Make sure TMPDIR directories exist!

4 files changed, 35 insertions, 25 deletions

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 36bc3da..bd50900 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -9,7 +9,7 @@ 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
+from gn3.fs_helpers import assert_paths_exist, get_tmpdir
 
 rqtl = Blueprint("rqtl", __name__)
 
diff --git a/gn3/app.py b/gn3/app.py
index c8f0c5a..955a9b3 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -28,6 +28,7 @@ from gn3.api.sampledata import sampledata
 from gn3.api.llm import gnqa
 from gn3.auth import oauth2
 from gn3.case_attributes import caseattr
+from gn3.fs_helpers import get_tmpdir
 
 
 def create_app(config: Union[Dict, str, None] = None) -> Flask:
@@ -57,6 +58,9 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     logging.info("Guix Profile: '%s'.", os.environ.get("GUIX_PROFILE"))
     logging.info("Python Executable: '%s'.", sys.executable)
 
+    if "TMPDIR" in os.environ:
+        app.config.from_envvar('TMPDIR')
+
     CORS(
         app,
         origins=app.config["CORS_ORIGINS"],
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 8b1b316..b53efbd 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -11,7 +11,7 @@ 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, assert_path_exists
+from gn3.fs_helpers import get_hash_of_files, assert_path_exists, get_tmpdir
 
 from gn3.debug import __pk__
 
@@ -68,13 +68,11 @@ def process_rqtl_mapping(file_name: str) -> List:
 
     # Later I should probably redo this using csv.read to avoid the
     # awkwardness with removing quotes with [1:-1]
-    with open(
-        os.path.join(
-            current_app.config.get("TMPDIR", "/tmp"), "output", file_name
-        ),
-        "r",
-        encoding="utf-8",
-    ) as the_file:
+    outdir = os.path.join(get_tmpdir(),"output")
+    if not os.path.isdir(outdir):
+        os.mkdir(outdir)
+
+    with open( os.path.join(outdir,file_name),"r",encoding="utf-8") as the_file:
         for line in the_file:
             line_items = line.split(",")
             if line_items[1][1:-1] == "chr" or not line_items:
@@ -115,13 +113,11 @@ def pairscan_for_figure(file_name: str) -> Dict:
     figure_data = {}
 
     # Open the file with the actual results, written as a list of lists
-    with open(
-        os.path.join(
-            current_app.config.get("TMPDIR", "/tmp"), "output", file_name
-        ),
-        "r",
-        encoding="utf8",
-    ) as the_file:
+    outdir = os.path.join(get_tmpdir(),"output")
+    if not os.path.isdir(outdir):
+        os.mkdir(outdir)
+
+    with open( os.path.join(outdir,file_name),"r",encoding="utf-8") as the_file:
         lod_results = []
         for i, line in enumerate(the_file):
             if i == 0:  # Skip first line
@@ -322,15 +318,11 @@ def process_perm_output(file_name: str) -> Tuple[List, float, float]:
     suggestive and significant thresholds"""
 
     perm_results = []
-    with open(
-        os.path.join(
-            current_app.config.get("TMPDIR", "/tmp"),
-            "output",
-            "PERM_" + file_name,
-        ),
-        "r",
-        encoding="utf-8",
-    ) as the_file:
+    outdir = os.path.join(get_tmpdir(),"output")
+    if not os.path.isdir(outdir):
+        os.mkdir(outdir)
+
+    with open( os.path.join(outdir,file_name),"r",encoding="utf-8") as the_file:
         for i, line in enumerate(the_file):
             if i == 0:
                 # Skip header line
diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py
index 845c48b..1b226bc 100644
--- a/gn3/fs_helpers.py
+++ b/gn3/fs_helpers.py
@@ -13,6 +13,20 @@ from typing import List
 from typing import ValuesView
 from werkzeug.utils import secure_filename
 
+from flask import current_app
+
+def get_tmpdir() -> str:
+    """Get the temp directory from the FLASK tmpdir setting. If it is not set, set it to /tmp. Note
+    that the app should check for environment settings to initialize its TMPDIR.
+    """
+    tmpdir = current_app.config.get("TMPDIR")
+    if not tmpdir:
+        tmpdir = "/tmp"
+    if not os.path.isdir(tmpdir):
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), f"TMPDIR {tmpdir} is not a valid directory")
+
+    return tmpdir
+
 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):