Remove absolute paths and redundant file references

[benjaminhwilliams]

• Several experiment list files contain references to image file templates and/or mask files that refer to an absolute path.
• In some cases, the file name doesn't match the example image/mask files in the same directory, presumably the intended target of these references.
• In some cases, there is no matching file uploaded.

The latter two points aren't necessarily a problem until/unless someone writes a test that queries the linked mask/image file(s), but it seems sensible to make the uploaded data consistent and complete where possible, to avoid future test-writers getting caught out.

Examples:

$ grep -r "Users\|home"
l_cysteine_integrated/30_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_02_#####.cbf", 
l_cysteine_integrated/30_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_integrated/25_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_01_#####.cbf", 
l_cysteine_integrated/25_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_integrated/35_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_03_#####.cbf", 
l_cysteine_integrated/35_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_integrated/20_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_04_#####.cbf", 
l_cysteine_integrated/20_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
pdteet-2-lattice/sweep-04/indexed.expt:      "template": "/Users/graeme/data/i19-1-double-PdTEET/PdTEET_04_#####.cbf.gz", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_04_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_01_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_4_sweeps_scaled/scaled_30.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_02_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_30.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_4_sweeps_scaled/scaled_35.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_03_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_35.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
centroid_test_data/INTEGRATE.HKL:!NAME_TEMPLATE_OF_DATA_FRAMES=/Users/graeme/data/RU/1/X4_lots_M1S4_1_0???.cbf CB

[benjaminhwilliams]

A slightly more complete list:

$ grep -r "/dls/\|/Users/"
l_cysteine_integrated/30_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_02_#####.cbf", 
l_cysteine_integrated/30_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_integrated/25_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_01_#####.cbf", 
l_cysteine_integrated/25_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_integrated/35_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_03_#####.cbf", 
l_cysteine_integrated/35_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_integrated/20_integrated_experiments.json:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_04_#####.cbf", 
l_cysteine_integrated/20_integrated_experiments.json:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
vmxi_proteinase_k_sweeps/experiments_3.expt:      "template": "/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_46/images/image_17657_master.h5", 
vmxi_proteinase_k_sweeps/experiments_3.expt:      "mask": "/dls/science/users/hko55533/mx21314-30/VMXi-AB0813/well_46_image_17657/DEFAULT/NATIVE/SWEEP1/index/2_hot_mask_0.pickle", 
vmxi_proteinase_k_sweeps/experiments_0.expt:      "template": "/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_112/images/image_17578_master.h5", 
vmxi_proteinase_k_sweeps/experiments_0.expt:      "mask": "/dls/science/users/hko55533/mx21314-30/VMXi-AB0813/well_112_image_17578/DEFAULT/NATIVE/SWEEP1/index/2_hot_mask_0.pickle", 
vmxi_proteinase_k_sweeps/experiments_1.expt:      "template": "/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_12/images/image_17586_master.h5", 
vmxi_proteinase_k_sweeps/experiments_1.expt:      "mask": "/dls/science/users/hko55533/mx21314-30/VMXi-AB0813/well_12_image_17586/DEFAULT/NATIVE/SWEEP1/index/2_hot_mask_0.pickle", 
vmxi_proteinase_k_sweeps/experiments_2.expt:      "template": "/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_151/images/image_17607_master.h5", 
vmxi_proteinase_k_sweeps/experiments_2.expt:      "mask": "/dls/science/users/hko55533/mx21314-30/VMXi-AB0813/well_151_image_17607/DEFAULT/NATIVE/SWEEP1/index/2_hot_mask_0.pickle", 
vmxi_proteinase_k_sweeps/README.md:files="/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_12/images/image_17586_master.h5
vmxi_proteinase_k_sweeps/README.md:/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_46/images/image_17657_master.h5
vmxi_proteinase_k_sweeps/README.md:/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_112/images/image_17578_master.h5
vmxi_proteinase_k_sweeps/README.md:/dls/mx/data/mx21314/mx21314-30/VMXi-AB0813/well_151/images/image_17607_master.h5"
mpro-x0305_processed/indexed.expt:      "template": "/dls/i04-1/data/2020/lb18145-154/Mpro/Mpro-x0305/Mpro-x0305_1_####.cbf",
mpro-x0305_processed/imported.expt:      "template": "/dls/i04-1/data/2020/lb18145-154/Mpro/Mpro-x0305/Mpro-x0305_1_####.cbf",
mpro-x0305_processed/README.md:dials.import /dls/i04-1/data/2020/lb18145-154/Mpro/Mpro-x0305/*.cbf
pdteet-2-lattice/sweep-04/indexed.expt:      "template": "/Users/graeme/data/i19-1-double-PdTEET/PdTEET_04_#####.cbf.gz", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_04_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_01_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_20_25.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_4_sweeps_scaled/scaled_30.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_02_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_30.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
l_cysteine_4_sweeps_scaled/scaled_35.expt:      "template": "/Users/graeme/data/i19-1/l-cyst/l-cyst_03_#####.cbf", 
l_cysteine_4_sweeps_scaled/scaled_35.expt:      "mask": "/Users/graeme/Projects/l-cys/DEFAULT/NATIVE/SWEEP1/index/hot_mask_0.pickle", 
Binary file centroid_test_data/centroid_0007.cbf matches
Binary file centroid_test_data/centroid_0008.cbf matches
centroid_test_data/INTEGRATE.HKL:!NAME_TEMPLATE_OF_DATA_FRAMES=/Users/graeme/data/RU/1/X4_lots_M1S4_1_0???.cbf CB
Binary file centroid_test_data/centroid_0005.cbf matches
Binary file centroid_test_data/centroid_0003.cbf matches
Binary file centroid_test_data/centroid_0002.cbf matches
Binary file centroid_test_data/centroid_0006.cbf matches
Binary file centroid_test_data/centroid_0001.cbf matches
centroid_test_data/XDS.INP:!NAME_TEMPLATE_OF_DATA_FRAMES=/dls/i02/data/2013/nt5964-1/2013_02_08/GW/DNA/P1/X4/X4_lots_M1S4_1_????.cbf
Binary file centroid_test_data/centroid_0009.cbf matches
Binary file centroid_test_data/centroid_0004.cbf matches