Getting Rqtl to run on fallback

8 files changed, 34 insertions, 13 deletions

diff --git a/gn3/api/general.py b/gn3/api/general.py
index 69ec343..891f992 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -64,7 +64,7 @@ def run_r_qtl(geno_filestr, pheno_filestr):
     """Run r_qtl command using the written rqtl_wrapper program
 
     """
-    rqtl_wrapper = current_app.config["RQTL_WRAPPER"]
+    rqtl_wrapper = 'scripts/rqtl_wrapper.R'
     cmd = (f"Rscript {rqtl_wrapper} "
            f"{geno_filestr} {pheno_filestr}")
     return jsonify(run_cmd(cmd)), 201
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 3893275..36bc3da 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -6,6 +6,7 @@ from flask import current_app
 from flask import jsonify
 from flask import request
 
+from gn3.debug import __pk__
 from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \
                                   process_rqtl_pairscan, process_perm_output
 from gn3.fs_helpers import assert_paths_exist
@@ -38,7 +39,7 @@ run the rqtl_wrapper script and return the results as JSON
                 rqtl_bool_kwargs.append(kwarg)
 
     rqtl_cmd = generate_rqtl_cmd(
-        rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
+        rqtl_wrapper_cmd='scripts/rqtl_wrapper.R',
         rqtl_wrapper_kwargs=rqtl_kwargs,
         rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs
     )
@@ -46,7 +47,7 @@ run the rqtl_wrapper script and return the results as JSON
     rqtl_output = {}
     if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"),
                                        "output", rqtl_cmd.get('output_file'))):
-        os.system(rqtl_cmd.get('rqtl_cmd'))
+        os.system(__pk__(rqtl_cmd.get('rqtl_cmd')))
 
     if "pairscan" in rqtl_bool_kwargs:
         rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'), genofile)
diff --git a/gn3/commands.py b/gn3/commands.py
index 79e1e7e..7a9ba67 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -154,12 +154,14 @@ def run_cmd(cmd: str, success_codes: Tuple = (0,), env: Optional[str] = None) ->
     """Run CMD and return the CMD's status code and output as a dict"""
     parsed_cmd = json.loads(cmd)
     parsed_env = (json.loads(env) if env is not None else None)
+
     results = subprocess.run(
         parsed_cmd, capture_output=True, shell=isinstance(parsed_cmd, str),
         check=False, env=parsed_env)
     out = str(results.stdout, 'utf-8')
     if results.returncode not in success_codes:  # Error!
         out = str(results.stderr, 'utf-8')
+        current_app.logger.debug(out)
     return {"code": results.returncode, "output": out}
 
 def run_async_cmd(
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index f082482..8b1b316 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,5 +1,7 @@
 """Procedures related to R/qtl computations"""
 import os
+import sys
+import logging
 from bisect import bisect
 from typing import Dict, List, Tuple, Union
 
@@ -9,8 +11,9 @@ from flask import current_app
 
 from gn3.commands import compose_rqtl_cmd
 from gn3.computations.gemma import generate_hash_of_string
-from gn3.fs_helpers import get_hash_of_files
+from gn3.fs_helpers import get_hash_of_files, assert_path_exists
 
+from gn3.debug import __pk__
 
 def generate_rqtl_cmd(
     rqtl_wrapper_cmd: str,
@@ -21,6 +24,8 @@ def generate_rqtl_cmd(
     dict of keyword arguments, return the full rqtl_wrapper command and an
     output filename generated from a hash of the genotype and phenotype files"""
 
+    assert_path_exists(rqtl_wrapper_cmd)
+
     # Generate a hash from contents of the genotype and phenotype files
     _hash = get_hash_of_files(
         [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]]
@@ -60,6 +65,7 @@ def process_rqtl_mapping(file_name: str) -> List:
     """Given an output file name, read in R/qtl results and return
     a List of marker objects"""
     marker_obs = []
+
     # Later I should probably redo this using csv.read to avoid the
     # awkwardness with removing quotes with [1:-1]
     with open(
diff --git a/gn3/debug.py b/gn3/debug.py
index ccfcba1..acc2402 100644
--- a/gn3/debug.py
+++ b/gn3/debug.py
@@ -1,9 +1,12 @@
 """Debug utilities"""
 import logging
+from flask import current_app
+
 logger = logging.getLogger(__name__)
 
 def __pk__(*args):
     value = args[-1]
     title_vals = " => ".join(args[0:-1])
-    logger.debug("%s: %s", title_vals, value)
+    current_app.logger.setLevel(logging.DEBUG) # Force debug level since we assume we are using it!
+    current_app.logger.debug("%s: %s", title_vals, value)
     return value
diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py
index 74e7ada..845c48b 100644
--- a/gn3/fs_helpers.py
+++ b/gn3/fs_helpers.py
@@ -13,14 +13,19 @@ from typing import List
 from typing import ValuesView
 from werkzeug.utils import secure_filename
 
+def assert_path_exists(path: str, throw_error: bool = True) -> bool:
+    """Throw error if any of them do not exist."""
+    if not os.path.isfile(path):
+        if throw_error:
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
+        else:
+            return False
+    return True
+
 def assert_paths_exist(paths: ValuesView, throw_error: bool = True) -> bool:
     """Given a list of PATHS, throw error if any of them do not exist."""
     for path in paths:
-        if not os.path.isfile(path):
-            if throw_error:
-                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
-            else:
-                return False
+        assert_path_exists(path,throw_error)
     return True
 
 def get_hash_of_files(files: List[str]) -> str:
diff --git a/gn3/settings.py b/gn3/settings.py
index 1e794ff..04aa129 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -11,12 +11,10 @@ import tempfile
 BCRYPT_SALT = "$2b$12$mxLvu9XRLlIaaSeDxt8Sle"  # Change this!
 DATA_DIR = ""
 GEMMA_WRAPPER_CMD = os.environ.get("GEMMA_WRAPPER", "gemma-wrapper")
-RQTL_WRAPPER_CMD = os.environ.get("RQTL_WRAPPER")
 CACHEDIR = ""
 REDIS_URI = "redis://localhost:6379/0"
 REDIS_JOB_QUEUE = "GN3::job-queue"
 TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir())
-RQTL_WRAPPER = "rqtl_wrapper.R"
 
 # SPARQL endpoint
 SPARQL_ENDPOINT = os.environ.get(
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index 2ac8faa..0d1f2ff 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -3,6 +3,12 @@ library(qtl)
 library(stringi)
 library(stringr)
 
+
+tmp_dir = Sys.getenv("TMPDIR")
+if (!dir.exists(tmp_dir)) {
+  tmp_dir = "/tmp"
+}
+
 option_list = list(
   make_option(c("-g", "--geno"), type="character", help=".geno file containing a dataset's genotypes"),
   make_option(c("-p", "--pheno"), type="character", help="File containing two columns - sample names and values"),
@@ -56,7 +62,7 @@ geno_file = opt$geno
 pheno_file = opt$pheno
 
 # Generate randomized filename for cross object
-cross_file = file.path(opt$outdir, "cross", paste(stri_rand_strings(1, 8), ".cross", sep = ""))
+cross_file = file.path(tmp_dir, "output", paste(stri_rand_strings(1, 8), ".cross", sep = ""))
 
 trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }