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Errors in update script #1

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oesteban opened this issue Jan 11, 2022 · 0 comments
Open

Errors in update script #1

oesteban opened this issue Jan 11, 2022 · 0 comments
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bug Something isn't working

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@oesteban
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2022-01-11T10:00:07.2110701Z # github.com:22 SSH-2.0-babeld-d2b829ee
2022-01-11T10:00:07.2875825Z Agent pid 16
2022-01-11T10:00:07.2952838Z Identity added: (stdin) ((stdin))
2022-01-11T10:00:07.2954826Z Installing TemplateFlow Archive super-dataset ...
2022-01-11T10:00:07.4989743Z [INFO] Cloning dataset to Dataset(/github/workspace/templateflow) 
2022-01-11T10:00:07.4991878Z [INFO] Attempting to clone from [email protected]:templateflow/templateflow.git to /github/workspace/templateflow 
2022-01-11T10:00:08.1086830Z [INFO] Start enumerating objects 
2022-01-11T10:00:08.1198294Z [INFO] Start counting objects 
2022-01-11T10:00:08.1322719Z [INFO] Start compressing objects 
2022-01-11T10:00:08.1517801Z [INFO] Start receiving objects 
2022-01-11T10:00:08.1938253Z [INFO] Start resolving deltas 
2022-01-11T10:00:08.2212651Z [INFO] Completed clone attempts for Dataset(/github/workspace/templateflow) 
2022-01-11T10:00:08.4178654Z [INFO] Unable to parse git config from origin 
2022-01-11T10:00:08.8846646Z [INFO] Remote origin does not have git-annex installed; setting annex-ignore 
2022-01-11T10:00:08.8856452Z [INFO] This could be a problem with the git-annex installation on the remote. Please make sure that git-annex-shell is available in PATH when you ssh into the remote. Once you have fixed the git-annex installation, run: git annex enableremote origin 
2022-01-11T10:00:08.9236367Z [INFO] access to 1 dataset sibling public-s3 not auto-enabled, enable with:
2022-01-11T10:00:08.9239522Z | 		datalad siblings -d "/github/workspace/templateflow" enable -s public-s3 
2022-01-11T10:00:08.9255659Z install(ok): /github/workspace/templateflow (dataset)
2022-01-11T10:00:08.9616488Z Installing template tpl-RESILIENT ...
2022-01-11T10:00:09.2069968Z [INFO] Cloning dataset to Dataset(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:09.2072082Z [INFO] Attempting to clone from [email protected]:templateflow/templateflow.git/tpl-RESILIENT to /github/workspace/templateflow/tpl-RESILIENT 
2022-01-11T10:00:09.6193200Z [INFO] Attempting to clone from https://github.com/templateflow/tpl-RESILIENT.git to /github/workspace/templateflow/tpl-RESILIENT 
2022-01-11T10:00:09.8716226Z [INFO] Start enumerating objects 
2022-01-11T10:00:09.8724232Z [INFO] Start counting objects 
2022-01-11T10:00:09.8758764Z [INFO] Start compressing objects 
2022-01-11T10:00:09.8811849Z [INFO] Start receiving objects 
2022-01-11T10:00:09.8925278Z [INFO] Start resolving deltas 
2022-01-11T10:00:09.9019257Z [INFO] Completed clone attempts for Dataset(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:10.2669633Z [INFO] Remote origin not usable by git-annex; setting annex-ignore 
2022-01-11T10:00:10.2713435Z [INFO] https://github.com/templateflow/tpl-RESILIENT.git/config download failed: Not Found 
2022-01-11T10:00:11.2879037Z [INFO] Reset branch 'master' to 776f4a6c (from 8e11fcf1) to avoid a detached HEAD 
2022-01-11T10:00:11.3095523Z install(ok): /github/workspace/templateflow/tpl-RESILIENT (dataset) [Installed subdataset in order to get /github/workspace/templateflow/tpl-RESILIENT]
2022-01-11T10:00:11.3467986Z Updating template tpl-RESILIENT ...
2022-01-11T10:00:11.4951655Z [WARNING] path constraints for subdataset updates ignored, because `recursive` option was not given 
2022-01-11T10:00:11.5084583Z [INFO] Fetching updates for Dataset(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:11.5086651Z [INFO] Start fetching remotes for AnnexRepo(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:11.5087913Z [INFO] Fetching remote origin 
2022-01-11T10:00:11.6723922Z [INFO] Fetching remote gin-src 
2022-01-11T10:00:12.1364304Z [INFO] Finished fetching remotes for AnnexRepo(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:12.2648779Z merge(ok): . (dataset) [Merged origin/master]
2022-01-11T10:00:12.2649733Z update(ok): . (dataset)
2022-01-11T10:00:12.2650511Z action summary:
2022-01-11T10:00:12.2651264Z   merge (ok: 1)
2022-01-11T10:00:12.2651989Z   update (ok: 1)
2022-01-11T10:00:12.2884818Z Configuring g-Node/GIN remote ...
2022-01-11T10:00:12.2886208Z /github/workspace/templateflow/tpl-RESILIENT /github/workspace/templateflow
2022-01-11T10:00:15.8147075Z .: gin(+) [https://gin.g-node.org/templateflow/tpl-RESILIENT (git)]
2022-01-11T10:00:16.0624149Z [ERROR] Could not deduce RI type for None [network.py:__new__:423] (ValueError) 
2022-01-11T10:00:16.3138582Z Pushing to g-Node/GIN ...
2022-01-11T10:00:16.4759895Z [INFO] Determine push target 
2022-01-11T10:00:16.4765908Z [INFO] Push refspecs 
2022-01-11T10:00:17.0268807Z Host key verification failed.
2022-01-11T10:00:17.0366116Z [INFO] Transfer data 
2022-01-11T10:00:17.2060278Z [INFO] Update availability information 
2022-01-11T10:00:17.8179924Z CommandError: 'git -c diff.ignoreSubmodules=none -c [email protected]:/templateflow/tpl-RESILIENT.git.insteadof=https://gin.g-node.org/templateflow/tpl-RESILIENT fetch gin git-annex' failed with exitcode 128 under /github/workspace/templateflow/tpl-RESILIENT
2022-01-11T10:00:17.8182211Z Host key verification failed.
2022-01-11T10:00:17.8184557Z ConnectionOpenFailedError: 'ssh -fN -o ControlMaster=auto -o ControlPersist=15m -o ControlPath=/github/home/.cache/datalad/sockets/04ae1e9d [email protected]' failed with exitcode 255 [Failed to open SSH connection (could not start ControlMaster process)]
2022-01-11T10:00:17.8186870Z fatal: Could not read from remote repository.
2022-01-11T10:00:17.8187455Z 
2022-01-11T10:00:17.8188259Z Please make sure you have the correct access rights
2022-01-11T10:00:17.8189217Z and the repository exists.
2022-01-11T10:00:17.8422006Z Pushing to GitHub ...
2022-01-11T10:00:18.0053908Z [INFO] Determine push target 
2022-01-11T10:00:18.0058090Z [INFO] Push refspecs 
2022-01-11T10:00:18.1017200Z [INFO] Transfer data 
2022-01-11T10:00:18.1018216Z [INFO] Update availability information 
2022-01-11T10:00:18.4038449Z CommandError: 'git -c diff.ignoreSubmodules=none push --progress --porcelain origin master git-annex:git-annex' failed with exitcode 128 under /github/workspace/templateflow/tpl-RESILIENT
2022-01-11T10:00:18.4041009Z fatal: could not read Username for 'https://github.com': No such device or address
2022-01-11T10:00:18.4284800Z Pushing super-dataset ...
2022-01-11T10:00:18.4285923Z /github/workspace/templateflow
2022-01-11T10:00:19.1539317Z add(ok): tpl-RESILIENT (file)
2022-01-11T10:00:19.1540400Z save(ok): . (dataset)
2022-01-11T10:00:19.1541536Z action summary:
2022-01-11T10:00:19.1542367Z   add (ok: 1)
2022-01-11T10:00:19.1543148Z   save (ok: 1)
2022-01-11T10:00:19.3395832Z [INFO] Determine push target 
2022-01-11T10:00:19.3403127Z [INFO] Push refspecs 
2022-01-11T10:00:19.9129590Z [INFO] Transfer data 
2022-01-11T10:00:19.9130620Z [INFO] Update availability information 
2022-01-11T10:00:20.7101579Z [INFO] Start enumerating objects 
2022-01-11T10:00:20.7108044Z [INFO] Start counting objects 
2022-01-11T10:00:20.7116941Z [INFO] Start compressing objects 
2022-01-11T10:00:20.7123657Z [INFO] Start writing objects 
2022-01-11T10:00:20.7603400Z [INFO] Start resolving deltas 
2022-01-11T10:00:21.0446071Z [INFO] Finished 
2022-01-11T10:00:21.0457450Z [INFO] Finished push of Dataset(/github/workspace/templateflow) 
2022-01-11T10:00:21.0463310Z publish(ok): . (dataset) [refs/heads/git-annex->origin:refs/heads/git-annex d45a637..e22b16f]
2022-01-11T10:00:21.0465014Z publish(ok): . (dataset) [refs/heads/master->origin:refs/heads/master dafec50..3321e07]
2022-01-11T10:00:21.0762451Z Exporting to S3 bucket ...
2022-01-11T10:00:21.3402688Z .: s3(?) [git]
2022-01-11T10:00:21.3642299Z /github/workspace/templateflow/tpl-RESILIENT /github/workspace/templateflow
2022-01-11T10:00:21.5700774Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-1 recursively 
2022-01-11T10:00:21.5723133Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-4 recursively 
2022-01-11T10:00:21.5756404Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-2 recursively 
2022-01-11T10:00:21.5779134Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-3 recursively 
2022-01-11T10:01:10.3471506Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3473568Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3475514Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3483627Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3485660Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3487518Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3489831Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3491544Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3493873Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3495936Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3497796Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3499620Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3501441Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3503232Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3506405Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3508269Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3510165Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3511867Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3513706Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3515374Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3517024Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3518556Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3520399Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3522286Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3523955Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3525632Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3527269Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3529266Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3530568Z get(ok): cohort-1 (directory)
2022-01-11T10:01:10.3531530Z get(ok): cohort-2 (directory)
2022-01-11T10:01:10.3532476Z get(ok): cohort-4 (directory)
2022-01-11T10:01:10.3533434Z get(ok): cohort-3 (directory)
2022-01-11T10:01:10.3534221Z action summary:
2022-01-11T10:01:10.3534998Z   get (notneeded: 2, ok: 32)
2022-01-11T10:01:10.4504117Z   Set both AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY to use S3
2022-01-11T10:01:10.4505284Z unexport s3 template_description.json 
2022-01-11T10:01:10.4506580Z failed
2022-01-11T10:01:10.5920691Z export s3 .datalad/.gitattributes ok
2022-01-11T10:01:10.6138665Z export s3 .datalad/config ok
2022-01-11T10:01:10.6359721Z export s3 .gitattributes ok
2022-01-11T10:01:10.6532299Z export s3 .github/workflows/update-superdataset.yml ok
2022-01-11T10:01:10.6720267Z export s3 LICENSE ok
2022-01-11T10:01:10.6908522Z export s3 cohort-1/tpl-RESILIENT_cohort-1_T1w.nii.gz ok
2022-01-11T10:01:10.7138210Z export s3 cohort-1/tpl-RESILIENT_cohort-1_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:10.7323382Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:10.7500965Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:10.7706206Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:10.7904963Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:10.8081949Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-brain_mask.nii.gz ok
2022-01-11T10:01:10.8270461Z export s3 cohort-2/tpl-RESILIENT_cohort-2_T1w.nii.gz ok
2022-01-11T10:01:10.8469561Z export s3 cohort-2/tpl-RESILIENT_cohort-2_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:10.8640272Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:10.8834516Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:10.9037333Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:10.9226817Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:10.9420451Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-brain_mask.nii.gz ok
2022-01-11T10:01:10.9629634Z export s3 cohort-3/tpl-RESILIENT_cohort-3_T1w.nii.gz ok
2022-01-11T10:01:10.9813594Z export s3 cohort-3/tpl-RESILIENT_cohort-3_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:11.0005282Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:11.0182650Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:11.0373811Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:11.0639476Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:11.0812388Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-brain_mask.nii.gz ok
2022-01-11T10:01:11.0993694Z export s3 cohort-4/tpl-RESILIENT_cohort-4_T1w.nii.gz ok
2022-01-11T10:01:11.1189594Z export s3 cohort-4/tpl-RESILIENT_cohort-4_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:11.1365474Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:11.1531792Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:11.1695269Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:11.1999317Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:11.2176213Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-brain_mask.nii.gz ok
2022-01-11T10:01:11.2350110Z export s3 template_description.json ok
2022-01-11T10:01:11.2502044Z (recording state in git...)
2022-01-11T10:01:11.2583808Z export: 1 failed
2022-01-11T10:01:11.2739091Z /github/workspace/templateflow
@oesteban oesteban added the bug Something isn't working label Jan 11, 2022
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