From a0aaa85dded056951b233fba1dfcfc4fd5d4f356 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Fri, 30 Jun 2023 15:03:06 -0700 Subject: [PATCH 01/13] fix: update post-command in user-license --- qa-heal.planx-pla.net/manifests/hatchery/hatchery.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json index 25ab8ee69..493164aa9 100644 --- a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json @@ -85,7 +85,7 @@ "lifecycle-post-start": [ "/bin/sh", "-c", - "(while true; do [ -d ~/pd ] && [ -f ~/pd/stata.lic ] && cp ~/pd/stata.lic /usr/local/stata17/; sleep 1; done) & export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" + "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" ], "user-uid": 1000, "fs-gid": 100, From 671591aeaeb8c9956d78285d6d477db8fc9ed7ca Mon Sep 17 00:00:00 2001 From: George Thomas Date: Wed, 5 Jul 2023 15:01:16 -0700 Subject: [PATCH 02/13] Use new branch for user license workspace --- qa-heal.planx-pla.net/manifests/hatchery/hatchery.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json index 493164aa9..2d811359c 100644 --- a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json @@ -68,7 +68,7 @@ "cpu-limit": "1.0", "memory-limit": "2Gi", "name": "(Generic, User-licensed) Stata Notebook ", - "image": "quay.io/cdis/stata-heal:master", + "image": "quay.io/cdis/stata-heal:feat_stata-license", "env": {}, "args": [ "--NotebookApp.base_url=/lw-workspace/proxy/", From 79a8b2c134c2fc8cefb37e3dc5c6a428b2a312e3 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Wed, 5 Jul 2023 15:03:45 -0700 Subject: [PATCH 03/13] Use new branch for user license workspace --- qa-heal.planx-pla.net/manifests/hatchery/hatchery.json | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json index bd6da7b2c..44c6191e3 100644 --- a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json @@ -68,15 +68,11 @@ "cpu-limit": "1.0", "memory-limit": "2Gi", "name": "(Generic, User-licensed) Stata Notebook ", -<<<<<<< HEAD "image": "quay.io/cdis/stata-heal:feat_stata-license", - "env": {}, -======= - "image": "quay.io/cdis/stata-heal:george-portal", + "env": { "FRAME_ANCESTORS": "https://qa-heal.planx-pla.net" }, ->>>>>>> 9c5e6cc91ce95657fb671bf65a6ac4dc529cbdec "args": [ "--NotebookApp.base_url=/lw-workspace/proxy/", "--NotebookApp.password=''", From 0334fe15d47bc07bc5498ede2ae1f9b1e39ac8b2 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Wed, 5 Jul 2023 15:04:27 -0700 Subject: [PATCH 04/13] Remove blank line --- qa-heal.planx-pla.net/manifests/hatchery/hatchery.json | 1 - 1 file changed, 1 deletion(-) diff --git a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json index 44c6191e3..55f9431fe 100644 --- a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json @@ -69,7 +69,6 @@ "memory-limit": "2Gi", "name": "(Generic, User-licensed) Stata Notebook ", "image": "quay.io/cdis/stata-heal:feat_stata-license", - "env": { "FRAME_ANCESTORS": "https://qa-heal.planx-pla.net" }, From 37aff044058afc6a49cec3d0c1b4fb62f39ad291 Mon Sep 17 00:00:00 2001 From: Pauline <4224001+paulineribeyre@users.noreply.github.com> Date: Wed, 12 Jul 2023 21:36:52 +0200 Subject: [PATCH 05/13] qa-jcoin update stata workspaces --- .../manifests/hatchery/hatchery.json | 39 +++++++++++++++++-- 1 file changed, 36 insertions(+), 3 deletions(-) diff --git a/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json b/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json index 13a61f368..1dbf84acd 100644 --- a/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json @@ -80,8 +80,8 @@ "target-port": 8888, "cpu-limit": "1.0", "memory-limit": "2Gi", - "name": "User-licensed Stata Notebook", - "image": "quay.io/cdis/stata-heal:master", + "name": "(Generic, User-licensed) Stata Notebook ", + "image": "quay.io/cdis/stata-heal:feat_stata-license", "env": { "FRAME_ANCESTORS": "https://qa-jcoin.planx-pla.net" }, @@ -101,7 +101,40 @@ "lifecycle-post-start": [ "/bin/sh", "-c", - "(while true; do [ -d ~/pd ] && [ -f ~/pd/stata.lic ] && cp ~/pd/stata.lic /usr/local/stata17/; sleep 1; done) & export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" + "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" + ], + "user-uid": 1000, + "fs-gid": 100, + "user-volume-location": "/home/jovyan/pd", + "gen3-volume-location": "/home/jovyan/.gen3" + }, + { + "target-port": 8888, + "cpu-limit": "1.0", + "memory-limit": "2Gi", + "name": "(Generic, Limited Gen3-licensed) Stata Notebook", + "image": "quay.io/cdis/stata-heal:jupyter_pystata_licensed__latest", + "env": { + "FRAME_ANCESTORS": "https://qa-jcoin.planx-pla.net" + }, + "args": [ + "--NotebookApp.base_url=/lw-workspace/proxy/", + "--NotebookApp.password=''", + "--NotebookApp.token=''", + "--NotebookApp.shutdown_no_activity_timeout=5400", + "--NotebookApp.quit_button=False" + ], + "command": [ + "/bin/bash", + "/tmp/wait_for_license.sh" + ], + "path-rewrite": "/lw-workspace/proxy/", + "use-tls": "false", + "ready-probe": "/lw-workspace/proxy/", + "lifecycle-post-start": [ + "/bin/sh", + "-c", + "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" ], "user-uid": 1000, "fs-gid": 100, From 338398e3f7ada0e7980b92d222ff352ff34c9dd6 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Fri, 14 Jul 2023 13:37:01 -0700 Subject: [PATCH 06/13] chore/update jupyter pystata repo name --- qa-heal.planx-pla.net/manifests/hatchery/hatchery.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json index 55f9431fe..c3ec37ea9 100644 --- a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json @@ -68,7 +68,7 @@ "cpu-limit": "1.0", "memory-limit": "2Gi", "name": "(Generic, User-licensed) Stata Notebook ", - "image": "quay.io/cdis/stata-heal:feat_stata-license", + "image": "quay.io/cdis/jupyter-pystata-user-licensed:feat_stata-license", "env": { "FRAME_ANCESTORS": "https://qa-heal.planx-pla.net" }, @@ -99,7 +99,7 @@ "cpu-limit": "1.0", "memory-limit": "2Gi", "name": "(Generic, Limited Gen3-licensed) Stata Notebook", - "image": "quay.io/cdis/stata-heal:jupyter_pystata_licensed__latest", + "image": "quay.io/cdis/jupyter-pystata-gen3-licensed:feat_stata-license", "env": { "FRAME_ANCESTORS": "https://qa-heal.planx-pla.net" }, From f62d2ae0010421656fbf919569989fa718f8ff46 Mon Sep 17 00:00:00 2001 From: Mingfei Shao <2475897+mfshao@users.noreply.github.com> Date: Mon, 17 Jul 2023 10:12:21 -0500 Subject: [PATCH 07/13] updates for new metadata format (#2531) --- .secrets.baseline | 210 ++++++++--------- qa-heal.planx-pla.net/manifest.json | 6 +- .../metadata/aggregate_config.json | 216 +++++++----------- qa-heal.planx-pla.net/portal/gitops.json | 129 ++--------- 4 files changed, 207 insertions(+), 354 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 7d7b64372..81f368733 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -75,6 +75,10 @@ { "path": "detect_secrets.filters.allowlist.is_line_allowlisted" }, + { + "path": "detect_secrets.filters.common.is_baseline_file", + "filename": ".secrets.baseline" + }, { "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", "min_level": 2 @@ -6927,714 +6931,714 @@ "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "e894c0677072bafbeb02f54595d584328e44e04c", "is_verified": false, - "line_number": 144 + "line_number": 137 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "5b5ed6f027020a9eba9483ca3583400a579326c6", "is_verified": false, - "line_number": 150 + "line_number": 143 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "518513f30e09f3aac67af3f7a3ace2dcce46401c", "is_verified": false, - "line_number": 156 + "line_number": 149 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f345f5bc9fb969aa1ead477ce0c89933e8da69d2", "is_verified": false, - "line_number": 162 + "line_number": 155 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "63ef9ab7e5f2c2bd7690117aa3e38cac54ecc067", "is_verified": false, - "line_number": 168 + "line_number": 161 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "3c34cd9b8fe6dd953e8ff02c6066fe6460a0a829", "is_verified": false, - "line_number": 174 + "line_number": 167 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "18bcd4ed4267206365091e054ada17f89a6d2a62", "is_verified": false, - "line_number": 180 + "line_number": 173 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "d7a9296e1517c85826ab949abaae07442f8f15fc", "is_verified": false, - "line_number": 279 + "line_number": 260 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "3a4a8a3057b65b67edc597200bb046599096a33c", "is_verified": false, - "line_number": 294 + "line_number": 275 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "26f4706f71ffaa7394698257a5f8b5744cad4655", "is_verified": false, - "line_number": 301 + "line_number": 282 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "476735d5922f7bf2ce403a7afb217864ff5cde60", "is_verified": false, - "line_number": 349 + "line_number": 330 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "dcba8bcf616d53d32351a2dad1e2cf2a2f344c52", "is_verified": false, - "line_number": 363 + "line_number": 344 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "fbda6414e58f721b8fb83ea02de930f6cd34c8e6", "is_verified": false, - "line_number": 370 + "line_number": 351 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "dde9364282d7afa55a107baa4d4d0ecbf80f4c8f", "is_verified": false, - "line_number": 377 + "line_number": 358 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "40f37fc310c50ae5a615f062ac109eadc14d3168", "is_verified": false, - "line_number": 384 + "line_number": 365 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "97a7db738d958338c7112931706bcbbb8df6bed4", "is_verified": false, - 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"line_number": 956 + "line_number": 900 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "9b68777479917d27b0ed60ef5a881524dd32d76e", "is_verified": false, - "line_number": 963 + "line_number": 907 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "d13a1bd4cc93d48d365bebe3a945d45b2a90c5a9", "is_verified": false, - "line_number": 982 + "line_number": 926 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "3111c9596494082a282733deec5cd35972541343", "is_verified": false, - "line_number": 985 + "line_number": 929 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "c13240f56f84c4a68a9f0765020df1b7dc57b3b4", "is_verified": false, - "line_number": 992 + "line_number": 936 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f1565b2bf1a1d9a827d196c42b86808d43fd3c5c", "is_verified": false, - "line_number": 999 + "line_number": 943 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "2e3c3459ae07130e7bd32755740431d73dee1bf5", "is_verified": false, - "line_number": 1006 + "line_number": 950 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "d856b7d922db2a8f3b995509b18b1df9731a1b01", "is_verified": false, - "line_number": 1013 + "line_number": 957 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "68f3e1f89974ee0a254ba5ad8e21f3875507de6f", "is_verified": false, - "line_number": 1034 + "line_number": 978 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "a70714f6811ca1984285a274d803d397a854f437", "is_verified": false, - "line_number": 1037 + "line_number": 981 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "6fc3b39e677ed0674bb766d511036cb644061b25", "is_verified": false, - "line_number": 1044 + "line_number": 988 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "59fd8c3f61f33197f02003e856946037d304692d", "is_verified": false, - "line_number": 1051 + "line_number": 995 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "cfc071d4b772406b421d6c11107af0452c7791a3", "is_verified": false, - "line_number": 1058 + "line_number": 1002 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "6497035d007fbb86db29830a98375a2d07441e26", "is_verified": false, - "line_number": 1077 + "line_number": 1021 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "60d65b9cd0ae04bf2d25698255f9fe9c97b5a9b3", "is_verified": false, - "line_number": 1080 + "line_number": 1024 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "36690c5f0476bf03772314800d25b8439bf0bc27", "is_verified": false, - "line_number": 1087 + "line_number": 1031 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "e6792e08a82410fff9037572786261320ce41799", "is_verified": false, - "line_number": 1094 + "line_number": 1038 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "4b3732ebb3fde431f4f3754c3e37cfbfd39ebc75", "is_verified": false, - "line_number": 1101 + "line_number": 1045 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "e301ed844716902def444c1ce6224999da4b5443", "is_verified": false, - "line_number": 1120 + "line_number": 1064 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "1677089ffb27fe27f8eb47b005d595adb249eaba", "is_verified": false, - "line_number": 1123 + "line_number": 1067 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "5c4e740e6edcce4b32ba215f376c46ff685f84ba", "is_verified": false, - "line_number": 1130 + "line_number": 1074 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "e42f676bca01cfa08a9dd66221ba4c1c965f8d4a", "is_verified": false, - "line_number": 1137 + "line_number": 1081 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f2b5ccaff2ce715767e90ba4ee942cb49c269e04", "is_verified": false, - "line_number": 1144 + "line_number": 1088 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "4829156f57536223a66876c11203f0232f16b0ba", "is_verified": false, - "line_number": 1163 + "line_number": 1107 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f6f71352db31c6a057b4f37e9dda102366e5e2ff", "is_verified": false, - "line_number": 1166 + "line_number": 1110 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "df8364d52aabf1d380a99bfb0ef6d6a34de461a6", "is_verified": false, - "line_number": 1173 + "line_number": 1117 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "632db2776362cbd194bcecda2f3a011ef09f0e5d", "is_verified": false, - "line_number": 1180 + "line_number": 1124 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "2bfc4e00f3a391f240d8cb6702b2daba2ef5fb26", "is_verified": false, - "line_number": 1187 + "line_number": 1131 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "93ef759d083104f19ae77c221f76a7d8a679a710", "is_verified": false, - "line_number": 1209 + "line_number": 1153 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "25988519ec331829f445662006767e0dd0abc130", "is_verified": false, - "line_number": 1216 + "line_number": 1160 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "43b25a71a5cf1293710ba14ba6ab577a1ae35563", "is_verified": false, - "line_number": 1223 + "line_number": 1167 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f7fddcb97ba38b1ca1979eb1de3088b812bdd834", "is_verified": false, - "line_number": 1230 + "line_number": 1174 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "b11396ee35dd076a7f08a2d02bfcdb9fd2c0b3ee", "is_verified": false, - "line_number": 1249 + "line_number": 1193 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "b364e8eafbf161dc1789e1e099be2c07f7690ecb", "is_verified": false, - "line_number": 1252 + "line_number": 1196 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "0b2a961e1f852d93ee413d2dbcfe2e09637ae92a", "is_verified": false, - "line_number": 1259 + "line_number": 1203 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "9860b5f9b5478bdb72cfeb2a6f40c7eb7106755e", "is_verified": false, - "line_number": 1266 + "line_number": 1210 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "a709cddb975dedf3c0a6931a710937206f734758", "is_verified": false, - "line_number": 1273 + "line_number": 1217 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f720282990073f87db353f82c9fe11bb5fd17330", "is_verified": false, - "line_number": 1292 + "line_number": 1236 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "cfe6faa430f539de6a804046e9f92f97c5573431", "is_verified": false, - "line_number": 1295 + "line_number": 1239 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "5c0e0176bf11adac3253cca8c4c2fe350f59eb73", "is_verified": false, - "line_number": 1302 + "line_number": 1246 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "79cde8590d0dedc41f2c0f1fdca767f0f5f6b2aa", "is_verified": false, - "line_number": 1309 + "line_number": 1253 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "35358c7055a2a6a8997239918588e01ed6ae1392", "is_verified": false, - "line_number": 1316 + "line_number": 1260 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "5a2cf84d549c25cf8c117adc380e8d501b6c3c82", "is_verified": false, - "line_number": 1335 + "line_number": 1279 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "2ab98077a4a68016d72b75f4d22fef06db6fd605", "is_verified": false, - "line_number": 1338 + "line_number": 1282 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "68463d5b987ed3868e08bd30c3ec5be831b952b7", "is_verified": false, - "line_number": 1345 + "line_number": 1289 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "ef62359609ac68617f0a01a4419a3dbd9af64f5c", "is_verified": false, - "line_number": 1352 + "line_number": 1296 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "963db3117b5c98e3645a9cdd9d77df9e5feb1302", "is_verified": false, - "line_number": 1359 + "line_number": 1303 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "8ed37aa21f5c9f21ade6e4dd2527bfde5c71ff87", "is_verified": false, - "line_number": 1378 + "line_number": 1322 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "e128ecc842f57ce57e883cc0ab67eaac557c520e", "is_verified": false, - "line_number": 1381 + "line_number": 1325 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "3bcefddae71fd94340005f4b81c06ff1644a9643", "is_verified": false, - "line_number": 1388 + "line_number": 1332 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "d4f7da97231deec20a5de30a8f9ec36cda85cf9c", "is_verified": false, - "line_number": 1395 + "line_number": 1339 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "499dd9a0da3623a288ad3c2bb6c08c787a4750f5", "is_verified": false, - "line_number": 1402 + "line_number": 1346 } ], "qa-ibd.planx-pla.net/manifest.json": [ @@ -7711,5 +7715,5 @@ } ] }, - "generated_at": "2023-07-06T21:37:41Z" + "generated_at": "2023-07-17T14:30:08Z" } diff --git a/qa-heal.planx-pla.net/manifest.json b/qa-heal.planx-pla.net/manifest.json index 34c2b2bef..650b47655 100644 --- a/qa-heal.planx-pla.net/manifest.json +++ b/qa-heal.planx-pla.net/manifest.json @@ -11,7 +11,7 @@ "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.06", "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.06", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.2.0", + "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:feat_mds-update", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.06", "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.06", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", @@ -20,10 +20,10 @@ "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.06", "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.1.1", "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.06", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.06", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:feat_nested-fields", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.06", "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2023.06", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.7.1", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:feat_supportNestedFieldNames", "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2023.06", "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.06", "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.06", diff --git a/qa-heal.planx-pla.net/metadata/aggregate_config.json b/qa-heal.planx-pla.net/metadata/aggregate_config.json index 9aed79a6d..020c96692 100644 --- a/qa-heal.planx-pla.net/metadata/aggregate_config.json +++ b/qa-heal.planx-pla.net/metadata/aggregate_config.json @@ -18,8 +18,11 @@ "type": "string" }, "investigators_name": { - "type": "string", - "default": "" + "type": "array", + "items": { + "type": "string" + }, + "default": [] }, "_hdp_uid": { "type": "string" @@ -31,65 +34,55 @@ "type": "array", "default": [] }, - "Data": { - "type": "object" - }, - "Data Availability": { + "study_metadata": { "type": "object", - "properties": { - "data_collection_finish_date": { - "type": "date" - }, - "data_collection_start_date": { - "type": "date" - }, - "data_release_finish_date": { - "type": "date" - }, - "data_release_start_date": { - "type": "date" + "data": { + "type": "object" + }, + "data_availability": { + "type": "object", + "properties": { + "data_collection_finish_date": { + "type": "date" + }, + "data_collection_start_date": { + "type": "date" + }, + "data_release_finish_date": { + "type": "date" + }, + "data_release_start_date": { + "type": "date" + } } + }, + "human_condition_applicability": { + "type": "object" + }, + "human_subject_applicability": { + "type": "object" + }, + "human_treatment_applicability": { + "type": "object" + }, + "metadata_location": { + "type": "object", + "properties": { + "other_study_websites": { + "type": "array" + } + } + }, + "minimal_info": { + "type": "object" + }, + "study_translational_focus": { + "type": "object" + }, + "study_type": { + "type": "object" } }, - "Human Condition Applicability": { - "type": "object" - }, - "Human Subject Applicability": { - "type": "object" - }, - "Human Treatment Applicability": { - "type": "object" - }, - "Metadata Location": { - "type": "object" - }, - "Minimal Info": { - "type": "object" - }, - "Study Translational Focus": { - "type": "object" - }, - "Study Type": { - "type": "object" - }, - "budget_start": { - "type": "date" - }, - "budget_end": { - "type": "date" - }, - "project_end_date": { - "type": "date" - }, - "date_added": { - "type": "date" - }, - "award_notice_date": { - "type": "date" - }, - "project_start_date": { - "type": "date" - }, "study_description_summary": {}, "project_title": {} }, @@ -138,7 +131,7 @@ "commons_url": "https://qa-heal.planx-pla.net/" }, "per_item_values": { - "9898044": { + "HDP00258": { "__manifest": [ { "md5sum": "459b157ad875428cda0c85e53b38eae9", @@ -193,7 +186,6 @@ "commons_name": "JCOIN", "keep_original_fields": true, "field_mappings": { - "_unique_id": "path:project_number", "_hdp_uid": "path:project_number", "__manifest": "path:__manifest" } @@ -219,56 +211,45 @@ "field_mappings": { "tags": [], "authz": "", - "sites": "", "study_description_summary": { "path": "description", "filters": [ "strip_html" ] }, + "study_metadata.minimal_info.study_description": { + "path": "description", + "filters": [ + "strip_html" + ] + }, "study_url": { "path": "ipcsr_study_id", "filters": [ "add_icpsr_source_url" ] }, + "study_metadata.metadata_location.other_study_websites": { + "path": "ipcsr_study_id", + "filters": [ + "add_icpsr_source_url" + ] + }, "location": "path:coverage[0]", - "subjects": "", "__manifest": "", - "study_name_title": "", "study_type": "", "institutions": "path:contributor", "year_awarded": "", "investigators_name": "path:creator", "project_title": "path:title", - "protocol_name": "", - "study_summary": "", - "dataset_1_type": "", - "dataset_2_type": "", - "dataset_3_type": "", - "dataset_4_type": "", - "dataset_5_type": "", + "study_metadata.minimal_info.study_name": "path:title", "project_number": "path:identifier", "_hdp_uid": "path:identifier", - "dataset_1_title": "", - "dataset_2_title": "", - "dataset_3_title": "", - "dataset_4_title": "", - "dataset_5_title": "", "administering_ic": "", "advSearchFilters": [], "dataset_category": "path:type", "research_program": "", - "research_question": "", - "study_description": "", - "clinical_trial_link": "", - "dataset_description": "", "research_focus_area": "", - "dataset_1_description": "", - "dataset_2_description": "", - "dataset_3_description": "", - "dataset_4_description": "", - "dataset_5_description": "", "data_availability": "pending", "data_resource": "ICPSR" }, @@ -455,51 +436,35 @@ "field_mappings": { "tags": [], "authz": "/programs/open", - "sites": "", "study_description_summary": "path:BriefSummary", + "study_metadata.minimal_info.study_description": "path:BriefSummary", "study_url": { "path": "NCTId", "filters": [ "add_clinical_trials_source_url" ] }, + "study_metadata.metadata_location.other_study_websites": { + "path": "NCTId", + "filters": [ + "add_clinical_trials_source_url" + ] + }, + "study_metadata.metadata_location.clinical_trials_study_ID": "path:NCTId", "location": "", "subjects": "path:EnrollmentCount", "__manifest": "", - "study_name_title": "", - "study_type": "", "institutions": "path:LeadSponsorName", "year_awarded": "", "investigators_name": "path:OverallOfficial[0].OverallOfficialName", "project_title": "path:BriefTitle", - "protocol_name": "", - "study_summary": "", - "dataset_1_type": "", - "dataset_2_type": "", - "dataset_3_type": "", - "dataset_4_type": "", - "dataset_5_type": "", + "study_metadata.minimal_info.study_name": "path:BriefTitle", "project_number": "path:OrgStudyId", "_hdp_uid": "path:OrgStudyId", - "dataset_1_title": "", - "dataset_2_title": "", - "dataset_3_title": "", - "dataset_4_title": "", - "dataset_5_title": "", - "administering_ic": "", "advSearchFilters": [], "dataset_category": "", "research_program": "", - "research_question": "", - "study_description": "", - "clinical_trial_link": "", - "dataset_description": "", "research_focus_area": "", - "dataset_1_description": "", - "dataset_2_description": "", - "dataset_3_description": "", - "dataset_4_description": "", - "dataset_5_description": "", "data_availability": "pending", "data_resource": "CinicalTrials.gov" }, @@ -659,55 +624,34 @@ "field_mappings": { "tags": [], "authz": "", - "sites": "", "study_description_summary": { "path": "description", "filters": [ "strip_html" ] }, + "study_metadata.minimal_info.study_description": { + "path": "description", + "filters": [ + "strip_html" + ] + }, "location": "United States", - "subjects": "", "__manifest": "", - "study_name_title": "", "study_type": "", "institutions": "Center for Public Health Law Research at the Temple University Beasley School of Law", "year_awarded": "", "investigators_name": "", "project_title": "path:title", - "protocol_name": "", - "study_summary": { - "path": "description", - "filters": [ - "strip_html" - ] - }, - "dataset_1_type": "", - "dataset_2_type": "", - "dataset_3_type": "", - "dataset_4_type": "", - "dataset_5_type": "", + "study_metadata.minimal_info.study_name": "path:title", "project_number": "path:id", "_hdp_uid": "path:id", - "dataset_1_title": "", - "dataset_2_title": "", - "dataset_3_title": "", - "dataset_4_title": "", - "dataset_5_title": "", "administering_ic": "NIDA", "advSearchFilters": [], "dataset_category": "", "research_program": "", - "research_question": "", "study_description": "Observational", - "clinical_trial_link": "", - "dataset_description": "", "research_focus_area": "", - "dataset_1_description": "", - "dataset_2_description": "", - "dataset_3_description": "", - "dataset_4_description": "", - "dataset_5_description": "", "data_availability": "pending", "data_resource": "PDAPS" }, diff --git a/qa-heal.planx-pla.net/portal/gitops.json b/qa-heal.planx-pla.net/portal/gitops.json index a35c333ff..5bfa630dd 100644 --- a/qa-heal.planx-pla.net/portal/gitops.json +++ b/qa-heal.planx-pla.net/portal/gitops.json @@ -149,14 +149,12 @@ "enabled": true, "inputSubtitle": "Examples: pain, buprenorphine, intervention", "searchableTextFields": [ - "study_description_summary", - "location", - "study_name_title", + "study_metadata.minimal_info.study_description", "institutions", "investigators_name", - "project_title", + "study_metadata.minimal_info.study_name", "project_number", - "appl_id", + "study_metadata.metadata_location.nih_application_id", "_hdp_uid", "dataset_1_title", "dataset_2_title", @@ -164,7 +162,6 @@ "dataset_4_title", "administering_ic", "research_program", - "research_question", "dataset_description", "dataset_1_description", "dataset_2_description", @@ -215,7 +212,7 @@ "studyColumns": [ { "name": "Project Title", - "field": "project_title", + "field": "study_metadata.minimal_info.study_name", "errorIfNotAvailable": false, "valueIfNotAvailable": "n/a" }, @@ -234,14 +231,14 @@ ], "studyPreviewField": { "name": "Summary", - "field": "study_description_summary", + "field": "study_metadata.minimal_info.study_description", "contentType": "string", "includeName": false, "includeIfNotAvailable": true, "valueIfNotAvailable": "No summary has been provided for this study." }, "detailView": { - "headerField": "project_title", + "headerField": "study_metadata.minimal_info.study_name", "tabs": [ { "tabName": "Study", @@ -251,7 +248,7 @@ "fields": [ { "type": "block", - "sourceField": "study_description_summary" + "sourceField": "study_metadata.minimal_info.study_description" } ] }, @@ -285,12 +282,6 @@ "label": "Research Program", "sourceField": "research_program", "default": "Not specified" - }, - { - "type": "text", - "label": "Research Question", - "sourceField": "research_question", - "default": "Not specified" } ] }, @@ -303,12 +294,6 @@ "sourceField": "institutions", "default": "Not specified" }, - { - "type": "text", - "label": "Location", - "sourceField": "location", - "default": "Not specified" - }, { "type": "text", "label": "Investigator(s)", @@ -370,8 +355,8 @@ }, { "type": "text", - "label": "Clinical Trial Link", - "sourceField": "clinical_trial_link", + "label": "Clinical Trial ID", + "sourceField": "study_metadata.metadata_location.clinical_trials_study_ID", "default": "Not specified" }, { @@ -487,36 +472,6 @@ } ] }, - { - "header": "Datasets", - "fields": [ - { - "type": "textList", - "sourceField": "study_list_of_data_files", - "label": "Study List of Data Files" - }, - { - "type": "textList", - "sourceField": "study_list_of_code_files", - "label": "Study List of Code Files" - }, - { - "type": "textList", - "sourceField": "study_list_of_documentation_files", - "label": "Study List of Documentation Files" - }, - { - "type": "text", - "sourceField": "dataset_category", - "label": "Dataset Category" - }, - { - "type": "text", - "sourceField": "study_data_last_update_date_time", - "label": "Study Data Last Update Date Time" - } - ] - }, { "header": "Data Availability", "fields": [ @@ -526,56 +481,6 @@ "label": "Data Availability" } ] - }, - { - "header": "Data Details", - "fields": [ - { - "type": "text", - "sourceField": "data_orientation", - "label": "Data Orientation" - }, - { - "type": "text", - "sourceField": "data_genre", - "label": "Data Genre" - }, - { - "type": "text", - "sourceField": "data_source", - "label": "Data Source" - }, - { - "type": "text", - "sourceField": "subject_data_unit_of_collection", - "label": "Subject Data Unit of Collection" - }, - { - "type": "text", - "sourceField": "subject_data_unit_of_analysis", - "label": "Subject Data Unit of Analysis" - }, - { - "type": "text", - "sourceField": "subject_data_unit_of_collection_expected_number", - "label": "Subject Data Unit of Collection Expected Number" - }, - { - "type": "text", - "sourceField": "subject_data_unit_of_analysis_expected_number", - "label": "Subject Data Unit of Analysis Expected Number" - }, - { - "type": "text", - "sourceField": "geographic_data_level_collected", - "label": "Georgraphic Data Level Collected" - }, - { - "type": "text", - "sourceField": "geographic_data_level_available", - "label": "Georgraphic Data Level Available" - } - ] } ] }, @@ -586,23 +491,23 @@ "header": "Resources/Repositories", "fields": [ { - "label": "Distributor Repository URL", - "sourceField": "distributor_repository_url", + "label": "Repository URL", + "sourceField": "repository_url", "type": "link" }, { - "label": "Repository Study ID", - "sourceField": "repository_study_id", + "label": "Repository Names", + "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_name", "type": "text" }, { - "label": "Distributory Repository Name", - "sourceField": "distributor_repository_name", + "label": "Repository Study IDs", + "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_study_ID", "type": "text" }, { - "label": "Repository ID", - "sourceField": "distributor_repository_id", + "label": "Repository Persistent IDs", + "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_persistent_ID", "type": "text" }, { From 4c4e6424d57b1574405b6e61fa99d11f058233b9 Mon Sep 17 00:00:00 2001 From: Mingfei Shao <2475897+mfshao@users.noreply.github.com> Date: Mon, 17 Jul 2023 17:11:55 -0500 Subject: [PATCH 08/13] fix: add back missing fields (#2532) --- .secrets.baseline | 192 +++++++++--------- .../metadata/aggregate_config.json | 10 + 2 files changed, 106 insertions(+), 96 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 81f368733..20b9f803c 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -6980,665 +6980,665 @@ "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "d7a9296e1517c85826ab949abaae07442f8f15fc", "is_verified": false, - "line_number": 260 + "line_number": 265 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "3a4a8a3057b65b67edc597200bb046599096a33c", "is_verified": false, - "line_number": 275 + "line_number": 280 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "26f4706f71ffaa7394698257a5f8b5744cad4655", "is_verified": false, - "line_number": 282 + "line_number": 287 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "476735d5922f7bf2ce403a7afb217864ff5cde60", "is_verified": false, - "line_number": 330 + "line_number": 335 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "dcba8bcf616d53d32351a2dad1e2cf2a2f344c52", "is_verified": false, - "line_number": 344 + "line_number": 349 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "fbda6414e58f721b8fb83ea02de930f6cd34c8e6", "is_verified": false, - "line_number": 351 + "line_number": 356 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "dde9364282d7afa55a107baa4d4d0ecbf80f4c8f", "is_verified": false, - 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"line_number": 1153 + "line_number": 1163 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "25988519ec331829f445662006767e0dd0abc130", "is_verified": false, - "line_number": 1160 + "line_number": 1170 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "43b25a71a5cf1293710ba14ba6ab577a1ae35563", "is_verified": false, - "line_number": 1167 + "line_number": 1177 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f7fddcb97ba38b1ca1979eb1de3088b812bdd834", "is_verified": false, - "line_number": 1174 + "line_number": 1184 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "b11396ee35dd076a7f08a2d02bfcdb9fd2c0b3ee", "is_verified": false, - "line_number": 1193 + "line_number": 1203 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "b364e8eafbf161dc1789e1e099be2c07f7690ecb", "is_verified": false, - "line_number": 1196 + "line_number": 1206 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "0b2a961e1f852d93ee413d2dbcfe2e09637ae92a", "is_verified": false, - "line_number": 1203 + "line_number": 1213 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "9860b5f9b5478bdb72cfeb2a6f40c7eb7106755e", "is_verified": false, - "line_number": 1210 + "line_number": 1220 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "a709cddb975dedf3c0a6931a710937206f734758", "is_verified": false, - "line_number": 1217 + "line_number": 1227 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "f720282990073f87db353f82c9fe11bb5fd17330", "is_verified": false, - "line_number": 1236 + "line_number": 1246 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "cfe6faa430f539de6a804046e9f92f97c5573431", "is_verified": false, - "line_number": 1239 + "line_number": 1249 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "5c0e0176bf11adac3253cca8c4c2fe350f59eb73", "is_verified": false, - "line_number": 1246 + "line_number": 1256 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "79cde8590d0dedc41f2c0f1fdca767f0f5f6b2aa", "is_verified": false, - "line_number": 1253 + "line_number": 1263 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "35358c7055a2a6a8997239918588e01ed6ae1392", "is_verified": false, - "line_number": 1260 + "line_number": 1270 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "5a2cf84d549c25cf8c117adc380e8d501b6c3c82", "is_verified": false, - "line_number": 1279 + "line_number": 1289 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "2ab98077a4a68016d72b75f4d22fef06db6fd605", "is_verified": false, - "line_number": 1282 + "line_number": 1292 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "68463d5b987ed3868e08bd30c3ec5be831b952b7", "is_verified": false, - "line_number": 1289 + "line_number": 1299 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "ef62359609ac68617f0a01a4419a3dbd9af64f5c", "is_verified": false, - "line_number": 1296 + "line_number": 1306 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "963db3117b5c98e3645a9cdd9d77df9e5feb1302", "is_verified": false, - "line_number": 1303 + "line_number": 1313 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "8ed37aa21f5c9f21ade6e4dd2527bfde5c71ff87", "is_verified": false, - "line_number": 1322 + "line_number": 1332 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "e128ecc842f57ce57e883cc0ab67eaac557c520e", "is_verified": false, - "line_number": 1325 + "line_number": 1335 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "3bcefddae71fd94340005f4b81c06ff1644a9643", "is_verified": false, - "line_number": 1332 + "line_number": 1342 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "d4f7da97231deec20a5de30a8f9ec36cda85cf9c", "is_verified": false, - "line_number": 1339 + "line_number": 1349 }, { "type": "Hex High Entropy String", "filename": "qa-heal.planx-pla.net/metadata/aggregate_config.json", "hashed_secret": "499dd9a0da3623a288ad3c2bb6c08c787a4750f5", "is_verified": false, - "line_number": 1346 + "line_number": 1356 } ], "qa-ibd.planx-pla.net/manifest.json": [ @@ -7715,5 +7715,5 @@ } ] }, - "generated_at": "2023-07-17T14:30:08Z" + "generated_at": "2023-07-17T21:46:18Z" } diff --git a/qa-heal.planx-pla.net/metadata/aggregate_config.json b/qa-heal.planx-pla.net/metadata/aggregate_config.json index 020c96692..83d51a43f 100644 --- a/qa-heal.planx-pla.net/metadata/aggregate_config.json +++ b/qa-heal.planx-pla.net/metadata/aggregate_config.json @@ -250,6 +250,11 @@ "dataset_category": "path:type", "research_program": "", "research_focus_area": "", + "dataset_1_title": "", + "dataset_2_title": "", + "dataset_3_title": "", + "dataset_4_title": "", + "dataset_5_title": "", "data_availability": "pending", "data_resource": "ICPSR" }, @@ -652,6 +657,11 @@ "research_program": "", "study_description": "Observational", "research_focus_area": "", + "dataset_1_title": "", + "dataset_2_title": "", + "dataset_3_title": "", + "dataset_4_title": "", + "dataset_5_title": "", "data_availability": "pending", "data_resource": "PDAPS" }, From 51d749fa01eed3803d74358457925c9ebb5b4e23 Mon Sep 17 00:00:00 2001 From: Mingfei Shao <2475897+mfshao@users.noreply.github.com> Date: Mon, 17 Jul 2023 21:30:07 -0500 Subject: [PATCH 09/13] Update manifest.json (#2533) --- qa-heal.planx-pla.net/manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qa-heal.planx-pla.net/manifest.json b/qa-heal.planx-pla.net/manifest.json index 650b47655..5b0afaa7a 100644 --- a/qa-heal.planx-pla.net/manifest.json +++ b/qa-heal.planx-pla.net/manifest.json @@ -17,7 +17,7 @@ "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "frontend-framework": "quay.io/cdis/frontend-framework:0.4.6", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.06", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.06", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:5.0.1", "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.1.1", "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.06", "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:feat_nested-fields", From 2e215f00b74e7208a9fd1701eba09ab507b9b993 Mon Sep 17 00:00:00 2001 From: Michy-Chan Date: Tue, 18 Jul 2023 10:34:37 -0500 Subject: [PATCH 10/13] update agg config for Canine Study Name --- qa-brh.planx-pla.net/metadata/aggregate_config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qa-brh.planx-pla.net/metadata/aggregate_config.json b/qa-brh.planx-pla.net/metadata/aggregate_config.json index 4f9ad1944..01d734238 100644 --- a/qa-brh.planx-pla.net/metadata/aggregate_config.json +++ b/qa-brh.planx-pla.net/metadata/aggregate_config.json @@ -193,7 +193,7 @@ "study_id": "path:clinical_study_designation", "study_description": "", "full_name": "path:clinical_study_name", - "short_name": "N/A", + "short_name": "path:clinical_study_name", "commons": "CRDC Integrated Canine Data Commons", "study_url": "N/A", "_subjects_count" : {"path":"numberOfCases", "default" : 0 }, From 4574968bff8d0f8b3a177244c0abec375a9c61e1 Mon Sep 17 00:00:00 2001 From: briennal <111100165+briennal@users.noreply.github.com> Date: Tue, 18 Jul 2023 12:37:29 -0400 Subject: [PATCH 11/13] Update manifest.json Update IndexD to 5.0.1 to resolve drs-pull command issues --- qa-brh.planx-pla.net/manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qa-brh.planx-pla.net/manifest.json b/qa-brh.planx-pla.net/manifest.json index b2c9b201b..039726952 100644 --- a/qa-brh.planx-pla.net/manifest.json +++ b/qa-brh.planx-pla.net/manifest.json @@ -14,7 +14,7 @@ "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.06", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.06", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.06", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:5.0.1", "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.1.2", "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.06", "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.06", From 3267be4b73877c497dc6d44c575886718e95a5e3 Mon Sep 17 00:00:00 2001 From: J Montgomery Maxwell Date: Tue, 18 Jul 2023 15:17:41 -0500 Subject: [PATCH 12/13] test new generic workspace iamge --- qa-brh.planx-pla.net/manifests/hatchery/hatchery.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/qa-brh.planx-pla.net/manifests/hatchery/hatchery.json b/qa-brh.planx-pla.net/manifests/hatchery/hatchery.json index 92cd7661c..59ece634f 100755 --- a/qa-brh.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-brh.planx-pla.net/manifests/hatchery/hatchery.json @@ -36,7 +36,7 @@ "cpu-limit": "2.0", "memory-limit": "8Gi", "name": "(Generic) Jupyter Lab Notebook with R Kernel", - "image": "quay.io/cdis/jupyter-superslim-r:1.0.4", + "image": "quay.io/cdis/brh-notebooks:generic_rkernel__74bc13c4cf39a164daec18234d9adfd4678a50e5", "env": { "FRAME_ANCESTORS": "https://qa-brh.planx-pla.net" }, @@ -133,4 +133,4 @@ "gen3-volume-location": "/home/jovyan/.gen3" } ] -} \ No newline at end of file +} From 870d3d703098231adfc6627dd3c964f3acbdc2ee Mon Sep 17 00:00:00 2001 From: PlanXCyborg <38964842+PlanXCyborg@users.noreply.github.com> Date: Fri, 21 Jul 2023 11:28:56 -0500 Subject: [PATCH 13/13] Updating CI env with integration202308 qa-ibd.planx-pla.net 1689781147 (#2540) * apply version integration202308 to qa-ibd.planx-pla.net * apply version integration202308 to qa-ibd.planx-pla.net * dummy commit --------- Co-authored-by: Hara Prasad Co-authored-by: Atharva Rane <41084525+atharvar28@users.noreply.github.com> --- qa-ibd.planx-pla.net/manifest.json | 52 +++++++++---------- .../manifests/hatchery/hatchery.json | 4 +- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/qa-ibd.planx-pla.net/manifest.json b/qa-ibd.planx-pla.net/manifest.json index 3c0410658..cd8a9d281 100644 --- a/qa-ibd.planx-pla.net/manifest.json +++ b/qa-ibd.planx-pla.net/manifest.json @@ -1,32 +1,32 @@ { "notes": [ - "This is the qa environment manifest.", + "This is the qa environment manifest", "That's all I have to say." ], "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.06", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.06", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:integration202308", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:integration202308", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.06", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.06", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.06", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.06", - "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2023.06", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.06", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.06", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.8.0", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:integration202308", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:integration202308", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:integration202308", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:integration202308", + "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:integration202308", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:integration202308", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:integration202308", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:integration202308", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.06", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2023.06", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.06", - "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2023.06", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.06", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:integration202308", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:integration202308", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:integration202308", + "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:integration202308", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:integration202308", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.06", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:0.16.1", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.06", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.06", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.06" + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:integration202308", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:integration202308", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:integration202308", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:integration202308", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:integration202308" }, "indexd": { "arborist": "true" @@ -39,7 +39,7 @@ "serviceAccountName": "jobs-qa-ibd-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2023.06", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:integration202308", "pull_policy": "Always", "env": [ { @@ -79,7 +79,7 @@ "serviceAccountName": "jobs-qa-ibd-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2023.06", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:integration202308", "pull_policy": "Always", "env": [ { @@ -119,7 +119,7 @@ "serviceAccountName": "jobs-qa-ibd-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2023.06", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:integration202308", "pull_policy": "Always", "env": [ { @@ -156,7 +156,7 @@ ], "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.06" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:integration202308" } }, "global": { @@ -210,4 +210,4 @@ "arborist": { "deployment_version": "2" } -} \ No newline at end of file +} diff --git a/qa-ibd.planx-pla.net/manifests/hatchery/hatchery.json b/qa-ibd.planx-pla.net/manifests/hatchery/hatchery.json index 43b414465..8e34d7f58 100644 --- a/qa-ibd.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-ibd.planx-pla.net/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2023.06", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:integration202308", "env": { "NAMESPACE": "qa-ibd", "HOSTNAME": "qa-ibd.planx-pla.net" @@ -230,4 +230,4 @@ "user-volume-location": "/home/jovyan/pd" } ] -} +} \ No newline at end of file