Update test-repo to use grapevne-helper

electron-app/postbuild_tests/modules.test.ts

@@ -595,13 +595,40 @@ describe('modules', () => {
 
   // Conda tests
   runif(is_installed(['mamba', 'conda'], 'any')).each([
-    ['conda', [path.join('results', 'conda', 'data.csv')]],
+    // Test: 1 (connect two modules)
+    [
+      [
+        // Modules to add to scene
+        'payload shell', // data-nodeid="n0"
+        'conda', // data-nodeid="n1"
+      ],
+      [
+        // Connections to make between modules
+        ['n0-out-source', 'n1-in-target'], // (nodeid)-(portname)-(porttype)
+      ],
+      [
+        // Expected output files
+        path.join('results', 'conda', 'data.csv'),
+      ],
+    ],
   ])(
     "Build and Test the conda workflow: module '%s'",
-    async (modulename, outfiles) => {
-      await BuildAndRun_SingleModuleWorkflow(driver, modulename, outfiles);
+    async (modulenames, connections, outfiles) => {
+      // Open settings pane
+      await driver.findElement(By.xpath('//div[@id="btnSidenavSettings"]')).click();
+
+      // Set snakemake command line arguments
+      const args = await driver.findElement(webdriver.By.id('inputBuilderSettingsSnakemakeArgs'));
+      await OverwriteInputField(args, '--cores 1 --use-conda');
+
+      // Close settings pane
+      await driver.findElement(By.xpath('//div[@id="btnSidenavBuilder"]')).click();
+      console.log('<<< test Set snakemake arguments list to use conda');
+
+      // Build and run workflow
+      await BuildAndRun_MultiModuleWorkflow(driver, modulenames, connections, outfiles);
     },
-    10 * ONE_MINUTE,
+    5 * ONE_MINUTE,
   ); // long timeout
 
   test(

electron-app/postbuild_tests/test-repo/workflows/MyNewProject/modules/MyNewModule2/config/config.yaml

@@ -0,0 +1,12 @@
+"input_namespace":
+  "payload_run$": "in"
+"output_namespace": "payload_run"
+"payload_run":
+  "name": "payload_run"
+  "type": "module"
+  "snakefile": "/Users/jsb/repos/jsbrittain/GRAPEVNE/electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/payload_run/workflow/Snakefile"
+  "config":
+    "input_namespace": "in"
+    "output_namespace": "payload_run"
+    "params":
+      "filename": "data.csv"

electron-app/postbuild_tests/test-repo/workflows/MyNewProject/modules/MyNewModule2/workflow/Snakefile

@@ -0,0 +1,8 @@
+configfile: "config/config.yaml"
+
+module payload_run:
+    snakefile:
+        config["payload_run"]["snakefile"]
+    config:
+        config["payload_run"]["config"]
+use rule * from payload_run exclude _test as payload_run_*

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run/.test.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+rm -rf results/out
+snakemake --cores 1 --use-conda --configfile=config/.test.yaml _test

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run/config/.test.yaml

@@ -0,0 +1,4 @@
+input_namespace: in
+output_namespace: out
+params:
+  filename: data.csv

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run/workflow/Snakefile

@@ -1,20 +1,22 @@
 configfile: "config/config.yaml"
+from grapevne_helper import *
 import shutil
 
-params = config["params"]
+init(workflow)
 
 rule copy:
     input:
-        expand(
-            "results/{indir}/{filename}",
-            indir=config["input_namespace"],
-            filename=params["filename"],
-        )
+        input(params("filename")),
     output:
-        expand(
-            "results/{outdir}/{filename}",
-            outdir=config["output_namespace"],
-            filename=params["filename"],
-        )
+        output(params("filename")),
     run:
         shutil.copy(input[0], output[0])
+
+rule _test:
+    input:
+        src=rules.copy.input[0],
+        dst=rules.copy.output[0],
+    run:
+        # Verify that the file has been copied correctly
+        with open(input.src) as src, open(input.dst) as dst:
+            assert src.read() == dst.read()

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run/workflow/grapevne_helper.py

@@ -0,0 +1,24 @@
+import sys
+import logging
+
+try:
+    from grapevne.helpers import *  # noqa: F403
+except ImportError:
+    import ensurepip
+    import subprocess
+
+    ensurepip.bootstrap()
+    subprocess.check_call(
+        [sys.executable, "-m", "pip", "install", "--upgrade", "grapevne"]
+    )
+    try:
+        from grapevne.helpers import *  # noqa: F403 F401
+    except ImportError:
+        logging.error("Failed to install grapevne. Exiting.")
+        sys.exit(1)
+
+# Tidy-up namespace
+del sys, logging
+
+# Dynamically export all names imported from grapevne
+__all__ = [name for name in dir() if not name.startswith("_")]

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run_multiport/.test.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+rm -rf results/out
+snakemake --cores 1 --use-conda --configfile=config/.test.yaml _test

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run_multiport/config/.test.yaml

@@ -0,0 +1,7 @@
+input_namespace:
+  in1: in1
+  in2: in2
+  in3: in3
+output_namespace: out
+params:
+  filename: data.csv

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run_multiport/workflow/Snakefile

@@ -3,22 +3,24 @@ Input namespaces: [in1, in2, in3]
 Copy file from first input namespace (in1) only
 """
 configfile: "config/config.yaml"
+from grapevne_helper import *
 import shutil
 
-params = config["params"]
+init(workflow)
 
 rule copy:
     input:
-        expand(
-            "results/{indir}/{filename}",
-            indir=config["input_namespace"]["in1"],
-            filename=params["filename"],
-        )
+        input(params("filename"), "in1"),
     output:
-        expand(
-            "results/{outdir}/{filename}",
-            outdir=config["output_namespace"],
-            filename=params["filename"],
-        )
+        output(params("filename")),
     run:
         shutil.copy(input[0], output[0])
+
+rule _test:
+    input:
+        src=rules.copy.input[0],
+        dst=rules.copy.output[0],
+    run:
+        # Verify that the file has been copied correctly
+        with open(input.src) as src, open(input.dst) as dst:
+            assert src.read() == dst.read()

electron-app/postbuild_tests/test-repo/workflows/single_modules/modules/copy_run_multiport/workflow/grapevne_helper.py

@@ -0,0 +1,24 @@
+import sys
+import logging
+
+try:
+    from grapevne.helpers import *  # noqa: F403
+except ImportError:
+    import ensurepip
+    import subprocess
+
+    ensurepip.bootstrap()
+    subprocess.check_call(
+        [sys.executable, "-m", "pip", "install", "--upgrade", "grapevne"]
+    )
+    try:
+        from grapevne.helpers import *  # noqa: F403 F401
+    except ImportError:
+        logging.error("Failed to install grapevne. Exiting.")
+        sys.exit(1)
+
+# Tidy-up namespace
+del sys, logging
+
+# Dynamically export all names imported from grapevne
+__all__ = [name for name in dir() if not name.startswith("_")]

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/conda/.test.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+rm -rf results/out
+snakemake --cores 1 --use-conda --configfile=config/.test.yaml _test

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/conda/config/.test.yaml

@@ -0,0 +1,4 @@
+input_namespace: in
+output_namespace: out
+params:
+  filename: data.csv

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/conda/workflow/Snakefile

@@ -1,23 +1,25 @@
 configfile: "config/config.yaml"
+from grapevne_helper import *
 
-params = config["params"]
+init(workflow)
 
 rule copy:
     input:
-        expand(
-            srcdir("../results/{indir}/{filename}"),
-            indir=config["input_namespace"],
-            filename=params["filename"],
-        )
+        input(params("filename")),
     output:
-        expand(
-            "results/{outdir}/{filename}",
-            outdir=config["output_namespace"],
-            filename=params["filename"],
-        )
+        output(params("filename")),
     conda:
         "envs/conda.yaml"
     shell:
         """
         cp {input} {output}
         """
+
+rule _test:
+    input:
+        src=rules.copy.input[0],
+        dst=rules.copy.output[0],
+    run:
+        # Verify that the file has been copied correctly
+        with open(input.src) as src, open(input.dst) as dst:
+            assert src.read() == dst.read()

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/conda/workflow/grapevne_helper.py

@@ -0,0 +1,24 @@
+import sys
+import logging
+
+try:
+    from grapevne.helpers import *  # noqa: F403
+except ImportError:
+    import ensurepip
+    import subprocess
+
+    ensurepip.bootstrap()
+    subprocess.check_call(
+        [sys.executable, "-m", "pip", "install", "--upgrade", "grapevne"]
+    )
+    try:
+        from grapevne.helpers import *  # noqa: F403 F401
+    except ImportError:
+        logging.error("Failed to install grapevne. Exiting.")
+        sys.exit(1)
+
+# Tidy-up namespace
+del sys, logging
+
+# Dynamically export all names imported from grapevne
+__all__ = [name for name in dir() if not name.startswith("_")]

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/container_touch/.test.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+rm -rf results
+snakemake --cores 1 --use-conda --configfile=config/.test.yaml

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/container_touch/config/.test.yaml

@@ -0,0 +1,17 @@
+input_namespace: null
+output_namespace: utility_touch
+utility_touch:
+  config:
+    input_namespace: null
+    output_namespace: utility_touch
+    params:
+      filename: data.csv
+  name: (Utility) touch
+  snakefile:
+    args:
+      - jsbrittain/snakeshack
+    function: github
+    kwargs:
+      branch: main
+      path: workflows/Utility/modules/touch/workflow/Snakefile
+  type: module

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/container_touch/workflow/Snakefile

@@ -6,7 +6,6 @@ module utility_touch:
             *config["utility_touch"]["snakefile"]["args"],
             **config["utility_touch"]["snakefile"]["kwargs"],
         )
-        )
     config:
         config["utility_touch"]["config"]
 use rule * from utility_touch as utility_touch_*

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/payload_run/.test.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+rm -rf results/out
+snakemake --cores 1 --use-conda --configfile=config/.test.yaml _test

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/payload_run/config/.test.yaml

@@ -0,0 +1,4 @@
+input_namespace: in
+output_namespace: out
+params:
+  filename: data.csv

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/payload_run/workflow/Snakefile

@@ -1,20 +1,26 @@
 configfile: "config/config.yaml"
 
+from grapevne_helper import *
 import os
 import pathlib
 import shutil
 
-params = config["params"]
+init(workflow)
 
 rule copy:
     input:
-        srcdir("../resources/file"),
+        resource("file"),
     output:
-        expand(
-            "results/{outdir}/{filename}",
-            outdir=config["output_namespace"],
-            filename=params["filename"],
-        )
+        output(params("filename")),
     run:
         pathlib.Path(os.path.dirname(output[0])).mkdir(parents=True, exist_ok=True)
         shutil.copy(input[0], output[0])
+
+rule _test:
+    input:
+        src=resource("file"),
+        dst=output(params("filename")),
+    run:
+        # Verify that the file has been copied correctly
+        with open(input.src) as src, open(input.dst) as dst:
+            assert src.read() == dst.read()

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/payload_run/workflow/grapevne_helper.py

@@ -0,0 +1,24 @@
+import sys
+import logging
+
+try:
+    from grapevne.helpers import *  # noqa: F403
+except ImportError:
+    import ensurepip
+    import subprocess
+
+    ensurepip.bootstrap()
+    subprocess.check_call(
+        [sys.executable, "-m", "pip", "install", "--upgrade", "grapevne"]
+    )
+    try:
+        from grapevne.helpers import *  # noqa: F403 F401
+    except ImportError:
+        logging.error("Failed to install grapevne. Exiting.")
+        sys.exit(1)
+
+# Tidy-up namespace
+del sys, logging
+
+# Dynamically export all names imported from grapevne
+__all__ = [name for name in dir() if not name.startswith("_")]

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/payload_shell/.test.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+rm -rf results/out
+snakemake --cores 1 --use-conda --configfile=config/.test.yaml _test

electron-app/postbuild_tests/test-repo/workflows/single_modules/sources/payload_shell/config/.test.yaml

@@ -0,0 +1,4 @@
+input_namespace: in
+output_namespace: out
+params:
+  filename: data.csv