ENCD-5433-refactor-not-bdd-not-indexing-tests (#3445)

.circleci/config.yml

@@ -71,7 +71,6 @@ jobs:
       - browser-tools/install-chromedriver
       - run:
           name: Run bdd tests
-          # collected 2189 items / 2119 deselected / 70 selected
           command: |
             bin/test -s -vv -m "bdd" --tb=short \
               --splinter-implicit-wait 10 \
@@ -87,8 +86,7 @@ jobs:
       - run:
           name: non bdd indexing tests
           command: |
-            # collected 2189 items / 2184 deselected / 5 selected
-            bin/test -s -vv -m "not bdd" -k test_indexing
+            bin/test -s -vv -m "indexing"
   not-bdd-non-indexing:
     executor: encoded-executor
     resource_class: large
@@ -97,8 +95,7 @@ jobs:
       - run:
           name: non bdd non indexing tests
           command: |
-            # collected 2189 items / 75 deselected / 2114 selected
-            bin/test -s -vv -m "not bdd" -k 'not test_indexing'
+            bin/test -s -vv -m "not bdd and not indexing"
   npm:
     executor: encoded-executor
     resource_class: large

circle-tests.sh

@@ -17,12 +17,12 @@ if [ "$1" == "bdd" ]; then
 fi
 
 if [ "$1" == "not-bdd-indexing" ]; then
-    bin/test -s -vv -m "not bdd" -k test_indexing
+    bin/test -s -vv -m "indexing"
     exit
 fi
 
 if [ "$1" == "not-bdd-non-indexing" ]; then
-    bin/test -s -vv -m "not bdd" -k 'not test_indexing'
+    bin/test -s -vv -m "not bdd and not indexing" 
     exit
 fi
 

src/encoded/tests/features/advanced_query_search.feature

@@ -1,4 +1,4 @@
-@advanced_query_search @usefixtures(workbook)
+@advanced_query_search @usefixtures(index_workbook)
 Feature: Search
     Background:
         When I visit "/search"

src/encoded/tests/features/antibodies.feature

@@ -1,4 +1,4 @@
-@antibodies @usefixtures(workbook)
+@antibodies @usefixtures(index_workbook)
 Feature: Antibodies
 
     Scenario: Collection

src/encoded/tests/features/audit.feature

@@ -6,7 +6,7 @@ Feature: Title
         And I wait for the content to load
         Then the title should contain the text "Audit – ENCODE"
 
-@audit @usefixtures(workbook)
+@audit @usefixtures(index_workbook)
 Feature: Audit
     Background:
         When I visit "/audit/?type=Experiment"

src/encoded/tests/features/batch_hubs.feature

@@ -1,4 +1,4 @@
-@batchhubs @usefixtures(workbook)
+@batchhubs @usefixtures(index_workbook)
 Feature: Batch Hubs
     Background:
         When I visit "/search/?type=Experiment&status=released"

src/encoded/tests/features/biosamples.feature

@@ -1,4 +1,4 @@
-@biosamples @usefixtures(workbook)
+@biosamples @usefixtures(index_workbook)
 Feature: Biosamples
 
     Scenario: Detail page

src/encoded/tests/features/cart.feature

@@ -1,4 +1,4 @@
-@cart @usefixtures(workbook)
+@cart @usefixtures(index_workbook)
 Feature: Cart
     Scenario: Search result cart toggles:
         When I visit "/search/?type=Experiment"

src/encoded/tests/features/conftest.py

@@ -29,7 +29,7 @@ def app(app_settings):
 
 @pytest.mark.fixture_cost(500)
 @pytest.yield_fixture(scope='session')
-def workbook(request, app):
+def index_workbook(request, app):
     from snovault import DBSESSION
     connection = app.registry[DBSESSION].bind.pool.unique_connection()
     connection.detach()
@@ -97,7 +97,7 @@ def splinter_window_size():
 
 # Depend on workbook fixture here to avoid remote browser timeouts.
 @pytest.fixture(scope='session')
-def browser(workbook, session_browser):
+def browser(index_workbook, session_browser):
     return session_browser
 
 

src/encoded/tests/features/experiments.feature

@@ -1,4 +1,4 @@
-@experiments @usefixtures(workbook)
+@experiments @usefixtures(index_workbook)
 Feature: Experiments
 
     Scenario: Collection

src/encoded/tests/features/forms.feature

@@ -1,4 +1,4 @@
-@forms @usefixtures(workbook,admin_user)
+@forms @usefixtures(index_workbook,admin_user)
 Feature: Edit forms
 
     Scenario: Save a change to an antibody

src/encoded/tests/features/generics.feature

@@ -1,4 +1,4 @@
-@generics @usefixtures(workbook)
+@generics @usefixtures(index_workbook)
 Feature: Generics
 
     Scenario Outline: Generics

src/encoded/tests/features/matrix_chip_seq.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: ChIP-seq matrix
         When I visit "/"

src/encoded/tests/features/matrix_entex.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: Matrix ENTEx
         When I visit "/"

src/encoded/tests/features/matrix_experiment.feature

@@ -10,7 +10,7 @@ Feature: Title
         And I wait for the content to load
         Then the title should contain the text "Matrix – ENCODE"
 
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Background:
         When I visit "/matrix/?type=Experiment&status=released"

src/encoded/tests/features/matrix_mouse_development.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: Mouse development matrix
         When I visit "/"

src/encoded/tests/features/matrix_reference_epigenome.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: Matrix Reference Epigenome
         When I visit "/"

src/encoded/tests/features/matrix_reference_epigenome_homo_sapien_all.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: Matrix Reference Epigenome
         When I visit "/"

src/encoded/tests/features/matrix_reference_epigenome_homo_sapien_nonroadmap.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: Matrix Reference Epigenome
         When I visit "/"

src/encoded/tests/features/matrix_reference_epigenome_mus_musculus.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: Matrix Reference Epigenome
         When I visit "/"

src/encoded/tests/features/matrix_sescc_stem_cell.feature

@@ -1,4 +1,4 @@
-@matrix @usefixtures(workbook)
+@matrix @usefixtures(index_workbook)
 Feature: Matrix
     Scenario: SESCC-Stem-Cell-Matrix
         When I visit "/"

src/encoded/tests/features/page.feature

@@ -1,4 +1,4 @@
-@page @usefixtures(workbook,admin_user)
+@page @usefixtures(index_workbook,admin_user)
 Feature: Portal pages
 
     Scenario: Render page layout

src/encoded/tests/features/report.feature

@@ -6,7 +6,7 @@ Feature: Title
         And I wait for the content to load
         Then the title should contain the text "Report – ENCODE"
 
-@report @usefixtures(workbook)
+@report @usefixtures(index_workbook)
 Feature: Report
     Background:
         When I visit "/report/?type=Experiment"

src/encoded/tests/features/search.feature

@@ -1,4 +1,4 @@
-@search @usefixtures(workbook)
+@search @usefixtures(index_workbook)
 Feature: Search
     Background:
         When I visit "/search"

src/encoded/tests/features/summary.feature

@@ -6,7 +6,7 @@ Feature: Title
         And I wait for the content to load
         Then the title should contain the text "Summary – ENCODE"
 
-@Summary @usefixtures(workbook)
+@Summary @usefixtures(index_workbook)
 Feature: Summary
     Background:
         When I visit "/summary/?type=Experiment&status=released"

src/encoded/tests/features/targets.feature

@@ -1,4 +1,4 @@
-@targets @usefixtures(workbook)
+@targets @usefixtures(index_workbook)
 Feature: Targets
 
     Scenario: Collection

src/encoded/tests/features/test_admin_user.py

@@ -3,7 +3,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook', 'admin_user'),
+    pytest.mark.usefixtures('index_workbook', 'admin_user'),
 ]
 
 

src/encoded/tests/features/test_audit.py

@@ -5,11 +5,11 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 
-def test_auditview(testapp, workbook):
+def test_auditview(testapp, index_workbook):
     res = testapp.get('/audit/?type=Experiment')
     assert res.json['matrix']
 

src/encoded/tests/features/test_batch_hubs.py

@@ -5,7 +5,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 scenarios(

src/encoded/tests/features/test_cart.py

@@ -5,7 +5,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 scenarios(

src/encoded/tests/features/test_generics.py

@@ -8,7 +8,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 scenarios('generics.feature', strict_gherkin=False)

src/encoded/tests/features/test_matrix.py

@@ -5,7 +5,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 scenarios(

src/encoded/tests/features/test_report.py

@@ -5,7 +5,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 scenarios(

src/encoded/tests/features/test_submitter_user.py

@@ -3,7 +3,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook', 'submitter_user'),
+    pytest.mark.usefixtures('index_workbook', 'submitter_user'),
 ]
 
 

src/encoded/tests/features/test_summary.py

@@ -5,7 +5,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 scenarios(

src/encoded/tests/features/test_trackhubs.py

@@ -1,5 +1,6 @@
 import pytest
 
+pytestmark = [pytest.mark.indexing]
 
 @pytest.mark.parametrize('expected', [
     "# http://localhost/batch_hub/type=Experiment/hub.txt",
@@ -9,7 +10,7 @@
     "genomesFile genomes.txt",
     "email encode-help@lists.stanford.edu"
 ])
-def test_hub(testapp, workbook, expected):
+def test_hub(testapp, index_workbook, expected):
     res = testapp.get("/batch_hub/type=Experiment/hub.txt")
     assert expected in res.text
 
@@ -22,7 +23,7 @@ def test_hub(testapp, workbook, expected):
     "genome hg19",
     "trackDb hg19/trackDb.txt",
 ])
-def test_genomes(testapp, workbook, expected):
+def test_genomes(testapp, index_workbook, expected):
     res = testapp.get("/batch_hub/type=Experiment/genomes.txt")
     assert expected in res.text
 
@@ -53,7 +54,7 @@ def test_genomes(testapp, workbook, expected):
     "        type bigBed",
     "        subGroups BS=IMR4590 EXP=ENCSR575ZXX REP=pool view=cSTATE",
 ])
-def test_dataset_trackDb(testapp, workbook, expected):
+def test_dataset_trackDb(testapp, index_workbook, expected):
     res = testapp.get("/annotations/ENCSR575ZXX/@@hub/hg19/trackDb.txt")
     assert expected in res.text
 
@@ -90,23 +91,23 @@ def test_dataset_trackDb(testapp, workbook, expected):
     "        altColor 115,31,0",
     "        subGroups BS=GM12878 EXP=ENCSR000DZQ REP=pool TARG=EBF1 view=bIDRT",
 ])
-def test_genomes(testapp, workbook, expected):
+def test_genomes(testapp, index_workbook, expected):
     res = testapp.get("/batch_hub/type=Experiment%2C%2caccession%3DENCSR000DZQ%2C%2caccession%3DENCSRENCSR575ZXX/hg19/trackDb.txt")
     assert expected in res.text
 
 
 @pytest.mark.parametrize('expected', [
     ""
 ])
-def test_fileset_files_trackDb(testapp, workbook, expected):
+def test_fileset_files_trackDb(testapp, index_workbook, expected):
     res = testapp.get("/publication-data/ENCSR727WCB/@@hub/hg19/trackDb.txt")
     assert expected in res.text
 
 
 @pytest.mark.parametrize('expected', [
     "# Empty composite for ENCSR000ACY.  It cannot be visualized at this time.",
 ])
-def test_experiment_trackDb(testapp, workbook, expected):
+def test_experiment_trackDb(testapp, index_workbook, expected):
     res = testapp.get("/experiments/ENCSR000ACY/@@hub/trackDb.txt")
     assert expected in res.text
 
@@ -115,28 +116,28 @@ def test_experiment_trackDb(testapp, workbook, expected):
     "genome hg38",
     "trackDb hg38/trackDb.txt",
 ])
-def test_genome_txt(testapp, workbook, expected):
+def test_genome_txt(testapp, index_workbook, expected):
     res = testapp.get("/batch_hub/type=Experiment&assembly=GRCh38/genomes.txt")
     assert expected in res.text
 
 @pytest.mark.parametrize('expected', [
     "GRCh38",
     "hg19"
 ])
-def test_assembly(testapp, workbook, expected):
+def test_assembly(testapp, index_workbook, expected):
     res = testapp.get("/experiments/ENCSR000AEN/")
     assert expected in res.json['assembly']
 
 
 @pytest.mark.parametrize('expected', [
     "/experiments/ENCSR000AEN/@@hub/hub.txt",
 ])
-def test_hub_field(testapp, workbook, expected):
+def test_hub_field(testapp, index_workbook, expected):
     res = testapp.get("/experiments/ENCSR000AEN/")
     assert expected in res.json['hub']
 
 
-def test_visualize(submitter_testapp, workbook):
+def test_visualize(submitter_testapp, index_workbook):
     expected = {
         'GRCh38': [
             "Ensembl",

src/encoded/tests/features/test_views.py

@@ -5,7 +5,7 @@
 
 pytestmark = [
     pytest.mark.bdd,
-    pytest.mark.usefixtures('workbook'),
+    pytest.mark.usefixtures('index_workbook'),
 ]
 
 scenarios(