Mercurial > repos > ximgchess > chap_test_20230411
changeset 100:e7fd2e5b53ba draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 01388c69776c82e48e84676a3d17d4623f5e08bd-dirty
| author | ximgchess |
|---|---|
| date | Wed, 24 May 2023 16:05:52 +0000 |
| parents | 8889fd666989 |
| children | 3d849a09d6c3 |
| files | saxswaxs/PIL5.poni saxswaxs/PIL5.tif saxswaxs/pipeline.yaml saxswaxs/reduce.xml saxswaxs/test_1d saxswaxs/test_1d_001/test_1d_PIL11_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_010.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_010.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_010.tiff tomo/pipeline_combine.yaml tomo/pipeline_find_center.yaml tomo/pipeline_reconstruct.yaml tomo/pipeline_reduce_nexus.yaml tomo/pipeline_reduce_yaml.yaml tomo/test.txt tomo/tmp.txt tomo/tomo_combine.xml tomo/tomo_macros.xml tomo/tomo_reduce.xml |
| diffstat | 48 files changed, 107 insertions(+), 144 deletions(-) [+] |
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--- a/saxswaxs/PIL5.poni Wed May 24 15:29:46 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -# Nota: C-Order, 1 refers to the Y axis, 2 to the X axis -# Calibration done at Wed Dec 1 09:43:02 2021 -poni_version: 2 -Detector: Pilatus300k -Detector_config: {} -Distance: 1.6482087488134558 -Poni1: 0.1678687786895594 -Poni2: 0.13236163515363114 -Rot1: 0.05582857735072926 -Rot2: -0.07300334677284326 -Rot3: 3.757385675073369e-05 -Wavelength: 1.2781876020248165e-10
--- a/saxswaxs/pipeline.yaml Wed May 24 15:29:46 2023 +0000 +++ b/saxswaxs/pipeline.yaml Wed May 24 16:05:52 2023 +0000 @@ -1,5 +1,14 @@ pipeline: + # Download example data + - common.URLReader: + url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main + headers: + PRIVATE-TOKEN: # your token here + - common.URLResponseProcessor + - common.ExtractArchiveWriter: + filename: . + # Collect map data - common.YAMLReader: filename: map.yaml @@ -10,12 +19,12 @@ force_overwrite: true # Integrate map detetcor data - - pipeline.MultiplePipelineItem: - items: - - common.YAMLReader: + - common.MultipleReader: + readers: + - YAMLReader: filename: map.yaml schema: MapConfig - - common.YAMLReader: + - YAMLReader: filename: integration.yaml schema: IntegrationConfig - common.IntegrateMapProcessor
--- a/saxswaxs/reduce.xml Wed May 24 15:29:46 2023 +0000 +++ b/saxswaxs/reduce.xml Wed May 24 16:05:52 2023 +0000 @@ -1,7 +1,7 @@ <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05"> <requirements> - <requirement type="package" version="0.0.8">chessanalysispipeline</requirement> - <requirement type="package" version="1.0.1">nexusformat</requirement> + <requirement type="package" version="0.0.3">chessanalysispipeline</requirement> + <requirement type="package" version="2.28.1">requests</requirement> <requirement type="package" version="2023.3.0">pyfai</requirement> <requirement type="package" version="1.10.7">pydantic</requirement> </requirements>
--- a/saxswaxs/test_1d Wed May 24 15:29:46 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -#F sample_14_align -#E 1637195555 -#D Wed Nov 17 19:32:35 2021 -#C spec User = chess_id3b - -#O0 mono monz mchi mony monx und_CL s0s s0n -#O1 s0t s0b s0x s0h s0z s0v mirzu mirzd -#O2 mirbu mirbd xu yu zu xd zld zrd -#O3 fpx att mirz mirth s3b s3t s3s s3n -#O4 s3z s3v s3x s3h s1b s1t s1s s1n -#O5 s1z s1v s1x s1h fl1x fl1z fl2x fl2z -#O6 waxx waxz1 waxz2 waxz waxtilt xmirx xmirz xmirphi -#O7 xmirth saxx saxy saxz andy andz zl2 xl2 -#O8 yl2 yr2 zru2 zrd2 xd7 zd7 xu7 zu7 -#O9 bedx_lo icvx icvz air_x p3y p3z nozx nozz -#O10 bedx bedx_galil s2b s2t s2s s2n s2z s2v -#O11 s2x s2h xrfx xrfy xrfz zd5 zru5 zlu5 -#O12 yd5 xd5 xu5 tabx5 zr6 zlu6 zld6 yr6 -#O13 yl6 xr6 th tth phi vtxx txr tyr -#O14 tzr txt tyt tzt txr2 tyr2 tzr2 txt2 -#O15 tyt2 tzt2 txr3 tyr3 tzr3 txt3 tyt3 tzt3 -#O16 txr4 tyr4 tzr4 txt4 tyt4 tzt4 txr5 tyr5 -#O17 tzr5 txt5 tyt5 tzt5 txr6 tyr6 tzr6 txt6 -#O18 tyt6 tzt6 txr7 tyr7 tzr7 txt7 tyt7 tzt7 -#O19 txr8 tyr8 tzr8 txt8 tyt8 tzt8 -#o0 mono monz mchi mony monx und s0s s0n -#o1 s0t s0b s0x s0h s0z s0v mirzu mirzd -#o2 mirbu mirbd xu yu zu xd zld zrd -#o3 fpx att mirz mirth s3b s3t s3s s3n -#o4 s3z s3v s3x s3h s1b s1t s1s s1n -#o5 s1z s1v s1x s1h fl1x fl1z fl2x fl2z -#o6 waxx waxz1 waxz2 waxz waxtilt xmirx xmirz xmirphi -#o7 xmirth saxx saxy saxz andy andz zl2 xl2 -#o8 yl2 yr2 zru2 zrd2 xd7 zd7 xu7 zu7 -#o9 bedx_lo icvx icvz air_x p3y p3z nozx nozz -#o10 bedx bedx_g s2b s2t s2s s2n s2z s2v -#o11 s2x s2h samx samy samz zd5 zru5 zlu5 -#o12 yd5 xd5 xu5 tabx5 zr6 zlu6 zld6 yr6 -#o13 yl6 xr6 th tth phi vtxx txr tyr -#o14 tzr txt tyt tzt txr2 tyr2 tzr2 txt2 -#o15 tyt2 tzt2 txr3 tyr3 tzr3 txt3 tyt3 tabz -#o16 txr4 tyr4 tzr4 txt4 tyt4 tzt4 txr5 tyr5 -#o17 tzr5 txt5 tyt5 tzt5 txr6 tyr6 tzr6 txt6 -#o18 tyt6 tzt6 txr7 tyr7 tzr7 crlx tyt7 crlz -#o19 txr8 tyr8 tzr8 txt8 bedy bedz -#J0 Seconds ic0_ni keyz icv_pos icv_sum tminus sec_2 diode -#J1 ic1 ic3 icv_lo icv_hi mot_pulse p11_r1 -#j0 sec ic0_ni keyz icv_pos icv_sum tminus sec_2 diode -#j1 ic1 ic3 icv_lo icv_hi pulses p11_r1 - - -#S 1 flyscan samx 140.9 141.5 10 0.1 -#D Wed Nov 17 19:35:47 2021 -#T 12 (Seconds) -#G0 0 -#G1 0 -#G3 0 -#G4 0 -#Q -#P0 -3.7830971 3.0011801 -0.22821594 -3.8 13.94 3.69 34.924802 35.874722 -#P1 20.129699 18.629511 35.399834 0.94995949 19.379555 1.5001232 9.3153197 6.2847224 -#P2 7.6113723e-07 -3.039743e-07 3.4829819 1.005207 -9.6873251 -4.7275845 -10.608966 -10.438151 -#P3 -10.972008 544.544 7.8 -3.4595 -0.004199987 0.34579999 1.76 2.1600002 -#P4 0.1708 0.35 1.96 0.4 -1.35 -0.85000006 -0.30000002 0.40000036 -#P5 -1.1 0.5 0.05 0.7 -1.5328934 -20.102657 -8.9922526 -3.4989075 -#P6 11.303603 27.619064 29.211176 28.415 0.796 -3.0517576e-08 0.058524542 3.516674e-09 -#P7 0.49999989 8 1 -6 170 5.1999999 -11.341377 -4.0548513 -#P8 0.91678883 0.91679319 -9.7110746 -7.5862294 1.1553852 -0.19508918 4.0468633 -0.2839906 -#P9 11.900876 0.13366788 2.9005861 -1.2465739 385.49999 70 -13.999995 9.9999998 -#P10 -4.3098231e-06 -174.51549 -1.2799991 -0.37999994 2.8299999 3.5300016 -0.83 0.9 -#P11 3.18 0.7 140.8975 26.999999 141.6 1.0000013 4.0000013 4.0000013 -#P12 6.8038999 -0.59999922 -0.59999922 292 -20.93269 -45.083693 -11.619761 4.6857093e-09 -#P13 1.5745194e-08 -8.0676912 8.5449218e-08 90 0 9.1661255e-07 -1.1665 0.3365 -#P14 11.4515 -0.4805 1.496 -10.1055 4.183 3.7555 0 -2.5 -#P15 -0.815 -9.995 -0.0065 -0.081 -9 14.9515 0.0045 -0.4 -#P16 9.228 -1.1635 -9.65 0.4 -4.3845 1.0185 -2.201 0 -#P17 0 -0.6 8.1215 2.5 55.4955 5.769 0 -4.1045 -#P18 -38.1255 -24.9045 0.234 0.234 7.609 1.2315 0.234 -0.1975 -#P19 -10.2505 -10.2505 -0.6675 -10.2505 0 0 -#N 9 -#L xrfx Seconds sec_2 diode ic1 ic3 icv_lo icv_hi mot_pulse -140.899995 0 0.302713 10898.0 14772.0 29927.0 93811.0 87169.0 0 -140.959995 0 0.100783 3615.0 4910.0 9950.0 30648.0 29072.0 0 -141.019995 0 0.099614 3592.0 4902.0 9951.0 30359.0 28781.0 0 -141.079995 0 0.099614 1264.0 4851.0 9819.0 30288.0 28727.0 0 -141.139995 0 0.099614 877.0 4709.0 9445.0 30411.0 28511.0 0 -141.199995 0 0.100398 631.0 4764.0 9537.0 30308.0 28751.0 0 -141.259995 0 0.100782 542.0 4804.0 9630.0 30359.0 28916.0 0 -141.319995 0 0.099614 625.0 4839.0 9743.0 30425.0 28762.0 0 -141.379995 0 0.099614 542.0 4787.0 9597.0 30298.0 28635.0 0 -141.439995 0 0.099614 665.0 4784.0 9599.0 30283.0 28662.0 0 -141.499995 0 0.146491 1248.0 6957.0 13906.0 44347.0 42023.0 0
--- a/tomo/pipeline_combine.yaml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/pipeline_combine.yaml Wed May 24 16:05:52 2023 +0000 @@ -1,11 +1,11 @@ pipeline: # Combine tomography stacks - - common.MultipleReader: - readers: - - NexusReader: + - pipeline.MultiplePipelineItem: + items: + - common.NexusReader: filename: reconstructed.nex - - YAMLReader: + - common.YAMLReader: filename: combine.yaml schema: TomoCombineConfig - tomo.TomoDataProcessor:
--- a/tomo/pipeline_find_center.yaml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/pipeline_find_center.yaml Wed May 24 16:05:52 2023 +0000 @@ -1,11 +1,11 @@ pipeline: # Find rotation axis centers for the tomography stacks - - common.MultipleReader: - readers: - - NexusReader: + - pipeline.MultiplePipelineItem: + items: + - common.NexusReader: filename: reduced.nex - - YAMLReader: + - common.YAMLReader: filename: find_center.yaml schema: TomoFindCenterConfig - tomo.TomoDataProcessor:
--- a/tomo/pipeline_reconstruct.yaml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/pipeline_reconstruct.yaml Wed May 24 16:05:52 2023 +0000 @@ -1,14 +1,14 @@ pipeline: # Reconstruct tomography stacks - - common.MultipleReader: - readers: - - NexusReader: + - pipeline.MultiplePipelineItem: + items: + - common.NexusReader: filename: reduced.nex - - YAMLReader: + - common.YAMLReader: filename: reconstruct.yaml schema: TomoReconstructConfig - - YAMLReader: + - common.YAMLReader: filename: centers.yaml schema: TomoFindCenterConfig - tomo.TomoDataProcessor:
--- a/tomo/pipeline_reduce_nexus.yaml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/pipeline_reduce_nexus.yaml Wed May 24 16:05:52 2023 +0000 @@ -1,11 +1,11 @@ pipeline: # Reduce tomography images - - common.MultipleReader: - readers: - - NexusReader: + - pipeline.MultiplePipelineItem: + items: + - common.NexusReader: filename: setup.nex - - YAMLReader: + - common.YAMLReader: filename: reduce.yaml schema: TomoReduceConfig - tomo.TomoDataProcessor:
--- a/tomo/pipeline_reduce_yaml.yaml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/pipeline_reduce_yaml.yaml Wed May 24 16:05:52 2023 +0000 @@ -1,12 +1,12 @@ pipeline: # Reduce tomography images - - common.MultipleReader: - readers: - - YAMLReader: + - pipeline.MultiplePipelineItem: + items: + - common.YAMLReader: filename: map.yaml schema: MapConfig - - YAMLReader: + - common.YAMLReader: filename: reduce.yaml schema: TomoReduceConfig - tomo.TomoDataProcessor:
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/test.txt Wed May 24 16:05:52 2023 +0000 @@ -0,0 +1,34 @@ +I had a Galaxy tool crash repeatedly on Friday and tried a bunch of things, but nothing helped. Today I tried it from scratch and kept notes: + +Removed everything in: + /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess +and in: +/nfs/chess/galaxy-dev/var/dependencies/_conda/envs + +Rebooted the ansible + +Made sure that the repo in the testtoolshed is up to date. + +Reinstall the CHAP tool at: +https://galaxy-dev.classe.cornell.edu/admin/toolshed +Watching its progress, I can see that it first clones the tool repo and then installs the tool dependencies. +When done, I have the following new content in the galaxy tree: +ls -al /nfs/chess/galaxy-dev/var/dependencies/_conda/envs: +drwxr-xr-x 3 galaxy galaxy 32 May 1 09:17 . +drwxr-xr-x 5 galaxy galaxy 52 Apr 28 08:40 .. +drwxr-xr-x 3 galaxy galaxy 26 May 1 09:18 chap_test_20230411 + +ls -al /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess: +drwxr-xr-x 6 galaxy galaxy 317 May 1 10:04 . +drwxr-xr-x 15 galaxy galaxy 226 Aug 29 2021 .. +drwxr-xr-x 12 galaxy galaxy 184 May 1 10:03 __ChessAnalysisPipeline@0.0.2 +-rw-r--r-- 1 galaxy galaxy 0 May 1 09:18 .conda_envs_dir_test +drwxr-xr-x 27 galaxy galaxy 4096 May 1 10:02 mulled-v1-0cd3a5ccc731743d38833d0396752d8219d106c20bb3bb478c34e74608ecb1c3 +drwxr-xr-x 26 galaxy galaxy 4096 May 1 09:51 mulled-v1-67ac3841866ce74ad34393f2abb6cc61f6651a9d3f3e677b9821c88c9b0a676e +drwxr-xr-x 12 galaxy galaxy 184 May 1 10:04 mulled-v1-b1085bc9e4a5d280004f5b197e8295b3ef5167ea9ea22a074defb863f1b86458 + +When running a Galaxy tool and only when I try to pip install certif-pyspec, it bombs with: +OSError: [Errno 30] Read-only file system: '__config__.cpython-310.pyc' + +See stdout and stderr in: +/nfs/chess/aux/reduced_data/user/galaxy-dev/jobs/002/2440/outputs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/tmp.txt Wed May 24 16:05:52 2023 +0000 @@ -0,0 +1,13 @@ +try: + from pyspec.file.spec import FileSpec + from pyspec.file.tiff import TiffFile +except: + import sys + home = '/home/galaxy' + localpippath = f'{home}/.local/lib/python3.11/site-packages' + if localpippath not in sys.path: + sys.path.insert(0, localpippath) + from pyspec.file.spec import FileSpec + from pyspec.file.tiff import TiffFile + +
--- a/tomo/tomo_combine.xml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/tomo_combine.xml Wed May 24 16:05:52 2023 +0000 @@ -7,7 +7,7 @@ <command detect_errors="exit_code"> <![CDATA[ mkdir tomo_combine_plots; - cp $input_file reconstruced.nex && + cp $input_file reconstructed.nex && cp $tool_config combine.yaml && CHAP --config $__tool_directory__/pipeline_combine.yaml
--- a/tomo/tomo_macros.xml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/tomo_macros.xml Wed May 24 16:05:52 2023 +0000 @@ -1,10 +1,10 @@ <macros> <token name="@TOOL_VERSION@">0.1.0</token> <token name="@PROFILE@">21.09</token> - <token name="@PYTHON_TEMPLATE_VERSION@">3.9</token> + <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.0.7">chessanalysispipeline</requirement> + <requirement type="package" version="0.0.8">chessanalysispipeline</requirement> <requirement type="package" version="1.1.0">lmfit</requirement> <requirement type="package" version="3.7.1">matplotlib</requirement> <requirement type="package" version="1.0.1">nexusformat</requirement> @@ -15,13 +15,17 @@ <xml name="citations"> <citations> <citation type="bibtex"> -@misc{githubChessAnalysisPipeline, - author = {LastTODO, FirstTODO}, - year = {TODO}, - title = {Tomography reconstruction}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/CHESSComputing/ChessAnalysisPipeline}, +@software{keara_soloway_2023_7963605, + author = {Keara Soloway and + Valentin Kuznetsov and + Rolf Verberg}, + title = {CHESSComputing/ChessAnalysisPipeline: v0.0.8}, + month = may, + year = 2023, + publisher = {Zenodo}, + version = {v0.0.8}, + doi = {10.5281/zenodo.7963605}, + url = {https://doi.org/10.5281/zenodo.7963605} }</citation> </citations> </xml>
--- a/tomo/tomo_reduce.xml Wed May 24 15:29:46 2023 +0000 +++ b/tomo/tomo_reduce.xml Wed May 24 16:05:52 2023 +0000 @@ -8,9 +8,12 @@ <![CDATA[ mkdir tomo_reduce_plots; #if str($map.type_selector) == "yaml" - $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' && cp $input_file map.yaml && - cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && + #if str($map.detector.type_selector) == "from_file" + cat $map.detector.detector_file $tool_config > reduce.yaml && + #else + cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && + #end if #else cp $input_file setup.nex && cp $tool_config reduce.yaml && @@ -46,14 +49,18 @@ <when value="yaml"> <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/> <conditional name="detector"> - <param name="type_selector" type="select" display="radio" label="Choose detector prefix"> + <param name="type_selector" type="select" display="radio" label="Choose detector"> <option value="andor2.yaml">andor2</option> <option value="manta.yaml">manta</option> <option value="retiga.yaml">retiga</option> + <option value="from_file">from file</option> </param> <when value="andor2.yaml"/> <when value="manta.yaml"/> <when value="retiga.yaml"/> + <when value="from_file"> + <param name="detector_file" type="data" format="yaml" optional="false" label="Detector config file"/> + </when> </conditional> </when> <when value="nexus">