added tests and refactoring of tests and added default user tests

src/frontend_celery/playwright/start_redis_for_tests.sh

@@ -0,0 +1,50 @@
+
+#!/bin/bash
+
+SCRIPT=$(readlink -f "$0")
+SCRIPTPATH=$(dirname "$SCRIPT")
+cd $SCRIPTPATH
+pwd
+ROOT=$(dirname $(dirname $(dirname "$SCRIPTPATH")))
+
+function waitForServer {
+  dist=$1
+  echo -n "Starting $dist"
+  # Give the server some time to start up. Look for a well-known
+  # bit of text in the log file. Try at most 50 times before giving up.
+  C=500
+  while :
+  do
+    grep ".* Ready to accept connections tcp" redis.log
+    if [ $? -eq 0 ]; then
+      echo " server started."
+      break
+    elif [ $C -gt 0 ]; then
+      echo -n "."
+      C=$((C-1))
+      sleep 1
+    else
+      echo " timeout!"
+      cat redis.log
+      exit 1
+    fi
+  done
+}
+
+set -o allexport
+extension=env_
+source $ROOT/.$extension$WEBAPP_ENV
+set +o allexport
+
+TOOLS=$ROOT/tools
+
+redis_path=$SCRIPTPATH/redis_for_tests
+
+# install keycloak for tests if it is missing
+if [ ! -d "${redis_path}" ]; then
+  $TOOLS/script/install_redis.sh -p $SCRIPTPATH -n redis_for_tests
+  sleep 5
+fi
+
+redis_for_tests/src/redis-server --port $REDIS_PORT > redis.log 2>&1 &
+waitForServer "Redis"

src/frontend_celery/playwright/start_tests.sh

@@ -45,17 +45,32 @@ fi
 # start keycloak - this also seeds keycloak
 $TESTDIR/start_keycloak_for_tests.sh
 
+# start redis
+$TESTDIR/start_redis_for_tests.sh
 
 # start heredivar
 $TESTDIR/start_heredivar_for_tests.sh
 
 
 # run tests
 cd $TESTDIR
-export TESTUSER=$TEST_READONLY
-export TESTUSERPW=$TEST_READONLY_PW
-pytest --screenshot=only-on-failure --browser firefox tests/read_only/ #-k 'test_private_list_actions or test_variant_list_add' #-k 'test_dev' --browser webkit --browser chromium --numprocesses 2
+
+# test read only
+#export TESTUSER=$TEST_READONLY
+#export TESTUSERPW=$TEST_READONLY_PW
+#pytest --screenshot=only-on-failure --browser firefox tests/read_only/ -k 'test_user_classify' #-k 'test_private_list_actions or test_variant_list_add' #-k 'test_dev' --browser webkit --browser chromium --numprocesses 2
+
+# test default user
+export TESTUSER=$TEST_USER
+export TESTUSERPW=$TEST_USER_PW
+pytest --screenshot=only-on-failure --browser firefox tests/default_user/ -k 'test_user_select_all_schemes' #-k 'test_private_list_actions or test_variant_list_add' #-k 'test_dev' --browser webkit --browser chromium --numprocesses 2
+
+# test superuser
+#export TESTUSER=$TEST_SUPERUSER
+#export TESTUSERPW=$TEST_SUPERUSER_PW
+# TODO...
 
 # stop services
 pkill -s 0 -e java
 pkill -s 0 -e python3
+pkill -s 0 -e redis-server

src/frontend_celery/playwright/tests/default_user/specific/test_consensus_classify.py

@@ -0,0 +1,30 @@
+
+from os import path
+import os
+import sys
+sys.path.append(path.dirname(path.dirname(path.dirname(path.abspath(__file__)))))
+import utils
+import re
+#from playwright.sync_api import Page, expect, sync_playwright
+from flask import url_for
+sys.path.append(path.dirname(path.dirname(path.dirname(path.dirname(path.abspath(__file__))))))
+import common.functions as functions
+import common.paths as paths
+import time
+from functools import partial
+from playwright.sync_api import expect
+import requests
+
+
+def test_consensus_classify(page, conn):
+    # seed database
+    user = utils.get_user()
+    user_id = conn.get_user_id(user["username"])
+
+    # insert variants
+    variant_id = conn.insert_variant(chr = "chr2", pos = "214730440", ref = "G", alt = "A", orig_chr = "chr2", orig_pos = "214730440", orig_ref = "G", orig_alt = "A", user_id = user_id) # chr2-214730440-G-A BARD1
+
+    # start the test
+    utils.login(page, user)
+
+    utils.nav(page.goto, utils.UNAUTHORIZED_STATI, url_for('variant.consensus_classify', variant_id = variant_id, _external = True))

src/frontend_celery/playwright/tests/default_user/unspecific/test_classify.py

@@ -0,0 +1,42 @@
+from os import path
+import os
+import sys
+sys.path.append(path.dirname(path.dirname(path.dirname(path.abspath(__file__)))))
+import utils
+import re
+#from playwright.sync_api import Page, expect, sync_playwright
+from flask import url_for
+sys.path.append(path.dirname(path.dirname(path.dirname(path.dirname(path.abspath(__file__))))))
+import common.functions as functions
+import common.paths as paths
+import time
+from functools import partial
+from playwright.sync_api import expect
+import requests
+
+
+
+
+def test_user_select_all_schemes(page, conn):
+    # seed database
+    user = utils.get_user()
+    user_id = conn.get_user_id(user["username"])
+
+    # insert variants
+    variant_id = conn.insert_variant(chr = "chr2", pos = "214730440", ref = "G", alt = "A", orig_chr = "chr2", orig_pos = "214730440", orig_ref = "G", orig_alt = "A", user_id = user_id) # chr2-214730440-G-A BARD1
+
+    # start the test
+    utils.login(page, user)
+
+    utils.nav(page.goto, utils.GOOD_STATI, url_for('variant.classify', variant_id = variant_id, _external = True))
+
+    # test that all classification schemes are selectable
+    classification_schemes = conn.get_classification_schemas()
+    for classification_scheme_id in classification_schemes:
+        classification_scheme_label = classification_schemes[classification_scheme_id]["description"]
+        page.select_option('select#scheme', label=classification_scheme_label)
+
+        # assert that all criteria are visible
+        criteria = classification_schemes[classification_scheme_id]["criteria"]
+        for criterium in criteria:
+            expect(page.locator("#" + criterium)).to_have_count(1)

src/frontend_celery/playwright/tests/read_only/specific/test_classify.py

@@ -0,0 +1,44 @@
+from os import path
+import os
+import sys
+sys.path.append(path.dirname(path.dirname(path.dirname(path.abspath(__file__)))))
+import utils
+import re
+#from playwright.sync_api import Page, expect, sync_playwright
+from flask import url_for
+sys.path.append(path.dirname(path.dirname(path.dirname(path.dirname(path.abspath(__file__))))))
+import common.functions as functions
+import common.paths as paths
+import time
+from functools import partial
+from playwright.sync_api import expect
+import requests
+
+
+
+
+def test_user_classify(page, conn):
+    # seed database
+    user = utils.get_user()
+    user_id = conn.get_user_id(user["username"])
+
+    # insert variants
+    variant_id = conn.insert_variant(chr = "chr2", pos = "214730440", ref = "G", alt = "A", orig_chr = "chr2", orig_pos = "214730440", orig_ref = "G", orig_alt = "A", user_id = user_id) # chr2-214730440-G-A BARD1
+
+    # start the test
+    utils.login(page, user)
+
+    utils.nav(page.goto, utils.UNAUTHORIZED_STATI, url_for('variant.classify', variant_id = variant_id, _external = True))
+
+def test_consensus_classify(page, conn):
+    # seed database
+    user = utils.get_user()
+    user_id = conn.get_user_id(user["username"])
+
+    # insert variants
+    variant_id = conn.insert_variant(chr = "chr2", pos = "214730440", ref = "G", alt = "A", orig_chr = "chr2", orig_pos = "214730440", orig_ref = "G", orig_alt = "A", user_id = user_id) # chr2-214730440-G-A BARD1
+
+    # start the test
+    utils.login(page, user)
+
+    utils.nav(page.goto, utils.UNAUTHORIZED_STATI, url_for('variant.consensus_classify', variant_id = variant_id, _external = True))

src/frontend_celery/playwright/tests/read_only/test_browse.py → src/frontend_celery/playwright/tests/read_only/unspecific/test_browse.py

@@ -3,7 +3,6 @@
 import sys
 sys.path.append(path.dirname(path.dirname(path.dirname(path.abspath(__file__)))))
 import utils
-from utils import Test_Connection
 import re
 #from playwright.sync_api import Page, expect, sync_playwright
 from flask import url_for
@@ -263,7 +262,7 @@ def test_consensus_classification_search(page, conn):
     ]
 
     # insert consensus classifications
-    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI")
+    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI", 'v1.0.0')
     conn.insert_consensus_classification(user_id = user_id, variant_id = all_variant_ids[0], consensus_classification = "1", comment = "TEST1", evidence_document = bytes("TESTEXAMPLE", 'utf-8'), date = functions.get_now(), scheme_id = classification_scheme_id, scheme_class = "1")
     conn.insert_consensus_classification(user_id = user_id, variant_id = all_variant_ids[1], consensus_classification = "2", comment = "TEST2", evidence_document = bytes("TESTEXAMPLE", 'utf-8'), date = functions.get_now(), scheme_id = classification_scheme_id, scheme_class = "2")
     conn.insert_consensus_classification(user_id = user_id, variant_id = all_variant_ids[2], consensus_classification = "3-", comment = "TEST3", evidence_document = bytes("TESTEXAMPLE", 'utf-8'), date = functions.get_now(), scheme_id = classification_scheme_id, scheme_class = "3")
@@ -359,7 +358,7 @@ def test_user_classification_search(page, conn):
     ]
 
     # insert consensus classifications
-    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI")
+    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI", 'v1.0.0')
     conn.insert_user_classification(variant_id = all_variant_ids[0], classification = "1", user_id = user_id, comment = "", date = functions.get_now(), scheme_id = classification_scheme_id, scheme_class = "1")
     conn.insert_user_classification(variant_id = all_variant_ids[1], classification = "2", user_id = user_id, comment = "", date = functions.get_now(), scheme_id = classification_scheme_id, scheme_class = "2")
     conn.insert_user_classification(variant_id = all_variant_ids[2], classification = "3-", user_id = user_id, comment = "", date = functions.get_now(), scheme_id = classification_scheme_id, scheme_class = "3")
@@ -429,7 +428,7 @@ def test_automatic_classification_splicing_search(page, conn):
     ]
 
     # insert consensus classifications
-    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI")
+    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI", 'v1.0.0')
     conn.insert_automatic_classification(variant_id = all_variant_ids[0], classification_scheme_id = classification_scheme_id, classification_splicing = "1", classification_protein = "2", tool_version = "1.0.0")
     conn.insert_automatic_classification(variant_id = all_variant_ids[1], classification_scheme_id = classification_scheme_id, classification_splicing = "2", classification_protein = "1", tool_version = "1.0.0")
     conn.insert_automatic_classification(variant_id = all_variant_ids[2], classification_scheme_id = classification_scheme_id, classification_splicing = "3", classification_protein = "1", tool_version = "1.0.0")
@@ -490,7 +489,7 @@ def test_automatic_classification_protein_search(page, conn):
     ]
 
     # insert consensus classifications
-    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI")
+    classification_scheme_id = conn.get_classification_scheme_id_from_alias("ACMG standard + SVI", 'v1.0.0')
     conn.insert_automatic_classification(variant_id = all_variant_ids[0], classification_scheme_id = classification_scheme_id, classification_splicing = "2", classification_protein = "1", tool_version = "1.0.0")
     conn.insert_automatic_classification(variant_id = all_variant_ids[1], classification_scheme_id = classification_scheme_id, classification_splicing = "1", classification_protein = "2", tool_version = "1.0.0")
     conn.insert_automatic_classification(variant_id = all_variant_ids[2], classification_scheme_id = classification_scheme_id, classification_splicing = "1", classification_protein = "3", tool_version = "1.0.0")

src/frontend_celery/playwright/tests/read_only/test_lists.py → src/frontend_celery/playwright/tests/read_only/unspecific/test_lists.py

@@ -3,7 +3,6 @@
 import sys
 sys.path.append(path.dirname(path.dirname(path.dirname(path.abspath(__file__)))))
 import utils
-from utils import Test_Connection
 import re
 #from playwright.sync_api import Page, expect, sync_playwright
 from flask import url_for
@@ -73,7 +72,7 @@ def test_variant_list_add(page):
 def test_private_list_actions(page, conn):
     # seed database
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    user_id = conn.get_last_insert_id()
+    user_id = conn.get_user_id("transient_tester")
 
     list_name = "priv_l"
     conn.insert_user_variant_list(user_id = user_id, list_name = list_name, public_read = False, public_edit = False)
@@ -95,7 +94,6 @@ def test_private_list_actions(page, conn):
     # try accessing the private list -> unauthorized
     utils.nav(page.goto, utils.UNAUTHORIZED_STATI, url_for('user.my_lists', view=list_id, _external=True))
 
-
     # try to add variants to the private list -> unauthorized
     get_data = {
         "selected_list_id": list_id,
@@ -127,7 +125,7 @@ def test_add_list(page, conn):
     # seed database
     user = utils.get_user()
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    other_user_id = conn.get_last_insert_id()
+    other_user_id = conn.get_user_id("transient_tester")
 
     private_list_name = "priv_l"
     conn.insert_user_variant_list(user_id = other_user_id, list_name = private_list_name, public_read = False, public_edit = False)
@@ -206,7 +204,7 @@ def test_subtract_list(page, conn):
     # seed database
     user = utils.get_user()
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    other_user_id = conn.get_last_insert_id()
+    other_user_id = conn.get_user_id("transient_tester")
 
     private_list_name = "priv_l"
     conn.insert_user_variant_list(user_id = other_user_id, list_name = private_list_name, public_read = False, public_edit = False)
@@ -294,7 +292,7 @@ def test_intersect_list(page, conn):
     # seed database
     user = utils.get_user()
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    other_user_id = conn.get_last_insert_id()
+    other_user_id = conn.get_user_id("transient_tester")
 
     private_list_name = "priv_l"
     conn.insert_user_variant_list(user_id = other_user_id, list_name = private_list_name, public_read = False, public_edit = False)
@@ -380,7 +378,7 @@ def test_duplicate_list(page, conn):
     # seed database
     user = utils.get_user()
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    other_user_id = conn.get_last_insert_id()
+    other_user_id = conn.get_user_id("transient_tester")
 
     list_name = "priv_l"
     conn.insert_user_variant_list(user_id = other_user_id, list_name = list_name, public_read = False, public_edit = False)
@@ -422,7 +420,7 @@ def test_delete_list(page, conn):
     # seed database
     user = utils.get_user()
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    other_user_id = conn.get_last_insert_id()
+    other_user_id = conn.get_user_id("transient_tester")
 
     list_name = "priv_l"
     conn.insert_user_variant_list(user_id = other_user_id, list_name = list_name, public_read = False, public_edit = False)
@@ -460,7 +458,7 @@ def test_modify_list_permissions(page, conn):
     # seed database
     user = utils.get_user()
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    other_user_id = conn.get_last_insert_id()
+    other_user_id = conn.get_user_id("transient_tester")
 
     list_name = "priv_l"
     conn.insert_user_variant_list(user_id = other_user_id, list_name = list_name, public_read = False, public_edit = False)
@@ -554,7 +552,7 @@ def test_modify_list_permissions(page, conn):
 def test_public_list_actions(page, conn):
     # seed database
     conn.insert_user(username = "transient_tester", first_name = "TRA", last_name = "TEST", affiliation = "AFF")
-    user_id = conn.get_last_insert_id()
+    user_id = conn.get_user_id("transient_tester")
 
     list_name = "publ_l"
     conn.insert_user_variant_list(user_id = user_id, list_name = list_name, public_read = True, public_edit = False)
@@ -571,7 +569,7 @@ def test_public_list_actions(page, conn):
 
     # is the list visible?
     utils.nav(page.goto, utils.GOOD_STATI, url_for('user.my_lists', _external=True))
-    expect(page.locator("tr[list_id='" + str(list_id) + "']")).to_have_count(0)
+    expect(page.locator("tr[list_id='" + str(list_id) + "']")).to_have_count(1)
 
     # try accessing the public list -> works
     utils.nav(page.goto, utils.GOOD_STATI, url_for('user.my_lists', view=list_id, _external=True))