Make ncores in workfow rewrite configurable

.env.example

@@ -5,3 +5,5 @@ BARTENDER_PRIVATE_KEY=private_key.pem
 # See docs/auth.md#session how generate a better secret
 SESSION_SECRET=<please replace with a better secret>
 # For social login see docs/auth.md
+# See docs/rewriter.md how to configure the workflow rewriting
+HADDOCK3_NCORES = 6

README.md

@@ -11,6 +11,7 @@ Uses
 - [bartender](https://github.com/i-VRESSE/bartender) for job execution.
 - [workflow-builder](https://github.com/i-VRESSE/workflow-builder) to construct a Haddock3 workflow config file.
 - [haddock3](https://github.com/haddocking/haddock3) to compute
+- [haddock3-analysis-components](https://github.com/i-VRESSE/haddock3-analysis-components) for analysis components.
 
 ```mermaid
 sequenceDiagram
@@ -33,6 +34,7 @@ npm install
 Configuration of the web application is done via `.env` file or environment variables.
 For configuration of authentication & authorization see [docs/auth.md](docs/auth.md).
 For configuration of job submission see [docs/bartender.md#configuration](docs/bartender.md#configuration).
+For configuration of how to rewrite the submitted workflow file see [docs/reewite.md](docs/reewite.md).
 Use [.env.example](./.env.example) as a template:
 
 ```shell

app/models/applicaton.server.ts

@@ -60,7 +60,14 @@ async function rewriteConfig(config_body: string) {
   table.mode = "local";
   table.postprocess = true;
   table.clean = true;
-  delete table.ncores;
+
+  const haddock3_ncores = getNCores();
+  if (haddock3_ncores > 0) {
+    table.ncores = haddock3_ncores;
+  } else {
+    delete table.ncores;
+  }
+  delete table.max_cpus;
   delete table.batch_type;
   delete table.queue;
   delete table.queue_limit;
@@ -76,6 +83,26 @@ async function rewriteConfig(config_body: string) {
   });
 }
 
+/**
+ *
+ * @returns Number of cores to use for haddock3. 0 means use default.
+ */
+function getNCores() {
+  let haddock3_ncores = 0;
+  if (
+    process.env.HADDOCK3_NCORES !== undefined &&
+    process.env.HADDOCK3_NCORES !== ""
+  ) {
+    haddock3_ncores = parseInt(process.env.HADDOCK3_NCORES);
+    if (isNaN(haddock3_ncores)) {
+      throw new Error(
+        `HADDOCK3_NCORES env var is not a number: ${process.env.HADDOCK3_NCORES}`
+      );
+    }
+  }
+  return haddock3_ncores;
+}
+
 export async function rewriteConfigInArchive(upload: Blob) {
   const zip = new JSZip();
   // Tried to give upload blob directly to loadAsync, but failed with

docs/rewrite.md

@@ -0,0 +1,11 @@
+# Workflow rewrite
+
+You can submit a workflow to the webapp that can contain any parameter that haddock3 cli accepts.
+However we do not want a user to tell the webapp for example which run dir, queue to use, which cns executable, etc.
+The webapp should control most of the [global parameters](https://github.com/i-VRESSE/workflow-builder/blob/main/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml) except molecules parameter and preprocess parameter.
+
+Currently the submitted workflow is rewritten at [app/models/applicaton.server.ts](app/models/applicaton.server.ts) to defaults fit for bartender job service.
+
+The following parameters can be rewritten with environment variables:
+
+- Number of CPU cores (ncores) with `HADDOCK3_NCORES` environment variable. If not set uses haddock3 default.