From 0c30617c24ace0bde14a32a2218aa93acbabeac7 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@stfc.ac.uk>
Date: Tue, 7 Nov 2017 15:14:38 +0000
Subject: [PATCH] Issue #75

Further problems with absolute paths where a keyerror would occur on the
executable. A fix has been applied where the os.path.basename is run
against the executable. This should at least allow longbow to match the
executables that it knows.
---
 longbow/corelibs/applications.py              | 22 +++++++------
 .../corelibs_applications/test_processjobs.py | 33 ++++++++++++++++++-
 2 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/longbow/corelibs/applications.py b/longbow/corelibs/applications.py
index 8e5fff1..2e2c666 100755
--- a/longbow/corelibs/applications.py
+++ b/longbow/corelibs/applications.py
@@ -147,7 +147,7 @@ def processjobs(jobs):
 
         filelist = []
         appplugins = getattr(apps, "PLUGINEXECS")
-        app = appplugins[jobs[job]["executable"]]
+        app = appplugins[os.path.basename(jobs[job]["executable"])]
         foundflags = []
         substitution = {}
 
@@ -180,7 +180,7 @@ def processjobs(jobs):
                 "The local job directory '{0}' cannot be found for job '{1}'"
                 .format(jobs[job]["localworkdir"], job))
 
-        # Detect command-line parameter substitutions.
+        # Hook to determine command-line parameter substitutions.
         try:
 
             substitution = getattr(
@@ -222,8 +222,9 @@ def _flagvalidator(job, foundflags):
     """Validate that required command-line flags are provided."""
     # Initialisation.
     appplugins = getattr(apps, "PLUGINEXECS")
-    app = appplugins[job["executable"]]
-    execdata = getattr(apps, app.lower()).EXECDATA[job["executable"]]
+    executable = os.path.basename(job["executable"])
+    app = appplugins[executable]
+    execdata = getattr(apps, app.lower()).EXECDATA[executable]
 
     # Final check for if any required flags are missing.
     flags = list(set(execdata["requiredfiles"]) - set(foundflags))
@@ -288,17 +289,17 @@ def _proccommandline(job, filelist, foundflags, substitution):
     """
     # Initialisation.
     appplugins = getattr(apps, "PLUGINEXECS")
-    app = appplugins[job["executable"]]
+    executable = os.path.basename(job["executable"])
+    app = appplugins[executable]
     args = list(job["executableargs"])
-    subexecs = getattr(
-        apps, app.lower()).EXECDATA[job["executable"]]["subexecutables"]
+    subexe = getattr(apps, app.lower()).EXECDATA[executable]["subexecutables"]
 
     try:
 
         for arg in args:
 
             if (arg != "<" and arg != ">" and arg[0] != "-" and
-                    arg not in subexecs):
+                    arg not in subexe):
 
                 foundflags = _procfiles(job, arg, filelist, foundflags,
                                         substitution)
@@ -318,7 +319,8 @@ def _procfiles(job, arg, filelist, foundflags, substitution):
     """Processor for finding flags and files."""
     # Initialisation.
     appplugins = getattr(apps, "PLUGINEXECS")
-    app = appplugins[job["executable"]]
+    executable = os.path.basename(job["executable"])
+    app = appplugins[executable]
     initargs = list(job["executableargs"])
 
     # Check for as many files as there are replicates (default of 1).
@@ -349,7 +351,7 @@ def _procfiles(job, arg, filelist, foundflags, substitution):
 
             _markfoundfiles(arg, initargs, foundflags)
 
-            # Search input file for any file dependencies.
+            # Hook to search input file for any file dependencies.
             try:
 
                 getattr(apps, app.lower()).file_parser(
diff --git a/tests/unit/corelibs_applications/test_processjobs.py b/tests/unit/corelibs_applications/test_processjobs.py
index 9a8508d..fe1c17e 100644
--- a/tests/unit/corelibs_applications/test_processjobs.py
+++ b/tests/unit/corelibs_applications/test_processjobs.py
@@ -98,7 +98,38 @@ def test_processjobs_pardir():
 
 @mock.patch('longbow.corelibs.applications._proccommandline')
 @mock.patch('longbow.corelibs.applications._flagvalidator')
-def test_processjobs_singlejob(m_validator, m_proccommandline):
+def test_processjobs_singlejob1(m_validator, m_proccommandline):
+
+    """Test for single job, make sure parameters are all set correctly."""
+
+    jobs = {
+        "jobone": {
+            "executableargs": ["-i", "input", "-c", "coords", "-p", "topol"],
+            "localworkdir": os.path.join(os.getcwd(),
+                                         "tests/standards/jobs/single"),
+            "executable": "/some/path/pmemd.MPI",
+            "upload-include": "",
+            "upload-exclude": ""
+        }
+    }
+
+    m_proccommandline.side_effect = _proccommandline
+
+    m_validator.return_value = None
+
+    processjobs(jobs)
+
+    assert jobs["jobone"]["upload-exclude"] == "*"
+    assert jobs["jobone"]["localworkdir"] == os.path.join(
+        os.getcwd(), "tests/standards/jobs/single")
+    assert jobs["jobone"]["executableargs"] == \
+        "/some/path/pmemd.MPI -i input -c coords -p topol"
+    assert jobs["jobone"]["upload-include"] == "input, coords, topol"
+
+
+@mock.patch('longbow.corelibs.applications._proccommandline')
+@mock.patch('longbow.corelibs.applications._flagvalidator')
+def test_processjobs_singlejob2(m_validator, m_proccommandline):
 
     """Test for single job, make sure parameters are all set correctly."""