Cleanup test and add mock server

.github/workflows/test.yml

@@ -42,6 +42,7 @@ jobs:
       run: |
         pip install -r requirements.txt
         pip install -r requirements-dev.txt
+        pip install mock-server
         make mock
         docker pull kbase/runtester
         docker tag kbase/runtester test/runtester
@@ -55,6 +56,10 @@ jobs:
         export KB_AUTH_TOKEN=bogus
         export KB_ADMIN_AUTH_TOKEN=bogus
         export KB_BASE_URL=https://ci.kbase.us/services
+        IP=$(ip route get 8.8.8.8 | head -1 |cut -d' ' -f7)
+        echo $IP
+        export TEST_URL="$IP:8888"
+        mock-server --dir=./test/mock-server --address=0.0.0.0 &
         make test
 
     - name: Failure logs

JobRunner/SpecialRunner.py

@@ -3,6 +3,8 @@
 from subprocess import Popen, PIPE
 from time import sleep, time
 from select import select
+import sys
+import logging
 
 
 class SpecialRunner:
@@ -135,14 +137,21 @@ def _batch_submit(self, stype, config, data, job_id, fin_q):
         submit = "%s_submit" % (stype)
         if "submit_script" not in params:
             raise ValueError("Missing submit script")
-        os.chdir(self.shareddir)
-        scr = params["submit_script"]
+        scr = os.path.join(self.shareddir, params["submit_script"])
         if not os.path.exists(scr):
             raise OSError("Submit script not found at %s" % (scr))
-        outfile = "%s.out" % (job_id)
-        errfile = "%s.err" % (job_id)
+        outfile = f"{self.shareddir}{job_id}.out"
+        errfile = f"{self.shareddir}{job_id}.err"
         cmd = [submit, scr, outfile, errfile]
-        proc = Popen(cmd, stdout=PIPE, stderr=PIPE)
+        logging.info(f"Submitting: {cmd}")
+        try:
+            proc = Popen(cmd, cwd=self.shareddir, stdout=PIPE, stderr=PIPE)
+        except Exception as e:
+            for q in fin_q:
+                q.put(["finished_special", job_id, {}])
+            sys.stderr.write(str(e))
+            return None
+
         stdout, stderr = proc.communicate()
         slurm_jobid = stdout.decode("utf-8").rstrip()
         out = Thread(
@@ -191,16 +200,15 @@ def _wdl_run(self, stype, config, data, job_id, queues):
             raise ValueError("Missing workflow script")
         if "inputs" not in params:
             raise ValueError("Missing inputs")
-        os.chdir(self.shareddir)
-        wdl = params["workflow"]
+        wdl = os.path.join(self.shareddir, params["workflow"])
         if not os.path.exists(wdl):
             raise OSError("Workflow script not found at %s" % (wdl))
 
-        inputs = params["inputs"]
+        inputs = os.path.join(self.shareddir, params["inputs"])
         if not os.path.exists(inputs):
             raise OSError("Inputs file not found at %s" % (inputs))
         cmd = ["wdl_run", inputs, wdl]
-        proc = Popen(cmd, bufsize=0, stdout=PIPE, stderr=PIPE)
+        proc = Popen(cmd, cwd=self.shareddir, bufsize=0, stdout=PIPE, stderr=PIPE)
         out = Thread(target=self._readio, args=[proc, job_id, queues])
         self.threads.append(out)
         out.start()

Makefile

@@ -13,6 +13,6 @@ mock:
 	docker build -t mock_app ./test/mock_app
 
 test:
-	nosetests -A "not online" -s -v --with-coverage --cover-package=JobRunner --cover-erase --cover-html --cover-html-dir=./test_coverage .
+	nosetests -A "not fullonline" -s -v --with-coverage --cover-package=JobRunner --cover-erase --cover-html --cover-html-dir=./test_coverage .
 
 

test/mock-server/services/auth/api/legacy/KBase/Sessions/Login/POST_200.json

@@ -0,0 +1,3 @@
+{
+    "user_id": "canon"
+}

test/mock-server/services/catalog/POST_200.json

@@ -0,0 +1,28 @@
+{
+  "version": "1.1",
+  "result": [
+    {
+      "registration_id": "1529602194173_fab31f45-9465-4e59-b65d-89040a54396f",
+      "released": 1,
+      "timestamp": 1529602194173,
+      "notes": "",
+      "docker_img_name": "dockerhub-ci.kbase.us/kbase:echo_test.4b5a37e6fed857c199df65191ba3344a467b8aa",
+      "git_commit_hash": "4b5a37e6fed857c199df65191ba3344a467b8aab",
+      "version": "0.0.1",
+      "narrative_methods": [
+        "example_method"
+      ],
+      "released_timestamp": null,
+      "module_name": "echo_test",
+      "dynamic_service": 0,
+      "local_functions": [],
+      "git_commit_message": "Add the message in the return dict",
+      "release_timestamp": 1665086800987,
+      "git_url": "https://github.com/jayrbolton/kb_echo_test",
+      "release_tags": [
+        "release"
+      ]
+    }
+  ],
+  "id": "24087040852079133"
+}

test/mock_data.py

@@ -1,6 +1,9 @@
+import os
+
+
 _IMAGE = "dockerhub-prod.kbase.us/kbase:rast_sdk."
 _IMAGE += "50b012d9b41b71ba31b30355627cf85f2611bc3e"
-_BASE = u"https://ci.kbase.us/services/"
+
 
 CATALOG_GET_MODULE_VERSION = {
     "registration_id": "1553870236585_bab74ed6-4699-47b5-b865-d7130b90f542",
@@ -45,29 +48,34 @@
     u"service_ver": u"4b5a37e6fed857c199df65191ba3344a467b8aab",
     u"wsid": 42906,
 }
-EE2_LIST_CONFIG = {
-    u"auth-service-url": _BASE + u"auth/api/legacy/KBase/Sessions/Login",
-    u"auth-service-url-allow-insecure": u"false",
-    u"auth-service-url-v2": _BASE + u"auth/api/V2/token",
-    u"awe.client.callback.networks": u"docker0,eth0",
-    u"awe.client.docker.uri": u"unix:///var/run/docker.sock",
-    u"catalog.srv.url": _BASE + u"catalog",
-    u"condor.docker.job.timeout.seconds": u"604800",
-    u"condor.job.shutdown.minutes": u"10080",
-    u"docker.registry.url": u"dockerhub-prod.kbase.us",
-    u"ee.server.version": u"0.2.11",
-    u"handle-url": _BASE + u"handle_service",
-    u"kbase-endpoint": u"https://ci.kbase.us/services",
-    u"ref.data.base": u"/kb/data",
-    u"ref_data_base": u"/kb/data",
-    u"external-url": _BASE + u"ee2",
-    u"shock-url": _BASE + u"shock-api",
-    u"srv.wiz.url": _BASE + u"service_wizard",
-    u"srv-wiz-url": _BASE + u"service_wizard",
-    u"time.before.expiration": u"10",
-    u"workspace-url": _BASE + u"ws",
-    u"scratch": "/tmp",
-}
+
+
+def ee2_list_config(base):
+    refdata = os.environ.get("KB_REF_DATA", "/kb/data")
+    res = {
+        u"auth-service-url": base + u"auth/api/legacy/KBase/Sessions/Login",
+        u"auth-service-url-allow-insecure": u"false",
+        u"auth-service-url-v2": base + u"auth/api/V2/token",
+        u"awe.client.callback.networks": u"docker0,eth0",
+        u"awe.client.docker.uri": u"unix:///var/run/docker.sock",
+        u"catalog.srv.url": base + u"catalog",
+        u"condor.docker.job.timeout.seconds": u"604800",
+        u"condor.job.shutdown.minutes": u"10080",
+        u"docker.registry.url": u"dockerhub-prod.kbase.us",
+        u"ee.server.version": u"0.2.11",
+        u"handle-url": base + u"handle_service",
+        u"kbase-endpoint": u"https://ci.kbase.us/services",
+        u"ref.data.base": refdata,
+        u"ref_data_base": refdata,
+        u"external-url": base + u"ee2",
+        u"shock-url": base + u"shock-api",
+        u"srv.wiz.url": base + u"service_wizard",
+        u"srv-wiz-url": base + u"service_wizard",
+        u"time.before.expiration": u"10",
+        u"workspace-url": base + u"ws",
+        u"scratch": "/tmp",
+    }
+    return res
 
 CATALOG_LIST_VOLUME_MOUNTS = [
     {