--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/cge/output/trash/test.py	Wed Dec 08 01:46:07 2021 +0000
@@ -0,0 +1,126 @@
+#!/usr/bin/env python3
+import unittest
+from subprocess import PIPE, run
+import os
+import shutil
+import sys
+from collections import namedtuple
+
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+
+from cgecore.cgefinder import CGEFinder
+from cge.resfinder import ResFinder
+from cge.pointfinder import PointFinder
+
+run_test_dir = "running_test"
+working_dir = os.path.dirname(os.path.realpath(__file__))
+
+test_names = ["test1", "test2", "test3", "test4"]
+
+
+class TestFinder(CGEFinder):
+
+    def __init__(results):
+        """
+        Marias minimalistic Finder class
+        """
+        self.results = results
+
+    def resistance_analysis_genes(self):
+        """
+        Running some analysis that yield results appropriate for resistance
+        type results
+        """
+        Gene = namedtuple("Gene",
+                          ["name", "length", "aln_ln", "aln_id", "aln_gaps",
+                           "name_variant", "acc", "query", "q_start", "q_end",
+                           "q_depth", "t_start", "t_end"])
+
+        analysis_results = {
+            "group1": {
+                "gene1": None, "gene2": None},
+            "group2": {
+                "gene3": None},
+            "group3": {},
+            "group4": {
+                "gene1": None}
+        }
+
+        analysis_results["group1"]["gene1"] = Gene(
+            "gene1", 1000, 890, 0.97, 2, "gene1b", "NC_SOMEGENE", "contig12",
+            24, 1024, 50, 1, 1000)
+        analysis_results["group1"]["gene2"] = Gene(
+            "gene2", 500, 500, 1, 0, None, "NC_SOMEGENE2", "contig3",
+            24, 1024, None, 1, 500)
+        analysis_results["group2"]["gene3"] = Gene(
+            "gene3", 5000, 4500, 0.85, 10, None, "NC_SOMEGENE3", None,
+            None, None, 50, 1, 5000)
+        analysis_results["group4"]["gene1"] = Gene(
+            "gene1", 1000, 890, 0.97, 2, "gene1b", "NC_SOMEGENE", "contig12",
+            24, 1024, 49.74, 1, 1000)
+
+        for group in analysis_results:
+            for name, gene in group.items():
+                self.results.add_gene(
+                    template_name=gene.name,
+                    template_length=gene.length,
+                    template_start_pos=gene.t_start,
+                    templare_end_pos=gene.t_end,
+                    aln_length=gene.aln_ln,
+                    aln_identity=gene.aln_id,
+                    aln_gaps=gene.aln_gaps,
+                    query_id=gene.query,
+                    query_start_pos=gene.q_start,
+                    query_end_pos=gene.q_end,
+                    query_depth=gene.q_depth
+                )
+
+    def resistance_analysis_mutations(self):
+        """
+        Running some analysis that yield results appropriate for resistance
+        type results
+        """
+        pass
+
+    def resistance_analysis_phenotypes(self):
+        """
+        Running some analysis that yield results appropriate for resistance
+        type results
+        """
+        pass
+
+
+class ResFinderRunTest(unittest.TestCase):
+
+    def setUp(self):
+        # Change working dir to test dir
+        os.chdir(working_dir)
+        # Does not allow running two tests in parallel
+        os.makedirs(run_test_dir, exist_ok=False)
+
+    def tearDown(self):
+        shutil.rmtree(run_test_dir)
+
+    def test_create_and_store_results_in_resistance_type(self):
+        """
+        Maria has created a CGE service. The service use the cge_core_module
+        to create a CGEFinder object, then runs some analysis which stores its
+        results using the output module.
+        """
+        # Maria records when the script is being run
+        run_start = time.gmtime(time.time())
+        run_start_cge = ",".join(run_start[0], run_start[1], run_start[2],
+                                 run_start[3], run_start[4], run_start[5])
+
+        # First she creates a few directories to store her output.
+        test1_dir = run_test_dir + "/" + test_names[0]
+        os.makedirs(test1_dir)
+
+        # Create
+        results = Resistance(date=run_start_cge, name="TestFinder", "0.01", "Fake_ID", dbs)
+        finder = TestFinder()
+        finder.resistance_analysis_genes()
+        finder.resistance_analysis_mutations()
+        finder.resistance_analysis_phenotypes()
+        out_str = results.dump_json()
+        results.dump_json("{}/data.json".format(test1_dir))