fix: Bugfix tes add files (#1133)

* add missing checkdir

* improve test with input/output

* remove

* format

* format

* format

* debug

* remove expected results

snakemake/executors/ga4gh_tes.py

@@ -315,7 +315,7 @@ def _get_task_inputs(self, job, jobscript, checkdir):
 
         return inputs
 
-    def _append_task_outputs(self, outputs, files):
+    def _append_task_outputs(self, outputs, files, checkdir):
         for file in files:
             obj = self._prepare_file(
                 filename=file,
@@ -329,15 +329,15 @@ def _append_task_outputs(self, outputs, files):
     def _get_task_outputs(self, job, checkdir):
         outputs = []
         # add output files to outputs
-        outputs = self._append_task_outputs(outputs, job.output)
+        outputs = self._append_task_outputs(outputs, job.output, checkdir)
 
         # add log files to outputs
         if job.log:
-            outputs = self._append_task_outputs(outputs, job.log)
+            outputs = self._append_task_outputs(outputs, job.log, checkdir)
 
         # add benchmark files to outputs
         if hasattr(job, "benchmark") and job.benchmark:
-            outputs = self._append_task_outputs(outputs, job.benchmark)
+            outputs = self._append_task_outputs(outputs, job.benchmark, checkdir)
 
         return outputs
 

tests/test_tes.py

@@ -23,11 +23,19 @@ def _validate_task(task):
 
 
 def _post_task(request, context):
+    outdir = dpath("test_tes")
     print("\n>>>> _post_task", file=sys.stderr)
     task = json.loads(request.body)
     print(task, file=sys.stderr)
     if _validate_task(task):
         context.status_code = 200
+        # create output file
+        print("\n     create output files in {}".format(outdir), file=sys.stderr)
+        with open("{}/test_output.txt".format(outdir), "w+") as f:
+            f.write("output")
+        # create log file
+        with open("{}/test_log.txt".format(outdir), "w+") as f:
+            f.write("log")
         return TEST_POST_RESPONSE
     else:
         context.status_code = 400
@@ -46,4 +54,12 @@ def test_tes(requests_mock):
         "GET", "{}/v1/tasks/id_1".format(TES_URL), json=_get_task
     )
     workdir = dpath("test_tes")
-    run(workdir, snakefile="Snakefile", tes=TES_URL, no_tmpdir=True, cleanup=False)
+    print("\n>>>> run workflow in {}".format(workdir), file=sys.stderr)
+    run(
+        workdir,
+        snakefile="Snakefile",
+        tes=TES_URL,
+        no_tmpdir=True,
+        cleanup=False,
+        forceall=True,
+    )

tests/test_tes/Snakefile

@@ -1,5 +1,11 @@
 
 rule all:
+    input:
+        "test_input.txt"
+    output:
+        "test_output.txt"
+    log:
+        "test_log.txt"
     shell:
         """
         echo "task submitted to tes"

tests/test_tes/test_input.txt

@@ -0,0 +1 @@
+test