Merge pull request #29 from DNAstack/isoseq-tests

Add xml_validator test for IsoSeq

README.md

@@ -15,7 +15,7 @@ If any step of the action fails, the check will fail; however if some task tests
 # GitHub action usage
 
 ```yaml
-- uses: dnastack/[email protected].7
+- uses: dnastack/[email protected].8
   with:
     # Configuration file where tests can be found
     # Default: wdl-ci.config.json
@@ -86,7 +86,7 @@ jobs:
         with:
           submodules: true
       - name: wdl-ci
-        uses: dnastack/[email protected].7
+        uses: dnastack/[email protected].8
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -114,7 +114,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/[email protected].7
+        uses: dnastack/[email protected].8
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -144,7 +144,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/[email protected].7
+        uses: dnastack/[email protected].8
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}

action.yml

@@ -50,19 +50,19 @@ runs:
           echo "WDL_CI_CUSTOM_TEST_WDL_DIR"=${{ inputs.wdl_ci_custom_test_wdl_dir }} >> $GITHUB_ENV
         fi
     - name: lint
-      uses: docker://dnastack/wdl-ci:v0.1.7
+      uses: docker://dnastack/wdl-ci:v0.1.8
       with:
         args: lint
     - name: detect-changes
-      uses: docker://dnastack/wdl-ci:v0.1.7
+      uses: docker://dnastack/wdl-ci:v0.1.8
       with:
         args: detect-changes
     - name: submit
-      uses: docker://dnastack/wdl-ci:v0.1.7
+      uses: docker://dnastack/wdl-ci:v0.1.8
       with:
         args: submit
     - name: monitor
-      uses: docker://dnastack/wdl-ci:v0.1.7
+      uses: docker://dnastack/wdl-ci:v0.1.8
       with:
         args: monitor --update-digests
       # If a test fails, still update task digests for any tests that succeeded
@@ -76,6 +76,6 @@ runs:
         default_author: github_actions
     - name: cleanup
       if: always()
-      uses: docker://dnastack/wdl-ci:v0.1.7
+      uses: docker://dnastack/wdl-ci:v0.1.8
       with:
         args: cleanup

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "wdl-testing-cli"
 description = "DNAstack WDL testing CLI"
-version = "v0.1.7"
+version = "v0.1.8"
 authors = [
     { name = "DNAstack", email = "[email protected]" }
 ]

src/wdlci/wdl_tests/count_columns.wdl

@@ -26,8 +26,9 @@ task count_columns {
 			current_run_output_column_count=$(sed 's;,;\t;g' ~{current_run_output} | awk '{print NF}' | sort -nu | tail -n 1)
 			validated_output_column_count=$(sed 's;,;\t;g' ~{validated_output} | awk '{print NF}' | sort -nu | tail -n 1)
 		else
-			current_run_output_column_count=$(awk '{print NF}' ~{current_run_output} | sort -nu | tail -n 1)
-			validated_output_column_count=$(awk '{print NF}' ~{validated_output} | sort -nu | tail -n 1)
+			# Disregard headers starting with `#`
+			current_run_output_column_count=$(sed '/^#/d' ~{current_run_output} | awk '{print NF}' | sort -nu | tail -n 1)
+			validated_output_column_count=$(sed '/^#/d' ~{validated_output} | awk '{print NF}' | sort -nu | tail -n 1)
 		fi
 
 		if [[ "$current_run_output_column_count" != "$validated_output_column_count" ]]; then

src/wdlci/wdl_tests/xml_validator.wdl

@@ -0,0 +1,47 @@
+version 1.0
+
+# Parse and validate XML file
+# Input type: XML files
+
+task xml_validator {
+	input {
+		File current_run_output
+		File validated_output
+	}
+
+	Int disk_size = ceil(size(current_run_output, "GB") + size(validated_output, "GB") + 50)
+
+	command <<<
+		set -euo pipefail
+
+		err() {
+			message=$1
+
+			echo -e "[ERROR] $message" >&2
+		}
+
+		if ! xmllint --noout ~{validated_output}; then
+			err "Validated XML file: [~{basename(validated_output)}] is invalid"
+			exit 1
+		else
+			if ! xmllint --noout ~{current_run_output}; then
+				err "Current run XML file: [~{basename(current_run_output)}] is invalid"
+				exit 1
+			else
+				echo "Current run XML file: [~{basename(current_run_output)}] is valid"
+			fi
+		fi
+	>>>
+
+	output {
+	}
+
+	runtime {
+		docker: "dnastack/dnastack-wdl-ci-tools:0.0.1"
+		cpu: 1
+		memory: "3.75 GB"
+		disk: disk_size + " GB"
+		disks: "local-disk " + disk_size + " HDD"
+		preemptible: 1
+	}
+}