Merge branch 'main' into ASReview2-nb

asreview · Jan 23, 2025 · e722d81 · e722d81
2 parents e1fc59e + 983dafa
commit e722d81
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Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/.github/workflows/workflow.yaml b/.github/workflows/workflow.yaml
@@ -120,7 +120,7 @@ jobs:
         ANSIBLE_HOST_KEY_CHECKING: "False"
       run: |
         echo "Sleeping to ensure instance is ready..."
-        sleep 10
+        sleep 20
         ansible-playbook ./asreview2-optuna/ansible/ansible_optuna_playbook.yml \
           --extra-vars "branch_name=${{ github.ref_name }} db_uri=${{ secrets.DB_API }}" \
           -u ubuntu --private-key ~/.ssh/id_rsa -i inventory.ini
diff --git a/asreview2-optuna/main.py b/asreview2-optuna/main.py
@@ -44,7 +44,7 @@
 
 
 def load_dataset(dataset_id):
-    if dataset_id == "Moran_2021":
+    if dataset_id == "Moran_2021_corrected":
         return pd.read_csv(Path("datasets", "Moran_2021_corrected_shuffled_raw.csv"))
 
     return sd.Dataset(dataset_id).to_frame().reset_index()

diff --git a/asreview2-optuna/synergy_studies_demo.jsonl b/asreview2-optuna/synergy_studies_demo.jsonl
@@ -9,7 +9,7 @@
 {"dataset_id": "Leenaars_2020", "prior_inclusions": [5158], "prior_exclusions": [2310]}
 {"dataset_id": "Meijboom_2021", "prior_inclusions": [194, 282], "prior_exclusions": [4]}
 {"dataset_id": "Menon_2022", "prior_inclusions": [46], "prior_exclusions": [880, 794, 655]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [974], "prior_exclusions": [228]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [981], "prior_exclusions": [229]}
 {"dataset_id": "Muthu_2021", "prior_inclusions": [676, 107], "prior_exclusions": [2316]}
 {"dataset_id": "Nelson_2002", "prior_inclusions": [266, 189], "prior_exclusions": [346, 328]}
 {"dataset_id": "Oud_2018", "prior_inclusions": [228], "prior_exclusions": [112]}
@@ -34,7 +34,7 @@
 {"dataset_id": "Leenaars_2020", "prior_inclusions": [6293], "prior_exclusions": [5630]}
 {"dataset_id": "Meijboom_2021", "prior_inclusions": [707, 247], "prior_exclusions": [148, 61, 97, 752, 42]}
 {"dataset_id": "Menon_2022", "prior_inclusions": [418], "prior_exclusions": [248]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3762], "prior_exclusions": [3938, 2905, 5278, 517]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3664], "prior_exclusions": [3940, 2904, 5278, 516]}
 {"dataset_id": "Muthu_2021", "prior_inclusions": [804], "prior_exclusions": [679]}
 {"dataset_id": "Nelson_2002", "prior_inclusions": [282, 183], "prior_exclusions": [94, 261, 69]}
 {"dataset_id": "Oud_2018", "prior_inclusions": [641, 478], "prior_exclusions": [646]}

diff --git a/asreview2-optuna/synergy_studies_full.jsonl b/asreview2-optuna/synergy_studies_full.jsonl
@@ -33,7 +33,7 @@
 {"dataset_id": "Leenaars_2020", "prior_inclusions": [4548], "prior_exclusions": [1789]}
 {"dataset_id": "Donners_2021", "prior_inclusions": [6], "prior_exclusions": [5, 92]}
 {"dataset_id": "Hall_2012", "prior_inclusions": [1476, 4543, 6963, 3258], "prior_exclusions": [6932]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3609], "prior_exclusions": [3804, 1724]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3587], "prior_exclusions": [3804, 1722]}
 {"dataset_id": "van_de_Schoot_2018", "prior_inclusions": [4327], "prior_exclusions": [4043, 3464]}
 {"dataset_id": "Walker_2018", "prior_inclusions": [2095], "prior_exclusions": [38191, 35217]}
 {"dataset_id": "van_der_Waal_2022", "prior_inclusions": [83], "prior_exclusions": [1785, 1739]}
@@ -110,7 +110,7 @@
 {"dataset_id": "Walker_2018", "prior_inclusions": [28131, 44136], "prior_exclusions": [4137, 40662, 13866, 33552]}
 {"dataset_id": "Donners_2021", "prior_inclusions": [235], "prior_exclusions": [110, 176]}
 {"dataset_id": "van_Dis_2020", "prior_inclusions": [7768, 2707, 564, 107, 2408], "prior_exclusions": [63, 6173]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3410, 137, 328], "prior_exclusions": [2765, 4060]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3287, 42, 296], "prior_exclusions": [2766, 4061]}
 {"dataset_id": "Leenaars_2020", "prior_inclusions": [6541], "prior_exclusions": [4519]}
 {"dataset_id": "Hall_2012", "prior_inclusions": [4241], "prior_exclusions": [200]}
 {"dataset_id": "Jeyaraman_2020", "prior_inclusions": [1021, 174], "prior_exclusions": [1060]}
@@ -137,7 +137,7 @@
 {"dataset_id": "van_de_Schoot_2018", "prior_inclusions": [4461], "prior_exclusions": [3740, 2884, 3363, 2525, 1422]}
 {"dataset_id": "Radjenovic_2013", "prior_inclusions": [624], "prior_exclusions": [228, 1881]}
 {"dataset_id": "Wassenaar_2017", "prior_inclusions": [2808], "prior_exclusions": [2233]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [1568], "prior_exclusions": [597, 3659, 4265]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [1637], "prior_exclusions": [596, 3661, 4265]}
 {"dataset_id": "Menon_2022", "prior_inclusions": [295], "prior_exclusions": [632, 856, 792]}
 {"dataset_id": "Brouwer_2019", "prior_inclusions": [12605, 36578, 18057], "prior_exclusions": [37118, 16097, 30195]}
 {"dataset_id": "Oud_2018", "prior_inclusions": [682, 162, 641, 376], "prior_exclusions": [174, 946]}
@@ -175,7 +175,7 @@
 {"dataset_id": "van_der_Waal_2022", "prior_inclusions": [1757], "prior_exclusions": [494, 1840, 778]}
 {"dataset_id": "Leenaars_2019", "prior_inclusions": [2639], "prior_exclusions": [1750, 5672, 2634]}
 {"dataset_id": "Brouwer_2019", "prior_inclusions": [16870, 24076], "prior_exclusions": [23371]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [881], "prior_exclusions": [4100, 1905]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [934], "prior_exclusions": [4100, 1903]}
 {"dataset_id": "Meijboom_2021", "prior_inclusions": [808, 184], "prior_exclusions": [641, 149, 592]}
 {"dataset_id": "Jeyaraman_2020", "prior_inclusions": [409], "prior_exclusions": [603, 22, 1017]}
 {"dataset_id": "Bos_2018", "prior_inclusions": [2304], "prior_exclusions": [2680, 2532]}
@@ -193,12 +193,12 @@
 {"dataset_id": "Muthu_2021", "prior_inclusions": [1809, 1273, 1939, 1248, 2499, 1226], "prior_exclusions": [2361, 1517, 2013]}
 {"dataset_id": "Walker_2018", "prior_inclusions": [44557, 28782], "prior_exclusions": [31357]}
 {"dataset_id": "Appenzeller-Herzog_2019", "prior_inclusions": [555, 1606, 1655, 2839], "prior_exclusions": [1564, 1552, 122, 1103]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [4468, 2277], "prior_exclusions": [4172]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [4516, 2232], "prior_exclusions": [4172]}
 {"dataset_id": "Appenzeller-Herzog_2019", "prior_inclusions": [142], "prior_exclusions": [1813]}
 {"dataset_id": "Nelson_2002", "prior_inclusions": [286], "prior_exclusions": [83]}
 {"dataset_id": "Hall_2012", "prior_inclusions": [3038, 1230, 4560, 779, 4877], "prior_exclusions": [6035]}
 {"dataset_id": "Radjenovic_2013", "prior_inclusions": [4598], "prior_exclusions": [3483, 5186]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [5346, 1881, 1108, 2762], "prior_exclusions": [2602]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [5263, 1937, 1163, 2707], "prior_exclusions": [2601]}
 {"dataset_id": "Walker_2018", "prior_inclusions": [16169], "prior_exclusions": [34623]}
 {"dataset_id": "Sep_2021", "prior_inclusions": [107], "prior_exclusions": [132]}
 {"dataset_id": "Bos_2018", "prior_inclusions": [2039, 36, 2304, 3141, 2925, 2751], "prior_exclusions": [4177]}
@@ -225,7 +225,7 @@
 {"dataset_id": "Jeyaraman_2020", "prior_inclusions": [552], "prior_exclusions": [239, 543]}
 {"dataset_id": "Bos_2018", "prior_inclusions": [2039], "prior_exclusions": [4182, 1304, 4194]}
 {"dataset_id": "Jeyaraman_2020", "prior_inclusions": [1120, 1159, 552, 168, 1062, 30], "prior_exclusions": [39]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [1086], "prior_exclusions": [1034, 4880]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [1163], "prior_exclusions": [1034, 4876]}
 {"dataset_id": "Radjenovic_2013", "prior_inclusions": [5760], "prior_exclusions": [983, 1750]}
 {"dataset_id": "van_Dis_2020", "prior_inclusions": [7154, 4079], "prior_exclusions": [3810, 7948]}
 {"dataset_id": "Hall_2012", "prior_inclusions": [1183, 2571, 2686], "prior_exclusions": [6969, 3576, 7746]}
@@ -245,6 +245,6 @@
 {"dataset_id": "Leenaars_2020", "prior_inclusions": [7105, 7109, 115, 890], "prior_exclusions": [1310, 1536]}
 {"dataset_id": "van_de_Schoot_2018", "prior_inclusions": [2545, 4154, 831], "prior_exclusions": [11, 3816, 3598, 670]}
 {"dataset_id": "Walker_2018", "prior_inclusions": [19168, 8350, 2095, 42631], "prior_exclusions": [27602, 18004, 28836, 44316]}
-{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3586], "prior_exclusions": [3375, 4173]}
+{"dataset_id": "Moran_2021_corrected", "prior_inclusions": [3569], "prior_exclusions": [3376, 4172]}
 {"dataset_id": "Radjenovic_2013", "prior_inclusions": [1395, 4598, 400], "prior_exclusions": [2333, 4435, 3860]}
 {"dataset_id": "Muthu_2021", "prior_inclusions": [1454, 1940], "prior_exclusions": [1077]}