From 92e891450ca233421455c4d9f16bea75806ffd7d Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Tue, 4 Jul 2023 12:12:16 +0100
Subject: [PATCH] refactor render environment variables -> read
---
src/slurm/job.rs | 21 +++++----------------
1 file changed, 5 insertions(+), 16 deletions(-)
diff --git a/src/slurm/job.rs b/src/slurm/job.rs
index 11ef868..7dfd760 100644
--- a/src/slurm/job.rs
+++ b/src/slurm/job.rs
@@ -35,7 +35,7 @@ impl JobRequest {
let header: Header = render_header(&&self.pipeline_param);
let callback: Callback = render_callback(&&self.pipeline_param);
- let vars: EnvVars = render_environment_variables(&&self);
+ let vars: EnvVars = read_environment_variables();
let workflow: Workflow = render_nxf(&globus_path, &&self.pipeline_param, &wd.path);
let job = JobTemplate { header, callback, vars, workflow };
@@ -202,22 +202,11 @@ fn render_header(param: &PipelineParam) -> Header {
Header { content: tt.render("header", &context).expect("Rendered document") }
}
-/// Render environment variables using TinyTemplate
-fn render_environment_variables(request: &JobRequest) -> EnvVars {
- /// included environment variables template
+/// Read environment variables from template
+fn read_environment_variables() -> EnvVars {
+ /// included environment variables template, everything is static
static ENV_VARS: &str = include_str!(concat!(env!("CARGO_MANIFEST_DIR"), "/data/templates/env_vars.txt"));
- let mut tt = TinyTemplate::new();
- // html escape breaks JSON
- tt.set_default_formatter(&tinytemplate::format_unescaped);
- tt.add_template("env_var", ENV_VARS).expect("Template");
-
- // todo: set globus base url dynamically
- let globus_base_url: String = "https://g-1504d5.dd271.03c0.data.globus.org".to_string();
- let guest_collection_id = request.globus_details.guest_collection_id.clone();
- let message: String = serde_json::to_string(&request).expect("Deserialised");
- let context = EnvVarContext { globus_base_url, guest_collection_id, message };
-
- EnvVars { content: tt.render("env_var", &context).expect("Rendered document") }
+ EnvVars { content: ENV_VARS.to_string() }
}
/// Render the workflow commands using TinyTemplate
--
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