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ebi-ait / hca-ebi-dev-team

Repository for hca ebi dev team agile management. See zenhub board
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Error creating test data pull request #506

Closed ami-day closed 1 year ago

ami-day commented 2 years ago

See https://github.com/HumanCellAtlas/schema-test-data/issues/25

ESapenaVentura commented 1 year ago

@ami-day to regenerate test data with a mock file

ami-day commented 1 year ago

Done, project uuid is: 4a77b2c4-da3c-4391-a345-12be491e199b Still getting connectivity issues even though my wifi at campus and home are working as usual.

Enumerating objects: 60, done. Counting objects: 100% (60/60), done. Delta compression using up to 8 threads Compressing objects: 100% (45/45), done. Writing objects: 78% (37/47), 145.62 MiB | 569.00 KiB/s

It stays at 78% for what seems like forever

ami-day commented 1 year ago 
(gsutil) C02ZL0J4LVDN:schema-test-data ami$ sh src/pull_test_data.sh
Please input the test project UUID
4a77b2c4-da3c-4391-a345-12be491e199b
yes
Verifying it's a valid project UUID
200
Found project in ingest
Pushing the dataset to the branch, please make sure you have gsutil configured
fatal: A branch named 'release-data-04/10/2022' already exists.

WARNING: gsutil rsync uses hashes when modification time is not available at
both the source and destination. Your crcmod installation isn't using the
module's C extension, so checksumming will run very slowly. If this is your
first rsync since updating gsutil, this rsync can take significantly longer than
usual. For help installing the extension, please see "gsutil help crcmod".

Building synchronization state...
If you experience problems with multiprocessing on MacOS, they might be related to https://bugs.python.org/issue33725. You can disable multiprocessing by editing your .boto config or by adding the following flag to your command: `-o "GSUtil:parallel_process_count=1"`. Note that multithreading is still available even if you disable multiprocessing.

Starting synchronization...
If you experience problems with multiprocessing on MacOS, they might be related to https://bugs.python.org/issue33725. You can disable multiprocessing by editing your .boto config or by adding the following flag to your command: `-o "GSUtil:parallel_process_count=1"`. Note that multithreading is still available even if you disable multiprocessing.

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Copying gs://broad-dsp-monster-hca-dev-ebi-staging/staging/4a77b2c4-da3c-4391-a345-12be491e199b/metadata/specimen_from_organism/28f0b2fe-3841-4b8f-8421-4180d2b1f7a3_2022-10-04T16:25:20.553000Z.json...
Copying gs://broad-dsp-monster-hca-dev-ebi-staging/staging/4a77b2c4-da3c-4391-a345-12be491e199b/staging_area.json...
Copying gs://broad-dsp-monster-hca-dev-ebi-staging/staging/4a77b2c4-da3c-4391-a345-12be491e199b/metadata/specimen_from_organism/a442abf8-289f-467d-8302-1d0e94a35279_2022-10-04T16:25:20.572000Z.json...
Copying gs://broad-dsp-monster-hca-dev-ebi-staging/staging/4a77b2c4-da3c-4391-a345-12be491e199b/metadata/specimen_from_organism/04d5edb8-b1e2-4a36-bdc5-a79bc8e1ea24_2022-10-04T16:25:20.589000Z.json...
| [77/77 files][ 61.9 KiB/ 61.9 KiB] 100% Done                                  
Operation completed over 77 objects/61.9 KiB.                                    
Creating a new branch with name 'release-data-04/10/2022'
[detached HEAD e8bdbf6] Added new data, corresponding to release on 04/10/2022
 21 files changed, 388 insertions(+), 44 deletions(-)
 create mode 100644 tests/data/AP3_file.h5ad
 create mode 100644 tests/data/Test_S1_L001_R1_001.fastq.gz
 create mode 100644 tests/data/Test_S1_L001_R2_001.fastq.gz
 create mode 100644 tests/descriptors/analysis_file/caf6d2a8-2272-5689-b3d8-9c97370d6c29_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/descriptors/sequence_file/8da4bdb9-ab64-5a90-8bce-f0ed5106ea41_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/descriptors/sequence_file/de17aa7d-be28-53c1-b7a3-1f4b3989e3e6_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/links/1ed68210-eaba-531d-ba9e-db80164d65ef_2021-01-01T00:00:00.000000Z_90bf705c-d891-5ce2-aa54-094488b445c6.json
 create mode 100644 tests/links/7a330531-ec7f-5aee-84d4-2ba24d66e93b_2021-01-01T00:00:00.000000Z_90bf705c-d891-5ce2-aa54-094488b445c6.json
 create mode 100644 tests/metadata/analysis_file/caf6d2a8-2272-5689-b3d8-9c97370d6c29_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/metadata/cell_suspension/6ff38054-9296-5d4c-b238-6a3b01a15175_2021-01-01T00:00:00.000000Z.json
 rename tests/metadata/process/{296b47c2-7c35-5fdb-bb11-95323011507c_2021-01-01T00:00:00.000000Z.json => 1ed68210-eaba-531d-ba9e-db80164d65ef_2021-01-01T00:00:00.000000Z.json} (86%)
 rename tests/metadata/process/{c352fa85-1de7-5ec1-9ecc-3f283cad54ca_2021-01-01T00:00:00.000000Z.json => 7a330531-ec7f-5aee-84d4-2ba24d66e93b_2021-01-01T00:00:00.000000Z.json} (86%)
 create mode 100644 tests/metadata/process/9c7b713c-6975-5484-9ff8-45725aa27a80_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/metadata/process/a3843530-046c-5ec0-bbf4-a4f0929b60af_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/metadata/process/e18171e4-1780-50f9-bd0f-4cbc28d3f642_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/metadata/sequence_file/8da4bdb9-ab64-5a90-8bce-f0ed5106ea41_2021-01-01T00:00:00.000000Z.json
 create mode 100644 tests/metadata/sequence_file/de17aa7d-be28-53c1-b7a3-1f4b3989e3e6_2021-01-01T00:00:00.000000Z.json
 delete mode 100644 tests/metadata/treatment_protocol/0f959f0b-5efa-5cc8-9c46-097b0cb574d5_2021-01-01T00:00:00.000000Z.json
Enumerating objects: 60, done.
Counting objects: 100% (60/60), done.
Delta compression using up to 8 threads
Compressing objects: 100% (45/45), done.
Writing objects:  78% (37/47), 240.77 MiB | 549.00 KiB/s
ami-day commented 1 year ago

Re-do tomorrow with treatment protocol included.

ami-day commented 1 year ago

Added treatment protocol and uploaded to ingest staging. Waiting for approval of pull request for the updated Schema_Test_Data.xlsx Template file.

ESapenaVentura commented 1 year ago

We should test if excel file generates same test data