From 1b228835e9525990db99243cb4f0d07aa6e01bc3 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 10 May 2022 12:29:42 +0200
Subject: [PATCH] refactor: require settings input always

---
 modules/sratools/prefetch/meta.yml            |  5 ++--
 .../prefetch/templates/retry_with_backoff.sh  |  4 +---
 tests/modules/sratools/prefetch/main.nf       | 23 ++-----------------
 .../modules/sratools/prefetch/nextflow.config |  3 ---
 .../sratools/prefetch/nextflow_mount.config   | 17 --------------
 tests/modules/sratools/prefetch/test.yml      | 16 ++-----------
 6 files changed, 7 insertions(+), 61 deletions(-)
 delete mode 100644 tests/modules/sratools/prefetch/nextflow_mount.config

diff --git a/modules/sratools/prefetch/meta.yml b/modules/sratools/prefetch/meta.yml
index f8c50a0d..a3a26522 100644
--- a/modules/sratools/prefetch/meta.yml
+++ b/modules/sratools/prefetch/meta.yml
@@ -25,9 +25,8 @@ input:
   - ncbi_settings:
       type: file
       description: >
-        Either a proper NCBI settings file or in case an existing file should be used,
-        a file with name EXISTS.
-      pattern: "*.mkfg | EXISTS"
+        An NCBI user settings file.
+      pattern: "*.mkfg"
 
 output:
   - meta:
diff --git a/modules/sratools/prefetch/templates/retry_with_backoff.sh b/modules/sratools/prefetch/templates/retry_with_backoff.sh
index 17395ef1..cec0ab43 100755
--- a/modules/sratools/prefetch/templates/retry_with_backoff.sh
+++ b/modules/sratools/prefetch/templates/retry_with_backoff.sh
@@ -40,9 +40,7 @@ retry_with_backoff() {
     echo "${output}"
 }
 
-if [[ "!{ncbi_settings.name}" != "EXISTS" ]]; then
-    export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
-fi
+export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
 
 retry_with_backoff !{args2} \
     prefetch \
diff --git a/tests/modules/sratools/prefetch/main.nf b/tests/modules/sratools/prefetch/main.nf
index eb579920..cf9794ab 100644
--- a/tests/modules/sratools/prefetch/main.nf
+++ b/tests/modules/sratools/prefetch/main.nf
@@ -4,31 +4,12 @@ nextflow.enable.dsl = 2
 
 include { SRATOOLS_PREFETCH } from '../../../../modules/sratools/prefetch/main.nf'
 
-workflow test_sratools_prefetch_with_settings_input {
-
-    file(params.settings_path).mkdirs()
-    def settings = file(params.settings_file)
-    settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
+workflow test_sratools_prefetch {
 
     input = [
         [ id:'test', single_end:false ], // meta map
         'DRR000774'
     ]
 
-    SRATOOLS_PREFETCH(input, settings)
+    SRATOOLS_PREFETCH(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
 }
-
-workflow test_sratools_prefetch_without_settings_input {
-
-    file(params.settings_path).mkdirs()
-    def settings = file(params.settings_file)
-    settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        'DRR000774'
-    ]
-
-    SRATOOLS_PREFETCH(input, file('EXISTS'))
-}
-
diff --git a/tests/modules/sratools/prefetch/nextflow.config b/tests/modules/sratools/prefetch/nextflow.config
index a6c70bd3..8730f1c4 100644
--- a/tests/modules/sratools/prefetch/nextflow.config
+++ b/tests/modules/sratools/prefetch/nextflow.config
@@ -1,6 +1,3 @@
-params.settings_path = '/tmp/.ncbi'
-params.settings_file = "${params.settings_path}/user-settings.mkfg"
-
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
diff --git a/tests/modules/sratools/prefetch/nextflow_mount.config b/tests/modules/sratools/prefetch/nextflow_mount.config
deleted file mode 100644
index 1a0eed2a..00000000
--- a/tests/modules/sratools/prefetch/nextflow_mount.config
+++ /dev/null
@@ -1,17 +0,0 @@
-params.settings_path = '/tmp/.ncbi'
-params.settings_file = "${params.settings_path}/user-settings.mkfg"
-
-env.NCBI_SETTINGS = params.settings_file
-
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: SRATOOLS_PREFETCH {
-        containerOptions = {
-            (workflow.containerEngine == 'singularity') ?
-            "-B ${params.settings_path}:${params.settings_path}" :
-            "-v ${params.settings_path}:${params.settings_path}"
-        }
-    }
-}
diff --git a/tests/modules/sratools/prefetch/test.yml b/tests/modules/sratools/prefetch/test.yml
index d747b9a6..a6c213f8 100644
--- a/tests/modules/sratools/prefetch/test.yml
+++ b/tests/modules/sratools/prefetch/test.yml
@@ -1,17 +1,5 @@
-- name: sratools prefetch test_sratools_prefetch_with_settings_input
-  command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch_with_settings_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
-  tags:
-    - sratools/prefetch
-    - sratools
-  files:
-    - path: output/sratools/DRR000774/DRR000774.sra
-      md5sum: 7647dba20c89c0e3d7ad13842f060eb0
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"
-
-- name: sratools prefetch test_sratools_prefetch_without_settings_input
-  command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch_without_settings_input -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow_mount.config
+- name: sratools prefetch test_sratools_prefetch
+  command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
   tags:
     - sratools/prefetch
     - sratools