add tests for ena_webin_cli

.gitignore

@@ -9,3 +9,6 @@ testing*
 null/
 .idea/
 test_data
+
+# Ignore Nextflow test output files, which may contain sensitive information and are not relevant to the repository.
+.nf-test*

modules/local/ena_webin_cli/main.nf

@@ -5,8 +5,11 @@ process ENA_WEBIN_CLI {
     container "quay.io/biocontainers/ena-webin-cli:9.0.1--hdfd78af_1"
 
     stageInMode 'copy'
-    secret 'WEBIN_ACCOUNT'
-    secret 'WEBIN_PASSWORD'
+    // Require authentication secrets for real runs, but not for mock testing.
+    if (!params.webincli_mock) {
+        secret 'WEBIN_ACCOUNT'
+        secret 'WEBIN_PASSWORD'
+    }
 
     input:
     tuple val(meta), path(submission_item), path(manifest)
@@ -29,12 +32,12 @@ process ENA_WEBIN_CLI {
     export ITEM_FULL_PATH=\$(readlink -f ${submission_item})
     sed 's|^FASTA\t.*|FASTA\t'"\${ITEM_FULL_PATH}"'|g' ${manifest} > ${prefix}_updated_manifest.manifest
 
-    ena-webin-cli \\
-        -context=genome \\
-        -manifest=${prefix}_updated_manifest.manifest \\
-        -userName="\${WEBIN_ACCOUNT}" \\
-        -password="\${WEBIN_PASSWORD}" \\
-        ${submit_or_validate} \\
+    ena-webin-cli \
+        -context=genome \
+        -manifest=${prefix}_updated_manifest.manifest \
+        -userName="\${WEBIN_ACCOUNT}" \
+        -password="\${WEBIN_PASSWORD}" \
+        ${submit_or_validate} \
         ${mode}
 
     mv webin-cli.report "${prefix}_webin-cli.report"
@@ -53,6 +56,10 @@ process ENA_WEBIN_CLI {
         # there was attempt to re-submit already submitted genome
         export STATUS="success"
         true
+    elif grep -q "Submission(s) validated successfully" "${prefix}_webin-cli.report"; then
+        # we ran with -validate flag
+        export STATUS="success"
+        true
     else
         export STATUS="failed"
         false

modules/local/ena_webin_cli/main.nf.test

@@ -0,0 +1,119 @@
+nextflow_process {
+    name "Test Process ENA_WEBIN_CLI"
+    script "modules/local/ena_webin_cli/main.nf"
+    process "ENA_WEBIN_CLI"
+
+    // Set WEBINCLI_TEST_MOCK=true to run against a mocked ena-webin-cli.
+    def useMocking = (System.getenv('WEBINCLI_TEST_MOCK') ?: 'false').toBoolean()
+    def launchDir = System.getProperty('user.dir')
+    def mockConfigPath = "${launchDir}/modules/local/ena_webin_cli/test-mocking/nextflow.config"
+
+    test("Run validate with no failures") {
+
+        if (useMocking) {
+            options "-c ${mockConfigPath}"
+        }
+
+        when {
+            params {
+                webincli_submit = false
+                webincli_mock = useMocking
+            }
+            process {
+                """
+                input[0] = Channel.of(
+                    tuple(
+                        [id: 'lachnospira_eligens'],
+                        file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz", checkIfExists: true),
+                        file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/lachnospira_eligens.manifest", checkIfExists: true)
+                    )
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                assert process.success
+                assert process.out.upload_status[0][1] == 'success'
+                def report_lines = path(process.out.webin_report[0][1]).readLines()
+                // When mocking it validates the parameters are passed correctly, but doesn't actually run the submission,
+                // so we check for the presence of the parameters in the report.
+                if (useMocking) {
+                    assert report_lines.any { it.contains("MOCK WEBIN RUN") }
+                    assert report_lines.any { it.contains("-context=genome") }
+                    assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") }
+                    assert report_lines.any { it.contains("-validate") }
+                }
+                assert report_lines.any { it.contains("Submission(s) validated successfully") }
+                assert snapshot(process.out.versions).match()
+            }
+        }
+
+    }
+
+    test("Run push with no failures") {
+        if (useMocking) {
+            options "-c ${mockConfigPath}"
+        }
+
+        setup {
+            run("GENERATE_TEST_DATA") {
+                script "./setup_test.nf"
+                process {
+                    """
+                    input[0] = Channel.of(
+                        file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/lachnospira_eligens.manifest", checkIfExists: true)
+                    )
+                    """
+                }
+            }
+
+        }
+
+        when {
+            params {
+                webincli_submit = true
+                test_upload = true
+                webincli_mock = useMocking
+            }
+            process {
+                """
+                def fasta = file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz", checkIfExists: true)
+
+                input[0] = GENERATE_TEST_DATA.out.test_manifest.map { manifest ->
+                    tuple(
+                        [id: 'lachnospira_eligens'],
+                        fasta,
+                        file(manifest)
+                    )
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                assert process.success
+                assert process.out.upload_status[0][1] == 'success'
+                def report_lines = path(process.out.webin_report[0][1]).readLines()
+                // When mocking it validates the parameters are passed correctly, but doesn't actually run the submission,
+                // so we check for the presence of the parameters in the report.
+                if (useMocking) {
+                    assert report_lines.any { it.contains("MOCK WEBIN RUN") }
+                    assert report_lines.any { it.contains("-context=genome") }
+                    assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") }
+                    assert report_lines.any { it.contains("-submit") }
+                    assert report_lines.any { it.contains("-test") }
+                }
+                assert report_lines.any { it.contains("Submission(s) validated successfully") }
+                assert report_lines.any { it.contains("The submission has been completed successfully") }
+                assert report_lines.any { it.contains("This was a TEST submission(s)") }
+                assert snapshot(process.out.versions).match()
+
+            }
+        }
+
+    }
+
+}

modules/local/ena_webin_cli/main.nf.test.snap

@@ -0,0 +1,26 @@
+{
+    "Run validate with no failures": {
+        "content": [
+            [
+                "versions.yml:md5,a38fb03bead632d71062a101d7889ded"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-29T14:09:00.202532371"
+    },
+    "Run push with no failures": {
+        "content": [
+            [
+                "versions.yml:md5,a38fb03bead632d71062a101d7889ded"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-29T14:01:42.491885321"
+    }
+}

modules/local/ena_webin_cli/setup_test.nf

@@ -0,0 +1,17 @@
+process GENERATE_TEST_DATA {
+    label 'process_low'
+    container "quay.io/biocontainers/ena-webin-cli:9.0.1--hdfd78af_1"
+
+    input:
+    path(manifest_template)
+
+    output:
+    path("*.manifest"), emit: test_manifest
+
+    script:
+    """
+    timestamp="\$(date +%s)"
+
+    sed -E "s/^(ASSEMBLYNAME\t[^\t]+)/\\1_\${timestamp}/" "${manifest_template}" > "lachnospira_eligens_dynamic_fixture.manifest"
+    """
+}

modules/local/ena_webin_cli/test-mocking/ena-webin-cli

@@ -0,0 +1,60 @@
+#!/usr/bin/env bash
+# Mock ena-webin-cli script for testing without credentials.
+set -euo pipefail
+
+# Verify that a real ena-webin-cli exists somewhere in PATH beyond this mock.
+real_bin="$(which -a ena-webin-cli 2>/dev/null | grep -v "$(realpath "$0")" | head -1 || true)"
+if [[ -z "$real_bin" ]]; then
+    echo "FATAL: No real ena-webin-cli found in PATH besides this mock." >&2
+    exit 666
+fi
+
+# Outputs the version of the real ena-webin-cli when called with -version, to allow testing of version parsing logic.
+if [[ "${1:-}" == "-version" ]]; then
+  echo $(${real_bin} -version 2>&1)
+  exit 0
+fi
+
+manifest=""
+action=""
+mode=""
+
+for arg in "$@"; do
+  case "$arg" in
+    -manifest=*)
+      manifest="${arg#-manifest=}"
+      ;;
+    -submit|-validate)
+      action="$arg"
+      ;;
+    -test)
+      mode="$arg"
+      ;;
+  esac
+done
+
+if [[ -z "$manifest" || -z "$action" ]]; then
+  echo "Mock ena-webin-cli: missing required arguments" >&2
+  exit 1
+fi
+
+prefix="$(basename "$manifest")"
+prefix="${prefix%_updated_manifest.manifest}"
+
+template_dir="${WEBINCLI_MOCK_TEMPLATE_DIR:-.}"
+if [[ "$action" == "-submit" ]]; then
+  template="$template_dir/mock_submit.report"
+else
+  template="$template_dir/mock_validate.report"
+fi
+
+if [[ ! -f "$template" ]]; then
+  echo "Mock template file not found: $template" >&2
+  exit 1
+fi
+
+sed \
+  -e "s|<PREFIX>|$prefix|g" \
+  -e "s|<ACTION>|$action|g" \
+  -e "s|<MODE>|$mode|g" \
+  "$template" > webin-cli.report

modules/local/ena_webin_cli/test-mocking/mock_submit.report

@@ -0,0 +1,5 @@
+INFO : MOCK WEBIN RUN
+INFO : command=ena-webin-cli -context=genome -manifest=<PREFIX>_updated_manifest.manifest <ACTION> <MODE>
+INFO : Submission(s) validated successfully
+INFO : The submission has been completed successfully
+INFO : This was a TEST submission(s)

modules/local/ena_webin_cli/test-mocking/mock_validate.report

@@ -0,0 +1,3 @@
+INFO : MOCK WEBIN RUN
+INFO : command=ena-webin-cli -context=genome -manifest=<PREFIX>_updated_manifest.manifest <ACTION> <MODE>
+INFO : Submission(s) validated successfully

modules/local/ena_webin_cli/test-mocking/nextflow.config

@@ -0,0 +1,12 @@
+params.testMockingDir = "${projectDir}/modules/local/ena_webin_cli/test-mocking"
+env {
+  WEBIN_ACCOUNT              = "mock_account"
+  WEBIN_PASSWORD             = "mock_password"
+  PATH                       = "${params.testMockingDir}:\$PATH"
+  WEBINCLI_MOCK_TEMPLATE_DIR = "${params.testMockingDir}"
+}
+process {
+  withName: 'ENA_WEBIN_CLI' {
+    containerOptions = "-v ${params.testMockingDir}:${params.testMockingDir}"
+  }
+}