Added writing output_schema and count_lines.sh when initializing a pi…

…peline interface #418

looper/const.py

@@ -88,6 +88,8 @@
     "DEBUG_JOBS",
     "DEBUG_COMMANDS",
     "DEBUG_EIDO_VALIDATION",
+    "LOOPER_GENERIC_OUTPUT_SCHEMA",
+    "LOOPER_GENERIC_COUNT_LINES",
 ]
 
 FLAGS = ["completed", "running", "failed", "waiting", "partial"]
@@ -206,6 +208,8 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
 SUBMISSION_FAILURE_MESSAGE = "Cluster resource failure"
 LOOPER_DOTFILE_NAME = "." + LOOPER_KEY + ".yaml"
 LOOPER_GENERIC_PIPELINE = "pipeline_interface.yaml"
+LOOPER_GENERIC_OUTPUT_SCHEMA = "output_schema.yaml"
+LOOPER_GENERIC_COUNT_LINES = "count_lines.sh"
 POSITIONAL = [PEP_CONFIG_FILE_KEY, "command"]
 SELECTED_COMPUTE_PKG = "package"
 EXTRA_KEY = "_cli_extra"

looper/utils.py

@@ -335,7 +335,7 @@ def init_generic_pipeline():
     # Destination one level down from CWD in pipeline folder
     dest_file = os.path.join(os.getcwd(), "pipeline", LOOPER_GENERIC_PIPELINE)
 
-    # Determine Generic Pipeline Interface
+    # Create Generic Pipeline Interface
     generic_pipeline_dict = {
         "pipeline_name": "default_pipeline_name",
         "pipeline_type": "sample",
@@ -355,6 +355,39 @@ def init_generic_pipeline():
             f"Pipeline interface file already exists `{dest_file}`. Skipping creation.."
         )
 
+    # Create Generic Output Schema
+    dest_file = os.path.join(os.getcwd(), "pipeline", LOOPER_GENERIC_OUTPUT_SCHEMA)
+    generic_output_schema_dict = {
+        "pipeline_name": "default_pipeline_name",
+        "samples": {
+            "number_of_lines": {
+                "type": "integer",
+                "description": "Number of lines in the input file.",
+            }
+        },
+    }
+    # Write file
+    if not os.path.exists(dest_file):
+        with open(dest_file, "w") as file:
+            yaml.dump(generic_output_schema_dict, file)
+        print(f"Output schema successfully created at: {dest_file}")
+    else:
+        print(f"Output schema file already exists `{dest_file}`. Skipping creation..")
+
+    # Create Generic countlines.sh
+    dest_file = os.path.join(os.getcwd(), "pipeline", LOOPER_GENERIC_COUNT_LINES)
+    shell_code = """#!/bin/bash
+linecount=`wc -l $1 | sed -E 's/^[[:space:]]+//' | cut -f1 -d' '`
+pipestat report -r $2 -i 'number_of_lines' -v $linecount -c $3
+echo "Number of lines: $linecount"
+    """
+    if not os.path.exists(dest_file):
+        with open(dest_file, "w") as file:
+            file.write(shell_code)
+        print(f"count_lines.sh successfully created at: {dest_file}")
+    else:
+        print(f"count_lines.sh file already exists `{dest_file}`. Skipping creation..")
+
     return True