fractal-server 2.4.2__py3-none-any.whl → 2.5.0a1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- fractal_server/__init__.py +1 -1
- fractal_server/app/db/__init__.py +4 -1
- fractal_server/app/models/v1/task.py +0 -5
- fractal_server/app/models/v2/workflowtask.py +2 -10
- fractal_server/app/routes/admin/v2.py +0 -30
- fractal_server/app/routes/api/v2/__init__.py +0 -4
- fractal_server/app/routes/api/v2/_aux_functions.py +11 -46
- fractal_server/app/routes/api/v2/workflow.py +23 -54
- fractal_server/app/routes/api/v2/workflowtask.py +9 -33
- fractal_server/app/routes/auth/_aux_auth.py +11 -5
- fractal_server/app/routes/auth/current_user.py +5 -1
- fractal_server/app/routes/auth/users.py +9 -8
- fractal_server/app/runner/v2/__init__.py +1 -4
- fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py +1 -4
- fractal_server/app/runner/v2/handle_failed_job.py +2 -9
- fractal_server/app/runner/v2/runner.py +42 -70
- fractal_server/app/runner/v2/runner_functions.py +0 -58
- fractal_server/app/runner/v2/runner_functions_low_level.py +7 -21
- fractal_server/app/schemas/user.py +17 -0
- fractal_server/app/schemas/v2/__init__.py +0 -1
- fractal_server/app/schemas/v2/dumps.py +2 -23
- fractal_server/app/schemas/v2/task.py +0 -5
- fractal_server/app/schemas/v2/workflowtask.py +4 -29
- fractal_server/migrations/env.py +4 -7
- fractal_server/migrations/naming_convention.py +7 -0
- fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py +1 -1
- fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py +97 -0
- {fractal_server-2.4.2.dist-info → fractal_server-2.5.0a1.dist-info}/METADATA +1 -1
- {fractal_server-2.4.2.dist-info → fractal_server-2.5.0a1.dist-info}/RECORD +32 -32
- fractal_server/app/routes/api/v2/task_legacy.py +0 -59
- fractal_server/app/runner/v2/v1_compat.py +0 -31
- {fractal_server-2.4.2.dist-info → fractal_server-2.5.0a1.dist-info}/LICENSE +0 -0
- {fractal_server-2.4.2.dist-info → fractal_server-2.5.0a1.dist-info}/WHEEL +0 -0
- {fractal_server-2.4.2.dist-info → fractal_server-2.5.0a1.dist-info}/entry_points.txt +0 -0
@@ -1,8 +1,8 @@
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fractal_server/__init__.py,sha256=
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fractal_server/__init__.py,sha256=1fM-hrX8GvZ3DcdEUtfHmLjQ5GtgW0uU1Sqd6Va9Mbo,24
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fractal_server/__main__.py,sha256=upYBkGYrkBnkS1rp4D_nb_1LS37QT4j-wxGX1ZMvR4A,5704
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fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
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fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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fractal_server/app/db/__init__.py,sha256=
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fractal_server/app/db/__init__.py,sha256=81rK9w1__Z6PJ5cEcChPVc-wI9YOK4fN--_5Opry0MQ,4119
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fractal_server/app/models/__init__.py,sha256=zt0Tiv91DWLg0daT8bkENz-LusihOJJX1h09UfHlAns,452
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fractal_server/app/models/linkusergroup.py,sha256=ufthlbLFAWMU_dJmsVZzVlQa_D9C9SmgydxypQ2Xq1U,309
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fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
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@@ -12,7 +12,7 @@ fractal_server/app/models/v1/dataset.py,sha256=99GDgt7njx8yYQApkImqp_7bHA5HH3Elv
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fractal_server/app/models/v1/job.py,sha256=QLGXcWdVRHaUHQNDapYYlLpEfw4K7QyD8TmcwhrWw2o,3304
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fractal_server/app/models/v1/project.py,sha256=JG7b5J9CzVNxua4MaMYpfB57xt2qjbXr5SnR7_oKQ70,819
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fractal_server/app/models/v1/state.py,sha256=m9gMZqqnm3oDpJNJp-Lht4kM7oO7pcEI7sL1g7LFvWU,1043
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fractal_server/app/models/v1/task.py,sha256=
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fractal_server/app/models/v1/task.py,sha256=uFXam7eu3Ye1Yt7_g7llCzY8BetmDRilsq5hR2C1Zbg,2640
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fractal_server/app/models/v1/workflow.py,sha256=dnY5eMaOe3oZv8arn00RNX9qVkBtTLG-vYdWXcQuyo4,3950
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fractal_server/app/models/v2/__init__.py,sha256=uLzdInqATSwi0bS_V4vKB-TqFrOFaXuxCAbU73c0f24,473
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fractal_server/app/models/v2/collection_state.py,sha256=nxb042i8tt8rCpmgbFJoBCYWU-34m0HdUfO9YurTp8k,588
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@@ -21,11 +21,11 @@ fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb
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fractal_server/app/models/v2/project.py,sha256=rAHoh5KfYwIaW7rTX0_O0jvWmxEvfo1BafvmcXuSSRk,786
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fractal_server/app/models/v2/task.py,sha256=Esf2j9c-0pGYjdbb__Ptpdx7NCAKVxqbQMoza524miU,1286
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fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
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fractal_server/app/models/v2/workflowtask.py,sha256=
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fractal_server/app/models/v2/workflowtask.py,sha256=iDuJYk8kp4PNqGmbKRtGI7y-QsbjkNd_gDsbMzL4i-g,1274
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fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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fractal_server/app/routes/admin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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fractal_server/app/routes/admin/v1.py,sha256=GIpZlwAwwwLGDWkBqywhtmp9TGsKLhGmZAdj1TDKJvE,13976
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fractal_server/app/routes/admin/v2.py,sha256=
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fractal_server/app/routes/admin/v2.py,sha256=hoEbH_sRJ-MaKMwhFp8c7SNObP0-Kmtgw1zbs_Z3nLY,12971
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fractal_server/app/routes/api/__init__.py,sha256=2IDheFi0OFdsUg7nbUiyahqybvpgXqeHUXIL2QtWrQQ,641
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fractal_server/app/routes/api/v1/__init__.py,sha256=Y2HQdG197J0a7DyQEE2jn53IfxD0EHGhzK1I2JZuEck,958
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fractal_server/app/routes/api/v1/_aux_functions.py,sha256=1YZdLch-Q1c44hQ_1ZEiijgWhLW6H3QEL5y5SHw5Ijk,13023
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@@ -36,8 +36,8 @@ fractal_server/app/routes/api/v1/task.py,sha256=OLASM6M4yfHvQgHQOuR5810jR2s0_W1H
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fractal_server/app/routes/api/v1/task_collection.py,sha256=VYxhtd_idBppgJM7-FCHikI2OKMAIz05fhV_TsJpWI8,9060
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fractal_server/app/routes/api/v1/workflow.py,sha256=2T93DuEnSshaDCue-JPmjuvGCtbk6lt9pFMuPt783t8,11217
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fractal_server/app/routes/api/v1/workflowtask.py,sha256=OYYConwJbmNULDw5I3T-UbSJKrbbBiAHbbBeVcpoFKQ,5785
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fractal_server/app/routes/api/v2/_aux_functions.py,sha256=
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fractal_server/app/routes/api/v2/__init__.py,sha256=301enf_GsL27_CnG6lSbMIeoz9-rrb3R2iDSs5pk4q8,1650
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fractal_server/app/routes/api/v2/_aux_functions.py,sha256=OLDwaZpkCr6q2heebmceGY5YvuKQy0-mVkkfcCp6kEc,13550
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fractal_server/app/routes/api/v2/dataset.py,sha256=Eilf_BAGjicIhqUiVwI86jlW45ineA5sVzxXW4b2GoQ,8329
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fractal_server/app/routes/api/v2/images.py,sha256=JR1rR6qEs81nacjriOXAOBQjAbCXF4Ew7M7mkWdxBU0,7920
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fractal_server/app/routes/api/v2/job.py,sha256=Bga2Kz1OjvDIdxZObWaaXVhNIhC_5JKhKRjEH2_ayEE,5157
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fractal_server/app/routes/api/v2/task.py,sha256=XgRnGBvSoI9VNJHtWZQ2Ide99f6elo7a2FN3GQkf0dU,8376
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fractal_server/app/routes/api/v2/task_collection.py,sha256=wEwP8VfsxhKPZ6K3v1Bnput_Zw0Cjhlaal0-e50feIQ,12337
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fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=6MW-l7xTCTbWKDSYDw8e_hnm5jFCJpgFL3UdvrHAaBk,6029
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fractal_server/app/routes/api/v2/workflowtask.py,sha256=HoHFnVRDa0Cw1oqTea1Of6A5ZhjGJeSTDTdI-SKP7Co,8063
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fractal_server/app/routes/api/v2/workflow.py,sha256=rMCcclz9aJAMSVLncUdSDGrgkKbn4KOCZTqZtqs2HDY,10428
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fractal_server/app/routes/api/v2/workflowtask.py,sha256=-3-c8DDnxGjMwWbX_h5V5OLaC_iCLXYzwWKBUaL-5wE,7060
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fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
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fractal_server/app/routes/auth/_aux_auth.py,sha256=G0-VwAq2UKlvKc5erCU8vhMQWA6gUgsRig9GmexEy74,3189
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fractal_server/app/routes/auth/current_user.py,sha256=E6fDWw8xGxgE816S9Mriow1OMOaxw8DIKAFcrGpiaIU,2106
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fractal_server/app/routes/auth/group_names.py,sha256=zvYDfhxKlDmbSr-oLXYy6WUVkPPTvzH6ZJtuoNdGZbE,960
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fractal_server/app/routes/auth/users.py,sha256=lMfcob_Bxz1j2EyddKeAoQPqMZTP40aOkiuk7Oeqo0E,6987
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fractal_server/app/schemas/_validators.py,sha256=1dTOYr1IZykrxuQSV2-zuEMZbKe_nGwrfS7iUrsh-sE,3461
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fractal_server/app/schemas/v1/workflow.py,sha256=tuOs5E5Q_ozA8if7YPZ07cQjzqB_QMkBS4u92qo4Ro0,4618
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fractal_server/app/schemas/v2/__init__.py,sha256=
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fractal_server/app/schemas/v2/__init__.py,sha256=kmM4NfSGIL0I4xVtnmMST20kfVo3nBBG-Ssk8vJAvLs,1979
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fractal_server/app/schemas/v2/dataset.py,sha256=dLT52tV4dSf2HrFNak4vdQEn8PT_04IUrGnd2z-AXIU,2599
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fractal_server/app/schemas/v2/dumps.py,sha256=
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+
fractal_server/app/schemas/v2/dumps.py,sha256=_iVgV98jb3gaKcOxX_halQFureKE81KTRIqbJsefw1s,1332
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fractal_server/app/schemas/v2/job.py,sha256=zfF9K3v4jWUJ7M482ta2CkqUJ4tVT4XfVt60p9IRhP0,3250
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fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Izxk9iL1vtwBJw,6243
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fractal_server/app/schemas/v2/project.py,sha256=u7S4B-bote1oGjzAGiZ-DuQIyeRAGqJsI71Tc1EtYE0,736
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fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
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fractal_server/app/schemas/v2/task.py,sha256=
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fractal_server/app/schemas/v2/task.py,sha256=xQfQxL2h-Vw0YL3yEiYvVIXTybE1lyRE0pPUu59nZes,4574
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fractal_server/app/schemas/v2/task_collection.py,sha256=8PG1bOqkfQqORMN0brWf6mHDmijt0bBW-mZsF7cSxUs,6129
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fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
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fractal_server/app/schemas/v2/workflowtask.py,sha256=
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fractal_server/app/schemas/v2/workflowtask.py,sha256=TN-mdkuE_EWet9Wk-xFrUwIt_tXYcw88WOKMnUcchKk,5665
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fractal_server/app/security/__init__.py,sha256=vuAE0sg2er0I2PAf7xCUHcxbMgxV1d8y6oJjO98n86o,11858
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fractal_server/config.py,sha256=R0VezSe2PEDjQjHEX2V29A1jMdoomdyECBjWNY15v_0,25049
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fractal_server/data_migrations/2_4_0.py,sha256=T1HRRWp9ZuXeVfBY6NRGxQ8aNIHVSftOMnB-CMrfvi8,2117
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@@ -160,11 +158,13 @@ fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLi
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fractal_server/logger.py,sha256=56wfka6fHaa3Rx5qO009nEs_y8gx5wZ2NUNZZ1I-uvc,5130
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fractal_server/main.py,sha256=NUvMd8C8kosulAcQ8pCFLnOGdLw7j-6RzcHxoNvSB7k,5003
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fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
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fractal_server/migrations/env.py,sha256=
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fractal_server/migrations/env.py,sha256=mEiX0TRa_8KAYBrUGJTx1cFJ5YAq_oNHHsFCp1raegk,2543
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fractal_server/migrations/naming_convention.py,sha256=htbKrVdetx3pklowb_9Cdo5RqeF0fJ740DNecY5de_M,265
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fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
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fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py,sha256
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fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py,sha256=-BSS9AFTPcu3gYC-sYbawSy4MWQQx8TfMb5BW5EBKmQ,1450
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fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
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fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py,sha256=Mob8McGYAcmgvrseyyYOa54E6Gsgr-4SiGdC-r9O4_A,1157
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fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py,sha256=5ROUgcoZOdjf8kMt6cxuvPhzHmV6xaCxvZEbhUEyZM4,3271
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fractal_server/migrations/versions/50a13d6138fd_initial_schema.py,sha256=zwXegXs9J40eyCWi3w0c_iIBVJjXNn4VdVnQaT3KxDg,8770
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fractal_server/migrations/versions/5bf02391cfef_v2.py,sha256=axhNkr_H6R4rRbY7oGYazNbFvPXeSyBDWFVbKNmiqs8,8433
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fractal_server/migrations/versions/70e77f1c38b0_add_applyworkflow_first_task_index_and_.py,sha256=Q-DsMzG3IcUV2Ol1dhJWosDvKERamBE6QvA2zzS5zpQ,1632
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@@ -207,8 +207,8 @@ fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kq
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fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
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fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
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fractal_server/zip_tools.py,sha256=xYpzBshysD2nmxkD5WLYqMzPYUcCRM3kYy-7n9bJL-U,4426
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fractal_server-2.
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fractal_server-2.5.0a1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
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fractal_server-2.5.0a1.dist-info/METADATA,sha256=qMNa2O2LVr-uNvS2djtZyio4-mk3FOHbIY_7N6Mh31k,4630
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fractal_server-2.5.0a1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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fractal_server-2.5.0a1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
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fractal_server-2.5.0a1.dist-info/RECORD,,
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@@ -1,59 +0,0 @@
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1
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from fastapi import APIRouter
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from fastapi import Depends
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from fastapi import HTTPException
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from fastapi import status
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from sqlmodel import select
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from fractal_server.app.db import AsyncSession
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from fractal_server.app.db import get_async_db
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from fractal_server.app.models import UserOAuth
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from fractal_server.app.models.v1 import Task as TaskV1
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from fractal_server.app.routes.auth import current_active_user
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from fractal_server.app.schemas.v2 import TaskLegacyReadV2
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from fractal_server.logger import set_logger
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router = APIRouter()
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logger = set_logger(__name__)
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@router.get("/", response_model=list[TaskLegacyReadV2])
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async def get_list_task_legacy(
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args_schema: bool = True,
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only_v2_compatible: bool = False,
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user: UserOAuth = Depends(current_active_user),
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db: AsyncSession = Depends(get_async_db),
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) -> list[TaskLegacyReadV2]:
|
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"""
|
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Get list of available legacy tasks
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"""
|
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stm = select(TaskV1)
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if only_v2_compatible:
|
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stm = stm.where(TaskV1.is_v2_compatible)
|
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res = await db.execute(stm)
|
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task_list = res.scalars().all()
|
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await db.close()
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if args_schema is False:
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for task in task_list:
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setattr(task, "args_schema", None)
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return task_list
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@router.get("/{task_id}/", response_model=TaskLegacyReadV2)
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async def get_task_legacy(
|
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task_id: int,
|
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user: UserOAuth = Depends(current_active_user),
|
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db: AsyncSession = Depends(get_async_db),
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) -> TaskLegacyReadV2:
|
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"""
|
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|
-
Get info on a specific legacy task
|
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-
"""
|
52
|
-
task = await db.get(TaskV1, task_id)
|
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-
await db.close()
|
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if not task:
|
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raise HTTPException(
|
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status_code=status.HTTP_404_NOT_FOUND,
|
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detail=f"TaskV1[{task_id}] not found",
|
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)
|
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return task
|
@@ -1,31 +0,0 @@
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from copy import deepcopy
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from pathlib import Path
|
3
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-
from typing import Any
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def convert_v2_args_into_v1(
|
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kwargs_v2: dict[str, Any],
|
8
|
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parallelization_level: str = "image",
|
9
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-
) -> dict[str, Any]:
|
10
|
-
kwargs_v1 = deepcopy(kwargs_v2)
|
11
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-
|
12
|
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zarr_url = kwargs_v1.pop("zarr_url")
|
13
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-
input_path = Path(zarr_url).parents[3].as_posix()
|
14
|
-
image_component = zarr_url.replace(input_path, "").lstrip("/")
|
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|
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if parallelization_level == "image":
|
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component = image_component
|
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elif parallelization_level == "well":
|
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-
component = str(Path(image_component).parent)
|
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elif parallelization_level == "plate":
|
20
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-
component = str(Path(image_component).parents[2])
|
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else:
|
22
|
-
raise ValueError(f"Invalid {parallelization_level=}.")
|
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|
-
|
24
|
-
kwargs_v1.update(
|
25
|
-
input_paths=[input_path],
|
26
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-
output_path=input_path,
|
27
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-
metadata={},
|
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-
component=component,
|
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-
)
|
30
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-
|
31
|
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return kwargs_v1
|
File without changes
|
File without changes
|
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|