboratories.immune-assay-data.workflow": patch
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---
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Improve empty input detection

‎pnpm-lock.yaml‎

Lines changed: 89 additions & 77 deletions
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‎pnpm-workspace.yaml‎

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@@ -4,6 +4,7 @@ packages:
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- software/coverage-mode-calc
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- software/fasta-to-tsv
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- software/xlsx-to-csv
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- software/check-content-empty
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- workflow
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- model
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- ui
@@ -15,13 +16,13 @@ catalog:
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'@milaboratories/ts-builder': 1.3.0
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'@milaboratories/ts-configs': 1.2.2
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'@platforma-sdk/workflow-tengo': 5.9.1
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'@platforma-sdk/model': 1.58.19
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'@platforma-sdk/ui-vue': 1.58.19
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'@platforma-sdk/tengo-builder': 2.4.27
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'@platforma-sdk/model': 1.58.22
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'@platforma-sdk/ui-vue': 1.58.25
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'@platforma-sdk/tengo-builder': 2.4.28
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'@platforma-sdk/package-builder': 3.11.6
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'@platforma-sdk/block-tools': 2.6.67
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'@platforma-sdk/block-tools': 2.6.68
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'@platforma-sdk/eslint-config': 1.2.0
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'@platforma-sdk/test': 1.58.20
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'@platforma-sdk/test': 1.58.24
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'@milaboratories/helpers': 1.13.7
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'@milaboratories/graph-maker': 1.2.3
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'@milaboratories/multi-sequence-alignment': 1.47.3

‎software/check-content-empty/package.json‎

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{
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"name": "@platforma-open/milaboratories.immune-assay-data.check-content-empty",
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"version": "1.0.0",
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"scripts": {
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"build": "pl-pkg build",
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"prepublishOnly": "pl-pkg prepublish",
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"do-pack": "rm -f *.tgz && pl-pkg build && pnpm pack && mv platforma-open*.tgz package.tgz",
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"changeset": "changeset",
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"version-packages": "changeset version"
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},
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"files": [
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"./dist/**/*"
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],
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"dependencies": {},
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"devDependencies": {
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"@platforma-sdk/package-builder": "catalog:",
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"@platforma-open/milaboratories.runenv-python-3": "catalog:"
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},
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"block-software": {
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"entrypoints": {
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"main": {
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"binary": {
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"artifact": {
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"type": "python",
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"registry": "platforma-open",
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"environment": "@platforma-open/milaboratories.runenv-python-3:3.12.10",
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"dependencies": {
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"toolset": "pip",
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"requirements": "requirements.txt"
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},
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"root": "./src"
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},
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"cmd": [
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"python",
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"{pkg}/main.py"
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]
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}
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}
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}
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}
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}

‎software/check-content-empty/src/main.py‎

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import argparse
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import sys
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def main():
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parser = argparse.ArgumentParser(description="Check if a file has a minimum number of non-empty lines.")
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parser.add_argument("-i", "--input", required=True, help="Input file path.")
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parser.add_argument("-n", "--min_lines", type=int, default=1, help="Minimum number of non-empty lines required to be considered 'not empty'.")
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args = parser.parse_args()
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try:
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count = 0
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with open(args.input, 'r') as f:
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for line in f:
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if line.strip():
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count += 1
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if count >= args.min_lines:
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break
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# print "true" if it's empty (count < min_lines), "false" if it has enough content
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print("true" if count < args.min_lines else "false")
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except FileNotFoundError:
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print(f"Error: File '{args.input}' not found.")
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sys.exit(1)
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except Exception as e:
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print(f"An unexpected error occurred: {e}")
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sys.exit(1)
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if __name__ == "__main__":
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main()

‎software/check-content-empty/src/requirements.txt‎

Whitespace-only changes.

‎workflow/package.json‎

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@@ -15,6 +15,7 @@
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"@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc": "workspace:*",
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"@platforma-open/milaboratories.immune-assay-data.fasta-to-tsv": "workspace:*",
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"@platforma-open/milaboratories.immune-assay-data.xlsx-to-csv": "workspace:*",
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"@platforma-open/milaboratories.immune-assay-data.check-content-empty": "workspace:*",
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"@platforma-open/soedinglab.software-mmseqs2": "catalog:"
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},
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"devDependencies": {

‎workflow/src/analysis.tpl.tengo‎

Lines changed: 14 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@ fastaToTsvSw := assets.importSoftware("@platforma-open/milaboratories.immune-ass
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addHeaderSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.add-header:main")
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covModeCalcSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc:main")
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xlsxToCsvSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.xlsx-to-csv:main")
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checkContentEmptySw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.check-content-empty:main")
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runAlignmentTpl := assets.importTemplate(":run-alignment")
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checkContentEmptyTpl := assets.importTemplate(":check-content-empty")
@@ -274,16 +275,24 @@ self.body(func(args) {
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arg("-o").arg("results_with_header.tsv").
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addFile("results.tsv", mmseqsOutput).
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saveFile("results_with_header.tsv").
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saveFileContent("results_with_header.tsv").
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run()
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mmseqsResultTsv := addHeaderRun.getFile("results_with_header.tsv")
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mmseqsResultContent := addHeaderRun.getFileContent("results_with_header.tsv")
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// Use subtemplate to check if file is empty
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// Check if results are empty (only header line or nothing)
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checkResultsRun := exec.builder().
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software(checkContentEmptySw).
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arg("-i").arg("input.file").
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arg("-n").arg("2"). // Require at least 2 non-empty lines (header + 1 data line)
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addFile("input.file", mmseqsResultTsv).
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saveStdoutContent().
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mem("8GiB").
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cpu(1).
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inLightQueue().
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run()
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checkResult := render.create(checkContentEmptyTpl, {
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content: mmseqsResultContent,
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mode: "headerOnly"
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content: checkResultsRun.getStdoutContent()
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})
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emptyResults := checkResult.output("result")
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‎workflow/src/check-content-empty.tpl.tengo‎

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Original file line numberDiff line numberDiff line change
@@ -4,18 +4,6 @@ text := import("text")
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self.defineOutputs("result")
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66
self.body(func(args) {
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content := string(args.content.getData())
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mode := args.mode
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isEmpty := false
11-
if mode == "raw" {
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// No header line (e.g. FASTA): empty content means no data
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isEmpty = text.trim_space(content) == ""
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} else if mode == "headerOnly" {
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// File has a header line (e.g. TSV with added header): empty means <= 1 line
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lines := text.split(text.trim_space(content), "\n")
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isEmpty = len(lines) <= 1
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}
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20-
return { result: isEmpty }
7+
// 'content' is the stdout of the check-software (already a "true"/"false" string)
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return { result: text.trim_space(string(args.content.getData())) == "true" }
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})

‎workflow/src/main.tpl.tengo‎

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Original file line numberDiff line numberDiff line change
@@ -16,6 +16,7 @@ processOutputsTpl := assets.importTemplate(":process-outputs")
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checkContentEmptyTpl := assets.importTemplate(":check-content-empty")
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prepareFastaSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.prepare-fasta:main")
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checkContentEmptySw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.check-content-empty:main")
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2021
wf.prepare(func(args){
2122
bundleBuilder := wf.createPBundleBuilder()
@@ -103,15 +104,23 @@ wf.body(func(args) {
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arg("--seq_col").arg("sequence").
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arg("--id_col").arg("seqId").
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saveFile("output.fasta").
106-
saveFileContent("output.fasta").
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run()
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clonesFasta := clonesFastaRun.getFile("output.fasta")
109-
clonesFastaContent := clonesFastaRun.getFileContent("output.fasta")
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111110
// Check if clones are empty before running mmseqs2
111+
checkClonesRun := exec.builder().
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software(checkContentEmptySw).
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arg("-i").arg("input.file").
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arg("-n").arg("1").
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addFile("input.file", clonesFasta).
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saveStdoutContent().
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mem("8GiB").
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cpu(1).
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inLightQueue().
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run()
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checkClonesResult := render.create(checkContentEmptyTpl, {
113-
content: clonesFastaContent,
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mode: "raw"
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content: checkClonesRun.getStdoutContent()
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})
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emptyClonesInput := checkClonesResult.output("result")
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