File Changes for kent

v359_base to v360_preview (2017-12-18 to 2018-01-08) v360

• src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c
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    57a332d97df6f6006f2b94f9e6f7fd2623ef516a Wed Dec 20 15:07:39 2017 -0800
    Changing sra_run to insdc_run as per V4 of metadata spec.
• src/hca/toHca/hcaStormToTabDir/hcaStormToTabDir.c
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    b99f908b84e7bbbe46f81c8c997f7ea9aeecf5c9 Tue Dec 12 17:13:22 2017 -0800
    First cut of V4 tagstorm to tab-dir utility. Still needs some work to connect the various types of sample together.
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    37accb7ce70ae0c9389661ada545a9ed46453ef4 Wed Dec 13 16:22:08 2017 -0800
    Linking various types of samples together with an id/derived_from fields.
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    0788f3b055293f4322288962340134441f11ff9a Thu Dec 14 12:03:00 2017 -0800
    Copying species info to all sample pieces.
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    118817ab7e80ee7f55eb7bd30710e777e515df65 Thu Dec 14 12:16:37 2017 -0800
    Moving naked sample fields to last sample in chain.
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    7a33dcbd529c98acb9ea151a51acb3f6b4290a1b Thu Dec 14 16:44:57 2017 -0800
    Moving donor.submitted_id field, making experimental_design a || separated array as EBI is doing in their spreadsheets, and making unwinding array of publications in project.publications.tsv.
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    bc8e64c384c3d1c590df66ae323207de19415287 Thu Dec 14 17:04:17 2017 -0800
    Handling submitters and contibutors.
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    f76cf9d4287628507e2c9cfe7b5fd4b1807d961a Thu Dec 14 17:11:54 2017 -0800
    Oops, reversed some fields.
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    331c418086187ca1ba157a6e348cc61f9e126390 Thu Dec 14 17:40:10 2017 -0800
    Rescuing the donor. and cell_suspension. and so forth form the sample* files field names.
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    7e0407f574cc747c239e3af9de078d91302532d9 Fri Dec 15 10:59:54 2017 -0800
    Making sample.donor.disease into a simple string variable rather than array of ontology objects in output.
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    1cfc0ba46262593dc90cd427ced6c318c3ab5d46 Fri Dec 15 11:12:24 2017 -0800
    Fixing a few wrinkels on sample_id.
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    41f861d4acd7703e2b57805da5f8d245d9756654 Fri Dec 15 11:29:16 2017 -0800
    Fixing a wrinkle in sample_id
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    bfab7701cb473e0e271e23fb9c91ccc8d2a39ebf Fri Dec 15 14:50:39 2017 -0800
    Refactoring some code so as to reuse some logic for different sample subobjects assay subobjects.
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    6486bc630c9e3c6873409aba22dfb1631bec3d70 Fri Dec 15 15:55:46 2017 -0800
    Adding in assay_id to appropriate tabs.
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    dab69af66431bf99c7a8325cf5467ba6c27f4ddc Tue Dec 19 16:43:20 2017 -0800
    Creating a tagStormCopyTags function that gets called about 8 times now and replaces about 4 lines of code. Starting to work on file tab.
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    6cc4ab64bdd73fa2759d000749ca43383c855bde Tue Dec 19 18:04:43 2017 -0800
    Second pass at adding file tab. Seems to work for the arrayExpress ones anyway.
• src/hca/v3v4/fieldsFromJson.py
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    34c386768b974eea58ea8f61b7c396641ab24e5c Mon Dec 4 15:33:50 2017 -0800
    A python script that reads a json schema and write out the fields it describes. Not totally robust. Just works on the HCA json schema well enough.
• src/hca/v3v4/v3_fields
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    a79774b4bdd70c5531339148277c84b9f7d3c209 Wed Nov 29 20:27:49 2017 -0800
    Working on v3 to v4 field-by-field conversion for tagstorms.
• src/hca/v3v4/v3v4
  • lines changed 284, context: html, text, full: html, text
    a79774b4bdd70c5531339148277c84b9f7d3c209 Wed Nov 29 20:27:49 2017 -0800
    Working on v3 to v4 field-by-field conversion for tagstorms.
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    5f0479c39a7257c46305e8eb377f4bbc5d49d8b7 Thu Nov 30 13:30:55 2017 -0800
    Saving another round of changes, a little more than half way through manual pass through file.
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    44cc15f9add4a8190119eab297e93b07a3efce80 Mon Dec 4 13:38:05 2017 -0800
    Done first pass of conversion table.
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    e09f0fdb9dcecb24b2dd2de24801c09c238139c1 Tue Dec 5 11:01:14 2017 -0800
    Removing some trailing .[] that just confuse things.
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    00a7e5a92d475d0d32cc17c8b146fab00b6d82af Tue Dec 12 13:40:50 2017 -0800
    Fixing typo of period for tab.
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    cfa79208aac247b068c2049273305dfa279d9965 Wed Dec 20 16:43:31 2017 -0800
    A little polishing.
• src/hca/v3v4/v4_fields
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    a79774b4bdd70c5531339148277c84b9f7d3c209 Wed Nov 29 20:27:49 2017 -0800
    Working on v3 to v4 field-by-field conversion for tagstorms.
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
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    20b34092c7789385fb83f73b95c5fe3356a45727 Wed Dec 20 16:46:42 2017 -0800
    Documenting recent changes to cdwWebBrowse
• src/hg/cirm/cdw/lib/resetCdw
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    f2920bdb18db3fe25189112594547986aab8095c Wed Dec 20 16:46:04 2017 -0800
    Fixing a wrong md5sum for a an assembly .2bit file. Also coping with option name change in cdwAddAssembly
• src/hg/oneShot/freen/freen.c
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    cf0b1e4a2737a97cd5d7d7fcf0ca60a871f5b94b Mon Dec 11 17:44:23 2017 -0800
    Working out some functions needed for substituting arrays.
• src/inc/tagSchema.h
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    fae178c6d7f74bf2ec5966d559e3ea66dae42923 Wed Dec 20 16:44:37 2017 -0800
    Adding some new library functions that help handle arrays of objects.
• src/lib/tagSchema.c
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    fae178c6d7f74bf2ec5966d559e3ea66dae42923 Wed Dec 20 16:44:37 2017 -0800
    Adding some new library functions that help handle arrays of objects.
• src/tagStorm/tagStormDeleteTags/tagStormDeleteTags.c
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    af9e74e1bed088d7e073bde9fc313d63029cb689 Tue Dec 12 11:18:28 2017 -0800
    Making tagStormDeleteTags handle tags that represent fields in arrays of objects.
• src/tagStorm/tagStormDeleteTags/tests/input/delete.tags
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    af9e74e1bed088d7e073bde9fc313d63029cb689 Tue Dec 12 11:18:28 2017 -0800
    Making tagStormDeleteTags handle tags that represent fields in arrays of objects.
• src/tagStorm/tagStormDeleteTags/tests/input/in.tags
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    af9e74e1bed088d7e073bde9fc313d63029cb689 Tue Dec 12 11:18:28 2017 -0800
    Making tagStormDeleteTags handle tags that represent fields in arrays of objects.
• src/tagStorm/tagStormInfo/tagStormInfo.c
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    b814e8fcbb40cc31b4346c7b86a75ec836d0d525 Wed Dec 20 16:47:42 2017 -0800
    Removing unneeded external function prototype.
• src/tagStorm/tagStormRenameTags/array.2col
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    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
• src/tagStorm/tagStormRenameTags/array.out
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    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
• src/tagStorm/tagStormRenameTags/array.tags
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    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
• src/tagStorm/tagStormRenameTags/tagStormRenameTags.c
  • lines changed 22, context: html, text, full: html, text
    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
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    d6347dce5eca5a6bcc426434f2ee7d8878921006 Wed Dec 20 16:49:01 2017 -0800
    Adding noArray option, useful when you want to rename array.1.something to scaler.something among other things.