fix: #5570 ssr error instanceof false

What kind of change does this PR introduce? (check at least one)

[x] Bugfix
[ ] Feature
[ ] Code style update
[ ] Refactor
[ ] Build-related changes
[ ] Other, please describe:

Does this PR introduce a breaking change? (check one)

[ ] Yes
[x] No

If yes, please describe the impact and migration path for existing applications:
The PR fulfills these requirements:

[x ] It's submitted to the dev branch for v2.x (or to a previous version branch), not the master branch
[x] When resolving a specific issue, it's referenced in the PR's title (e.g. fix #xxx[,#xxx], where "xxx" is the issue number)
[x] All tests are passing: https://github.com/vuejs/vue/blob/dev/.github/CONTRIBUTING.md#development-setup
[ ] New/updated tests are included

If adding a new feature, the PR's description includes:

[ ] A convincing reason for adding this feature (to avoid wasting your time, it's best to open a suggestion issue first and wait for approval before working on it)

Other information:
#5570

Thanks for the PR! See https://github.com/vuejs/vue/issues/5570#issuecomment-298489179


typo correction

as per user report #5183 , so corrected word  Grand to grant

@RAJU2529 : Thanks for your contribution! The author(s) have been notified to review your proposed change.

@RAJU2529 : Thanks for your contribution! The author(s) have been notified to review your proposed change.

(Sorry for making "noise" with my off-topic comment, but I just had to note the funny side here, that "Grand admin" looks rather close to "Grand Admiral" or something like that.) 😄

(Sorry for making "noise" with my off-topic comment, but I just had to note the funny side here, that "Grand admin" looks rather close to "Grand Admiral" or something like that.) 😄


CI: GH Pages cleanup and build

:tada: This PR is included in version 2.0.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Export function with public signature not allowed

This is my sub-case of https://typescript.codeplex.com/workitem/1312.
Consider trivial export of function:
module foo {
    function bar() {}
    export var pub = bar;
}

Compiler will complain about exporting private type bar. I could type it explicitly as ()=>void but it doesn't scale to real world usage like wrapping functions with potentially complex, generic signatures:
module foo {
    function wrap<T extends Function>(f: T): T {
        /* complex wrapping */
        return f;
    }

    /* complex generic signature */
    function _bar<T>() {}

    export var bar = wrap(_bar);
}

This feature is still not released, or am I mistaken? Running version 1.3 of the compiler.

This issue as described is fixed in 1.3. Can you post an example of something you'd expect to work that doesn't?

class Foo {}

var foo = new Foo();

export = foo;

I don't know if this is supposed to work or not. I'm getting the old "Exported variable 'foo' has or is using private type Foo" message.

That code compiles for me in 1.3 as long as --d isn't specified, which is the expected behavior.

@RyanCavanaugh My fault. You are totally right - it does compile. R# was giving me a hard time.

@thrandre off topic, but do you know if there's a way to get rid of resharpers incorrect warning about this? :)


where clause with associations is broken

In MetaWhere it was possible to do the following:
Post.where(user: User.first).to_sql
=> "SELECT posts.* FROM posts WHERE posts.user_id = 1"

In Squeel this produces:
Post.where(user: User.first).to_sql
=> "SELECT posts.* FROM posts WHERE posts.user = 1"

Which causes a MySql Error:
Mysql2::Error: Unknown column 'posts.user' in 'where clause':

ActiveRecord values were intentionally removed when transitioning from MetaWhere -> Squeel


Ran conda smithy register-ci and rerender.

Hi! This is the friendly automated conda-forge-linting service.
I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.


Test run against redis-rb master is failing on Travis CI

Looks like it's failing to resolve the dependencies, rather than failing to run against redis.rb. Possibly fixing this shows us whether #177 will have any failures too.
We should update the redisrb-master.gemfile so it installs on Travis CI.

Looks like tests are passing now

Tests are green across all supported platforms so I'm closing this for now


Improve script logic to detect if a change needs verification

The query parameter has now been replaced to expect a string in JSON
format.
It now checks all the patches from the last 8 hours by default.
Instead of querying using "to-groups" now it uses the repository ID.

LGTM


subprocess.CalledProcessError: Command 'set -o pipefail

I've trying to install and test using the AshekanziTrio reference from here ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio
I keep getting stalled at the annotation step for various reasons each time.  This is my latest error:
[2019-11-02T02:45Z] Annotate VCF file: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, gatk-haplotype
[2019-11-02T02:45Z] Annotate with dbSNP
[2019-11-02T02:45Z] =============================================
[2019-11-02T02:45Z] vcfanno version 0.3.2 [built with go1.12.1]
[2019-11-02T02:45Z] see: https://github.com/brentp/vcfanno
[2019-11-02T02:45Z] =============================================
[2019-11-02T02:45Z] vcfanno.go:115: found 1 sources from 1 files
[2019-11-02T02:45Z] vcfanno.go:145: using 2 worker threads to decompress bgzip file
[2019-11-02T02:45Z] vcfanno.go:194: Info Error: rs_ids not found in INFO >> this error/warning may occur many times. reporting once here...
[2019-11-02T02:53Z] vcfanno.go:248: annotated 418338 variants in 500.01 seconds (836.7 / second)
[2019-11-02T02:53Z] tabix index AshkenaziFam-annotated.vcf.gz
[2019-11-02T02:53Z] Filtering for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, gatk-haplotype
[2019-11-02T02:53Z] Removing variants with missing alts from<EMAIL_ADDRESS>[2019-11-02T02:53Z] bgzip AshkenaziFam-annotated-nomissingalt.vcf
[2019-11-02T02:53Z] tabix index AshkenaziFam-annotated-nomissingalt.vcf.gz
[2019-11-02T02:54Z] Cutoff-based soft filtering<EMAIL_ADDRESS>with TYPE="snp" && (MQRankSum < -12.5 || ReadPosRankSum < -8.0 || QD < 2.0 || FS > 60.0 || (QD < 10.0 && AD[0:1] / (AD[0:1] + AD[0:0]) < 0.25 && ReadPosRankSum < 0.0) || MQ < 30.0) : 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup
[2019-11-02T02:54Z] tabix index AshkenaziFam-annotated-nomissingalt-filterSNP.vcf.gz
[2019-11-02T02:54Z] Cutoff-based soft filtering<EMAIL_ADDRESS>with TYPE="indel" && (ReadPosRankSum < -20.0 || QD < 2.0 || FS > 200.0 || SOR > 10.0 || (QD < 10.0 && AD[0:1] / (AD[0:1] + AD[0:0]) < 0.25 && ReadPosRankSum < 0.0)) : 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup
[2019-11-02T02:54Z] tabix index AshkenaziFam-annotated-nomissingalt-filterSNP-filterINDEL.vcf.gz
[2019-11-02T02:54Z] Prioritization for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, gatk-haplotype
[2019-11-02T02:54Z] Finalizing variant calls: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, samtools
[2019-11-02T02:54Z] Calculating variation effects for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, samtools
[2019-11-02T02:54Z] Annotate VCF file: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, samtools
[2019-11-02T02:54Z] Annotate with dbSNP
[2019-11-02T02:54Z] =============================================
[2019-11-02T02:54Z] vcfanno version 0.3.2 [built with go1.12.1]
[2019-11-02T02:54Z] see: https://github.com/brentp/vcfanno
[2019-11-02T02:54Z] =============================================
[2019-11-02T02:54Z] vcfanno.go:115: found 1 sources from 1 files
[2019-11-02T02:54Z] vcfanno.go:145: using 2 worker threads to decompress bgzip file
[2019-11-02T02:54Z] vcfanno.go:194: Info Error: rs_ids not found in INFO >> this error/warning may occur many times. reporting once here...
[2019-11-02T03:02Z] vcfanno.go:248: annotated 500075 variants in 519.21 seconds (963.2 / second)
[2019-11-02T03:02Z] tabix index AshkenaziFam-annotated.vcf.gz
[2019-11-02T03:02Z] Filtering for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, samtools
[2019-11-02T03:02Z] Cutoff-based soft filtering<EMAIL_ADDRESS>with ((AC[0] / AN) <= 0.5 && max(FORMAT/DP) < 4 && %QUAL < 20) || (max(FORMAT/DP) < 13 && %QUAL < 10) || ((AC[0] / AN) > 0.5 && max(format/DP) < 4 && %QUAL < 50) : 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup
[2019-11-02T03:02Z] tabix index AshkenaziFam-annotated-filter.vcf.gz
[2019-11-02T03:02Z] Prioritization for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, samtools
[2019-11-02T03:02Z] Finalizing variant calls: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, platypus
[2019-11-02T03:02Z] Calculating variation effects for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, platypus
[2019-11-02T03:02Z] Annotate VCF file: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, platypus
[2019-11-02T03:02Z] Annotate with dbSNP
[2019-11-02T03:02Z] =============================================
[2019-11-02T03:02Z] vcfanno version 0.3.2 [built with go1.12.1]
[2019-11-02T03:02Z] see: https://github.com/brentp/vcfanno
[2019-11-02T03:02Z] =============================================
[2019-11-02T03:02Z] vcfanno.go:115: found 1 sources from 1 files
[2019-11-02T03:02Z] vcfanno.go:145: using 2 worker threads to decompress bgzip file
[2019-11-02T03:02Z] vcfanno.go:194: Info Error: rs_ids not found in INFO >> this error/warning may occur many times. reporting once here...
[2019-11-02T03:11Z] vcfanno.go:248: annotated 411560 variants in 489.52 seconds (840.8 / second)
[2019-11-02T03:11Z] tabix index AshkenaziFam-annotated.vcf.gz
[2019-11-02T03:11Z] Filtering for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, platypus
[2019-11-02T03:11Z] Cutoff-based soft filtering<EMAIL_ADDRESS>with (FR[0] <= 0.5 && TC < 4 && %QUAL < 20) || (TC < 13 && %QUAL < 10) || (FR[0] > 0.5 && TC < 4 && %QUAL < 50) : 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup
[2019-11-02T03:11Z] [W::bcf_hdr_check_sanity] GL should be declared as Number=G
[2019-11-02T03:11Z] tabix index AshkenaziFam-annotated-filter.vcf.gz
[2019-11-02T03:11Z] Prioritization for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, platypus
[2019-11-02T03:11Z] Finalizing variant calls: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, freebayes
[2019-11-02T03:11Z] Calculating variation effects for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, freebayes
[2019-11-02T03:11Z] Annotate VCF file: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, freebayes
[2019-11-02T03:11Z] Annotate with dbSNP
[2019-11-02T03:11Z] =============================================
[2019-11-02T03:11Z] vcfanno version 0.3.2 [built with go1.12.1]
[2019-11-02T03:11Z] see: https://github.com/brentp/vcfanno
[2019-11-02T03:11Z] =============================================
[2019-11-02T03:11Z] vcfanno.go:115: found 1 sources from 1 files
[2019-11-02T03:11Z] vcfanno.go:145: using 2 worker threads to decompress bgzip file
[2019-11-02T03:11Z] vcfanno.go:194: Info Error: rs_ids not found in INFO >> this error/warning may occur many times. reporting once here...
[2019-11-02T03:19Z] vcfanno.go:248: annotated 459101 variants in 502.86 seconds (913.0 / second)
[2019-11-02T03:19Z] tabix index AshkenaziFam-annotated.vcf.gz
[2019-11-02T03:19Z] Filtering for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, freebayes
[2019-11-02T03:19Z] Cutoff-based soft filtering<EMAIL_ADDRESS>with (AF[0] <= 0.5 && (max(FORMAT/DP) < 4 || (max(FORMAT/DP) < 13 && %QUAL < 10))) || (AF[0] > 0.5 && (max(FORMAT/DP) < 4 && %QUAL < 50)) : 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup
[2019-11-02T03:19Z] tabix index AshkenaziFam-annotated-filter.vcf.gz
[2019-11-02T03:19Z] Prioritization for 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, freebayes
[2019-11-02T03:19Z] multiprocessing: split_variants_by_sample
[2019-11-02T03:19Z] Timing: prepped BAM merging
[2019-11-02T03:19Z] Timing: validation
[2019-11-02T03:19Z] multiprocessing: compare_to_rm
[2019-11-02T03:19Z] Timing: ensemble calling
[2019-11-02T03:19Z] multiprocessing: combine_calls
[2019-11-02T03:19Z] Ensemble consensus calls for AshkenaziFam: gatk-haplotype,samtools,platypus,freebayes
[2019-11-02T03:19Z] Multi-allelic to single allele
[2019-11-02T03:19Z] normalize v0.5
[2019-11-02T03:19Z] options:     input VCF file                                  -
[2019-11-02T03:19Z]          [o] output VCF file                                 -
[2019-11-02T03:19Z]          [w] sorting window size                             10000
[2019-11-02T03:19Z]          [n] no fail on reference inconsistency for non SNPs true
[2019-11-02T03:19Z]          [q] quiet                                           false
[2019-11-02T03:19Z]          [d] debug                                           false
[2019-11-02T03:19Z]          [r] reference FASTA file<EMAIL_ADDRESS>[2019-11-02T03:19Z] decompose v0.5
[2019-11-02T03:19Z] options:     input VCF file        -
[2019-11-02T03:19Z]          [s] smart decomposition   true (experimental)
[2019-11-02T03:19Z]          [o] output VCF file       -
[2019-11-02T03:20Z] stats: no. variants                 : 395817
[2019-11-02T03:20Z]        no. biallelic variants       : 390828
[2019-11-02T03:20Z]        no. multiallelic variants    : 4989
[2019-11-02T03:20Z]        no. additional biallelics    : 5489
[2019-11-02T03:20Z]        total no. of biallelics      : 401306
[2019-11-02T03:20Z] Time elapsed: 4.38s
[2019-11-02T03:20Z] stats: biallelic
[2019-11-02T03:20Z]           no. left trimmed                      : 0
[2019-11-02T03:20Z]           no. right trimmed                     : 2359
[2019-11-02T03:20Z]           no. left and right trimmed            : 0
[2019-11-02T03:20Z]           no. right trimmed and left aligned    : 0
[2019-11-02T03:20Z]           no. left aligned                      : 26
[2019-11-02T03:20Z]        total no. biallelic normalized           : 2385
[2019-11-02T03:20Z]        multiallelic
[2019-11-02T03:20Z]           no. left trimmed                      : 0
[2019-11-02T03:20Z]           no. right trimmed                     : 0
[2019-11-02T03:20Z]           no. left and right trimmed            : 0
[2019-11-02T03:20Z]           no. right trimmed and left aligned    : 0
[2019-11-02T03:20Z]           no. left aligned                      : 0
[2019-11-02T03:20Z]        total no. multiallelic normalized        : 0
[2019-11-02T03:20Z]        total no. variants normalized            : 2385
[2019-11-02T03:20Z]        total no. variants observed              : 401306
[2019-11-02T03:20Z]        total no. reference observed             : 0
[2019-11-02T03:20Z] Time elapsed: 5.36s
[2019-11-02T03:20Z] tabix index AshkenaziFam-gatk-haplotype-noeff-decompose.vcf.gz
[2019-11-02T03:20Z] Multi-allelic to single allele
[2019-11-02T03:20Z] decompose v0.5
[2019-11-02T03:20Z] options:     input VCF file        -
[2019-11-02T03:20Z]          [s] smart decomposition   true (experimental)
[2019-11-02T03:20Z] normalize v         [o] output VCF file       -0.5
[2019-11-02T03:20Z] options:     input VCF file                                  -
[2019-11-02T03:20Z]          [o] output VCF file                                 -
[2019-11-02T03:20Z]          [w] sorting window size                             10000
[2019-11-02T03:20Z]          [n] no fail on reference inconsistency for non SNPs true
[2019-11-02T03:20Z]          [q] quiet                                           false
[2019-11-02T03:20Z]          [d] debug                                           false
[2019-11-02T03:20Z]          [r] reference FASTA file<EMAIL_ADDRESS>[2019-11-02T03:20Z] stats: no. variants                 : 462671
[2019-11-02T03:20Z]        no. biallelic variants       : 458527
[2019-11-02T03:20Z]        no. multiallelic variants    : 4144
[2019-11-02T03:20Z]        no. additional biallelics    : 4296
[2019-11-02T03:20Z]        total no. of biallelics      : 466967
[2019-11-02T03:20Z] Time elapsed: 4.23s
[2019-11-02T03:20Z] stats: biallelic
[2019-11-02T03:20Z]           no. left trimmed                      : 0
[2019-11-02T03:20Z]           no. right trimmed                     : 1657
[2019-11-02T03:20Z]           no. left and right trimmed            : 0
[2019-11-02T03:20Z]           no. right trimmed and left aligned    : 0
[2019-11-02T03:20Z]           no. left aligned                      : 13
[2019-11-02T03:20Z]        total no. biallelic normalized           : 1670
[2019-11-02T03:20Z]        multiallelic
[2019-11-02T03:20Z]           no. left trimmed                      : 0
[2019-11-02T03:20Z]           no. right trimmed                     : 0
[2019-11-02T03:20Z]           no. left and right trimmed            : 0
[2019-11-02T03:20Z]           no. right trimmed and left aligned    : 0
[2019-11-02T03:20Z]           no. left aligned                      : 0
[2019-11-02T03:20Z]        total no. multiallelic normalized        : 0
[2019-11-02T03:20Z]        total no. variants normalized            : 1670
[2019-11-02T03:20Z]        total no. variants observed              : 466967
[2019-11-02T03:20Z]        total no. reference observed             : 0
[2019-11-02T03:20Z] Time elapsed: 5.18s
[2019-11-02T03:20Z] tabix index AshkenaziFam-samtools-noeff-decompose.vcf.gz
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
[2019-11-02T03:20Z] Multi-allelic to single allele
[2019-11-02T03:20Z] decompose v0.5
[2019-11-02T03:20Z] options:     input VCF file        -
[2019-11-02T03:20Z]          [s] smart decomposition   truenormalize v (experimental)
[2019-11-02T03:20Z]          [o] output VCF file       0.5-
[2019-11-02T03:20Z] options:     input VCF file                                  -
[2019-11-02T03:20Z]          [o] output VCF file                                 -
[2019-11-02T03:20Z]          [w] sorting window size                             10000
[2019-11-02T03:20Z]          [n] no fail on reference inconsistency for non SNPs true
[2019-11-02T03:20Z]          [q] quiet                                           false
[2019-11-02T03:20Z]          [d] debug                                           false
[2019-11-02T03:20Z]          [r] reference FASTA file<EMAIL_ADDRESS>[2019-11-02T03:20Z] [W::bcf_hdr_check_sanity] GL should be declared as Number=G
[2019-11-02T03:21Z] stats: no. variants                 : 313938
[2019-11-02T03:21Z]        no. biallelic variants       : 312233
[2019-11-02T03:21Z]        no. multiallelic variants    : 1705
[2019-11-02T03:21Z]        no. additional biallelics    : 1962
[2019-11-02T03:21Z]        total no. of biallelics      : 315900
[2019-11-02T03:21Z] Time elapsed: 4.85s
[2019-11-02T03:21Z] stats: biallelic
[2019-11-02T03:21Z]           no. left trimmed                      : 0
[2019-11-02T03:21Z]           no. right trimmed                     : 1220
[2019-11-02T03:21Z]           no. left and right trimmed            : 0
[2019-11-02T03:21Z]           no. right trimmed and left aligned    : 1
[2019-11-02T03:21Z]           no. left aligned                      : 17
[2019-11-02T03:21Z]        total no. biallelic normalized           : 1238
[2019-11-02T03:21Z]        multiallelic
[2019-11-02T03:21Z]           no. left trimmed                      : 0
[2019-11-02T03:21Z]           no. right trimmed                     : 0
[2019-11-02T03:21Z]           no. left and right trimmed            : 0
[2019-11-02T03:21Z]           no. right trimmed and left aligned    : 0
[2019-11-02T03:21Z]           no. left aligned                      : 0
[2019-11-02T03:21Z]        total no. multiallelic normalized        : 0
[2019-11-02T03:21Z]        total no. variants normalized            : 1238
[2019-11-02T03:21Z]        total no. variants observed              : 315900
[2019-11-02T03:21Z]        total no. reference observed             : 0
[2019-11-02T03:21Z] Time elapsed: 5.39s
[2019-11-02T03:21Z] tabix index AshkenaziFam-platypus-noeff-decompose.vcf.gz
[2019-11-02T03:21Z] Multi-allelic to single allele
[2019-11-02T03:21Z] decompose v0.5
[2019-11-02T03:21Z] options:     input VCF file        -
[2019-11-02T03:21Z]          [s] smart decomposition   true (experimental)
[2019-11-02T03:21Z]          [o] output VCF file       -
[2019-11-02T03:21Z] normalize v0.5
[2019-11-02T03:21Z] options:     input VCF file                                  -
[2019-11-02T03:21Z]          [o] output VCF file                                 -
[2019-11-02T03:21Z]          [w] sorting window size                             10000
[2019-11-02T03:21Z]          [n] no fail on reference inconsistency for non SNPs true
[2019-11-02T03:21Z]          [q] quiet                                           false
[2019-11-02T03:21Z]          [d] debug                                           false
[2019-11-02T03:21Z]          [r] reference FASTA file<EMAIL_ADDRESS>[2019-11-02T03:22Z] stats: no. variants                 : 437621
[2019-11-02T03:22Z]        no. biallelic variants       : 434496
[2019-11-02T03:22Z]        no. multiallelic variants    : 3125
[2019-11-02T03:22Z]        no. additional biallelics    : 3212
[2019-11-02T03:22Z]        total no. of biallelics      : 440833
[2019-11-02T03:22Z] Time elapsed: 9.43s
[2019-11-02T03:22Z] stats: biallelic
[2019-11-02T03:22Z]           no. left trimmed                      : 0
[2019-11-02T03:22Z]           no. right trimmed                     : 987
[2019-11-02T03:22Z]           no. left and right trimmed            : 0
[2019-11-02T03:22Z]           no. right trimmed and left aligned    : 5
[2019-11-02T03:22Z]           no. left aligned                      : 15
[2019-11-02T03:22Z]        total no. biallelic normalized           : 1007
[2019-11-02T03:22Z]        multiallelic
[2019-11-02T03:22Z]           no. left trimmed                      : 0
[2019-11-02T03:22Z]           no. right trimmed                     : 0
[2019-11-02T03:22Z]           no. left and right trimmed            : 0
[2019-11-02T03:22Z]           no. right trimmed and left aligned    : 0
[2019-11-02T03:22Z]           no. left aligned                      : 0
[2019-11-02T03:22Z]        total no. multiallelic normalized        : 0
[2019-11-02T03:22Z]        total no. variants normalized            : 1007
[2019-11-02T03:22Z]        total no. variants observed              : 440833
[2019-11-02T03:22Z]        total no. reference observed             : 0
[2019-11-02T03:22Z] Time elapsed: 10.35s
[2019-11-02T03:22Z] tabix index AshkenaziFam-freebayes-noeff-decompose.vcf.gz
[2019-11-02T03:22Z] Ensemble intersection calling: AshkenaziFam
[2019-11-02T03:27Z] Timing: validation summary
[2019-11-02T03:27Z] Timing: structural variation
[2019-11-02T03:27Z] Timing: structural variation
[2019-11-02T03:27Z] Timing: structural variation ensemble
[2019-11-02T03:27Z] Timing: structural variation validation
[2019-11-02T03:27Z] multiprocessing: validate_sv
[2019-11-02T03:27Z] Timing: heterogeneity
[2019-11-02T03:27Z] Timing: population database
[2019-11-02T03:27Z] multiprocessing: prep_gemini_db
[2019-11-02T03:27Z] Not running gemini, input data not found: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup
[2019-11-02T03:27Z] Not running gemini, input data not found: 151002_7001448_0359_AC7F6GANXX_Sample_HG003-EEogPU_v02-KIT-Av5_TCTTCACA_L008_posiSrt_markDup
[2019-11-02T03:27Z] Not running gemini, input data not found: 151002_7001448_0359_AC7F6GANXX_Sample_HG004-EEogPU_v02-KIT-Av5_CCGAAGTA_L008_posiSrt_markDup
[2019-11-02T03:27Z] Annotating<EMAIL_ADDRESS>with vcfanno, using<EMAIL_ADDRESS>[2019-11-02T03:27Z] =============================================
[2019-11-02T03:27Z] vcfanno version 0.3.2 [built with go1.12.1]
[2019-11-02T03:27Z] see: https://github.com/brentp/vcfanno
[2019-11-02T03:27Z] =============================================
[2019-11-02T03:27Z] vcfanno.go:115: found 16 sources from 5 files
[2019-11-02T03:27Z] vcfanno.go:145: using 2 worker threads to decompress bgzip file
[2019-11-02T03:27Z] vcfanno.go:194: Info Error: AN not found in header >> this error/warning may occur many times. reporting once here...
[2019-11-02T03:27Z] vcfanno.go:194: Info Error: gnomad_an not found in INFO >> this error/warning may occur many times. reporting once here...
[2019-11-02T03:27Z] panic: runtime error: index out of range
[2019-11-02T03:27Z] goroutine 25906 [running]:
[2019-11-02T03:27Z] github.com/brentp/vcfanno/api.collect(0x7f1f7b523740, 0xc0057508d0, 0xc0016cbec0, 0x3, 0x4, 0xc000106c00, 0x1, 0x0, 0x0, 0x1, ...)
[2019-11-02T03:27Z] 	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:367 +0x2727
[2019-11-02T03:27Z] github.com/brentp/vcfanno/api.(*Annotator).AnnotateOne(0xc0000b2f40, 0x893ae0, 0xc0057508d0, 0x48d001, 0x0, 0x0, 0x0, 0x0, 0x0)
[2019-11-02T03:27Z] 	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:466 +0x1d7
[2019-11-02T03:27Z] github.com/brentp/vcfanno/api.(*Annotator).AnnotateEnds(0xc0000b2f40, 0x893ae0, 0xc0057508d0, 0x0, 0x0, 0x889500, 0xc007607230)
[2019-11-02T03:27Z] 	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:892 +0xaf2
[2019-11-02T03:27Z] main.main.func1(0x893ae0, 0xc0057508d0)
[2019-11-02T03:27Z] 	/home/brentp/go/src/github.com/brentp/vcfanno/vcfanno.go:182 +0x71
[2019-11-02T03:27Z] github.com/brentp/irelate.PIRelate.func1.1(0xc001a2cbd0, 0xc00531d300, 0x190, 0x190, 0xc0086401e0)
[2019-11-02T03:27Z] 	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:202 +0x89
[2019-11-02T03:27Z] created by github.com/brentp/irelate.PIRelate.func1
[2019-11-02T03:27Z] 	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:199 +0x89
[2019-11-02T03:27Z] Uncaught exception occurred
Traceback (most recent call last):
  File<EMAIL_ADDRESS>line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File<EMAIL_ADDRESS>line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail<EMAIL_ADDRESS>-p 7 -lua<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>|  bgzip -c ><EMAIL_ADDRESS>=============================================
vcfanno version 0.3.2 [built with go1.12.1]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 16 sources from 5 files
vcfanno.go:145: using 2 worker threads to decompress bgzip file
vcfanno.go:194: Info Error: AN not found in header >> this error/warning may occur many times. reporting once here...
vcfanno.go:194: Info Error: gnomad_an not found in INFO >> this error/warning may occur many times. reporting once here...
panic: runtime error: index out of range
goroutine 25906 [running]:
github.com/brentp/vcfanno/api.collect(0x7f1f7b523740, 0xc0057508d0, 0xc0016cbec0, 0x3, 0x4, 0xc000106c00, 0x1, 0x0, 0x0, 0x1, ...)
	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:367 +0x2727
github.com/brentp/vcfanno/api.(*Annotator).AnnotateOne(0xc0000b2f40, 0x893ae0, 0xc0057508d0, 0x48d001, 0x0, 0x0, 0x0, 0x0, 0x0)
	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:466 +0x1d7
github.com/brentp/vcfanno/api.(*Annotator).AnnotateEnds(0xc0000b2f40, 0x893ae0, 0xc0057508d0, 0x0, 0x0, 0x889500, 0xc007607230)
	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:892 +0xaf2
main.main.func1(0x893ae0, 0xc0057508d0)
	/home/brentp/go/src/github.com/brentp/vcfanno/vcfanno.go:182 +0x71
github.com/brentp/irelate.PIRelate.func1.1(0xc001a2cbd0, 0xc00531d300, 0x190, 0x190, 0xc0086401e0)
	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:202 +0x89
created by github.com/brentp/irelate.PIRelate.func1
	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:199 +0x89
' returned non-zero exit status 2.
Traceback (most recent call last):
  File<EMAIL_ADDRESS>line 245, in <module>
    main(**kwargs)
  File<EMAIL_ADDRESS>line 46, in main
    run_main(**kwargs)
  File<EMAIL_ADDRESS>line 50, in run_main
    fc_dir, run_info_yaml)
  File<EMAIL_ADDRESS>line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File<EMAIL_ADDRESS>line 188, in variant2pipeline
    samples = population.prep_db_parallel(samples, run_parallel)
  File<EMAIL_ADDRESS>line 401, in prep_db_parallel
    output = parallel_fn("prep_gemini_db", to_process)
  File<EMAIL_ADDRESS>line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File<EMAIL_ADDRESS>line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
  File<EMAIL_ADDRESS>line 921, in __call__
    if self.dispatch_one_batch(iterator):
  File<EMAIL_ADDRESS>line 759, in dispatch_one_batch
    self._dispatch(tasks)
  File<EMAIL_ADDRESS>line 716, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File<EMAIL_ADDRESS>line 182, in apply_async
    result = ImmediateResult(func)
  File<EMAIL_ADDRESS>line 549, in __init__
    self.results = batch()
  File<EMAIL_ADDRESS>line 225, in __call__
    for func, args, kwargs in self.items]
  File<EMAIL_ADDRESS>line 225, in <listcomp>
    for func, args, kwargs in self.items]
  File<EMAIL_ADDRESS>line 55, in wrapper
    return f(*args, **kwargs)
  File<EMAIL_ADDRESS>line 383, in prep_gemini_db
    return population.prep_gemini_db(*args)
  File<EMAIL_ADDRESS>line 40, in prep_gemini_db
    ann_vcf = run_vcfanno(gemini_vcf, data, decomposed)
  File<EMAIL_ADDRESS>line 119, in run_vcfanno
    decomposed=decomposed)
  File<EMAIL_ADDRESS>line 44, in run
    do.run(cmd.format(**locals()), message)
  File<EMAIL_ADDRESS>line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File<EMAIL_ADDRESS>line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail<EMAIL_ADDRESS>-p 7 -lua<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>|  bgzip -c ><EMAIL_ADDRESS>=============================================
vcfanno version 0.3.2 [built with go1.12.1]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 16 sources from 5 files
vcfanno.go:145: using 2 worker threads to decompress bgzip file
vcfanno.go:194: Info Error: AN not found in header >> this error/warning may occur many times. reporting once here...
vcfanno.go:194: Info Error: gnomad_an not found in INFO >> this error/warning may occur many times. reporting once here...
panic: runtime error: index out of range
goroutine 25906 [running]:
github.com/brentp/vcfanno/api.collect(0x7f1f7b523740, 0xc0057508d0, 0xc0016cbec0, 0x3, 0x4, 0xc000106c00, 0x1, 0x0, 0x0, 0x1, ...)
	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:367 +0x2727
github.com/brentp/vcfanno/api.(*Annotator).AnnotateOne(0xc0000b2f40, 0x893ae0, 0xc0057508d0, 0x48d001, 0x0, 0x0, 0x0, 0x0, 0x0)
	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:466 +0x1d7
github.com/brentp/vcfanno/api.(*Annotator).AnnotateEnds(0xc0000b2f40, 0x893ae0, 0xc0057508d0, 0x0, 0x0, 0x889500, 0xc007607230)
	/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:892 +0xaf2
main.main.func1(0x893ae0, 0xc0057508d0)
	/home/brentp/go/src/github.com/brentp/vcfanno/vcfanno.go:182 +0x71
github.com/brentp/irelate.PIRelate.func1.1(0xc001a2cbd0, 0xc00531d300, 0x190, 0x190, 0xc0086401e0)
	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:202 +0x89
created by github.com/brentp/irelate.PIRelate.func1
	/home/brentp/go/src/github.com/brentp/irelate/parallel.go:199 +0x89
' returned non-zero exit status 2.

I tried running just:
set -o pipefail<EMAIL_ADDRESS>-p 7 -lua<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>|  bgzip -c ><EMAIL_ADDRESS>
I got the error bash:

I went looking to see if the AshkenaziFam-ensemble-annotated-cre.vcfanno.vcf.gz was anywhere in my work directory and couldn't find it.
Any thoughts?

Sorry for the formatting, I'm not sure why it ended up looking this way.

The last error didn't show up in my post.  It was
bash<EMAIL_ADDRESS>No such file or directory

Taryn;
Thanks for the detailed report and apologies about the issue. Something problematic is happening when annotating the file with vcfanno. You should be able to reproduce by running without referencing the transactional directory (which doesn't exist outside of the bcbio run):
<EMAIL_ADDRESS>-p 7 -lua<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>|  bgzip -c > AshkenaziFam-ensemble-annotated-cre.vcfanno.vcf.gz

To isolate, we'd need to figure out what you're annotating with in the .conf and .lua files and see if there is something problematic there, or in the input ensemble VCF file. If you can share these so we could reproduce, that would help, or you could try adjusting the configuration in the vcfanno .conf file to see if you can isolate the annotation that's failing. Hope this helps and thanks much for the help debugging.

Thanks for your help.  Here are the .conf and .lua files (github was telling me they didn't support the file types so I added .txt to the end)
AshkenaziFam-ensemble-annotated-cre.vcfanno-combine.lua.txt
AshkenaziFam-ensemble-annotated-cre.vcfanno-combine.conf.txt
The clinvar.vcf.txt and the dbsnp-151.vcf.gz were in the variation folder when I downloaded bcbio_nextgen.  The dbNSFP.txt.gz and the gnomad_genome.vcf.gz were downloaded using
bcbio_nextgen.py upgrade --datatarget dbnsfp
bcbio_nextgen.py upgrade --datatarget gnomad
Gnomad took about 2 weeks to download.
When I ran the line you gave me I got the same error
vcfanno version 0.3.2 [built with go1.12.1]
see: https://github.com/brentp/vcfanno
vcfanno.go:115: found 16 sources from 5 files
vcfanno.go:145: using 2 worker threads to decompress bgzip file
vcfanno.go:194: Info Error: AN not found in header >> this error/warning may occur many times. reporting once here...
vcfanno.go:194: Info Error: gnomad_an not found in INFO >> this error/warning may occur many times. reporting once here...
panic: runtime error: index out of range
goroutine 32416 [running]:
github.com/brentp/vcfanno/api.collect(0x7f85f0f60868, 0xc001059f20, 0xc009cc1580, 0x6, 0x8, 0xc0000fcc00, 0x1, 0x0, 0x0, 0x1, ...)
/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:367 +0x2727
github.com/brentp/vcfanno/api.(*Annotator).AnnotateOne(0xc0000aef40, 0x893ae0, 0xc001059f20, 0xd6401, 0x0, 0x0, 0x0, 0x0, 0x0)
/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:466 +0x1d7
github.com/brentp/vcfanno/api.(*Annotator).AnnotateEnds(0xc0000aef40, 0x893ae0, 0xc001059f20, 0x0, 0x0, 0x889500, 0xc007e43aa0)
/home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:892 +0xaf2
main.main.func1(0x893ae0, 0xc001059f20)
/home/brentp/go/src/github.com/brentp/vcfanno/vcfanno.go:182 +0x71
github.com/brentp/irelate.PIRelate.func1.1(0xc001a669f0, 0xc005427980, 0x190, 0x190, 0xc0076bc000)
/home/brentp/go/src/github.com/brentp/irelate/parallel.go:202 +0x89
created by github.com/brentp/irelate.PIRelate.func1
/home/brentp/go/src/github.com/brentp/irelate/parallel.go:199 +0x89

When I removed all of the [postannotation]s from the .conf file I got the same error, but when I removed everything for gnomad I think it worked.
=============================================
vcfanno version 0.3.2 [built with go1.12.1]
see: https://github.com/brentp/vcfanno
vcfanno.go:115: found 8 sources from 3 files
vcfanno.go:145: using 2 worker threads to decompress bgzip file
vcfanno.go:194: Info Error: CLNSIG not found in INFO >> this error/warning may occur many times. reporting once here...
bix.go:251: chromosome MT not found in<EMAIL_ADDRESS>vcfanno.go:248: annotated 440673 variants in 878.06 seconds (501.9 / second)

Thanks for following up with all these details. My guess from looking through the configuration is the dbNSFP annotation:
#dbNSFP v3.5
[[annotation]]
<EMAIL_ADDRESS>names = ["CADD_phred","phyloP20way_mammalian","phastCons20way_mammalian","Vest3_score","Revel_score","Gerp_score"]
columns = [79,111,115,58,70,107]
ops = ["first","first","first","first","first","first"]

I believe it's the columns which can cause the index lookup error you're seeing. If that is the issue, it might be worth running without dbNSFP to see if that resolves the problem. If you really need dbNSFP annotations, @matthdsm might be able to help with debugging the underlying issue. Hope this helps and thanks again for the work to figure out the issue.

Thank you.  I've started rerunning it without dbNSFP to see if that works.  I would ultimately like to have the dbNSFP annotations.
P.S. I'm going to be away for the week so I won't be able to reply again until Saturday.

The program finished this time, but I am missing the gemini db files.  This isn't surprising to me because I had the following error during the run:
Not running gemini, input data not found: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup
[2019-11-02T03:27Z] Not running gemini, input data not found: 151002_7001448_0359_AC7F6GANXX_Sample_HG003-EEogPU_v02-KIT-Av5_TCTTCACA_L008_posiSrt_markDup
[2019-11-02T03:27Z] Not running gemini, input data not found: 151002_7001448_0359_AC7F6GANXX_Sample_HG004-EEogPU_v02-KIT-Av5_CCGAAGTA_L008_posiSrt_markDup
I'm not sure why those files would be missing or what part of the program would have them.  Should I open up a separate issue for this?

Taryn;
Thanks for following up, great to hear that at least identified the issue. I'm not as familiar with dbNSFP so not sure what changed with the column structure there, but hopefully the other annotations bcbio provides are useful.
For gemini, you'd need to install the gemini specific data with --datatarget gemini if you haven't already:
https://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#customizing-data-installation
and that should hopefully get gemini databases built as part of the process. This is going to be most useful with human build 37 where all the resources have been curated and prepared.
Hope this helps with getting a gemini database created if that's useful for your downstream analysis. Thanks again for the work debugging.

Hi @tathey, Brad,
Sorry to be MIA for a a while, I was on vacation.
As Brad said, the gemini datatarget is needed for bcbio to create the gemini db's. However, this is a simple check, and if you believe you have all required data installed, you can bypass this by adding gemini to the datatarget section in install-params.yaml.
As for your annotation issues, I think  the error might stem from the gnomad dataset. the config/data have been in flux, whereas dbNSFP hasn't been touched for a while, so it seems like thats a more likely candidate.
Cheers
M

Thanks for all the info.  My feeling is that it is dbNSFP because it wasn't running when I had the dbNSFP in my config file, but once I removed it the program ran to completion.
I've now discovered (with the help of CCM at SickKids) that vep isn't running and I'm not sure why.  I tried to run vep on my own using the following command:
unset PERL5LIB && export PATH=~/local/share/bcbio/anaconda/bin:"$PATH" && vep --vcf -o stdout -i ~/Pipeline_Tests/Test11/AshkenaziFam/work/gatk-haplotype/AshkenaziFam.vcf.gz --fork 7 --species homo_sapiens --no_stats --cache --offline --dir ~/local/share/bcbio/genomes/Hsapiens/GRCh37/vep --symbol --numbers --biotype --total_length --canonical --gene_phenotype --ccds --uniprot --domains --regulatory --protein --tsl --appris --af --max_af --af_1kg --af_esp --af_gnomad --pubmed --variant_class --allele_number --fasta ~/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa.gz --plugin LoF,human_ancestor_fa:~/local/share/bcbio/genomes/Hsapiens/GRCh37/variation/human_ancestor.fa.gz,loftee_path:~/local/share/bcbio/anaconda/share/ensembl-vep-97.3-0 --plugin G2P,file:~/Pipeline_Tests/Test11/AshkenaziFam/work/G2P.csv --plugin MaxEntScan,~/local/share/bcbio/anaconda/share/maxentscan-0_2004.04.21-1 --plugin SpliceRegion --sift b --polyphen b --hgvsg --hgvs --shift_hgvs 1 --merged | sed '/^#/! s/;;/;/g' | bgzip -c > ~/Pipeline_Tests/Test11/AshkenaziFam/work/AshkenaziFam-vepeffects.vcf.gz
The only part of this command that I was a little unsure of was "--plugin G2P,file:~/Pipeline_Tests/Test11/AshkenaziFam/work/G2P.csv"  I couldn't figure out if this was an input file or an output file, and I didn't find the vep documentations helpful.
When I did the run as written I did get an output file, but also had the following warnings:
WARNING: Failed to instantiate plugin LoF: Can't open ~/local/share/bcbio/anaconda/share/ensembl-vep-97.3-0/splice_data/donor_motifs/ese.txt: No such file or directory at<EMAIL_ADDRESS>line 212.
WARNING: Failed to instantiate plugin G2P: ERROR: No file specified or could not read from file file:~/Pipeline_Tests/Test11/AshkenaziFam/work/G2P.csv
WARNING: Failed to instantiate plugin MaxEntScan: ERROR: MaxEntScan directory not found
It would probably be easier if I could get vep running through the bcbio-nextgen pipeline, but I'm really not sure why it wasn't working.  I've attached the log files of this run (again with .txt added to the suffix). Any advice?
bcbio-nextgen.log.txt
bcbio-nextgen-commands.log.txt
bcbio-nextgen-debug.log.txt
Also, let me know if this should be a new issue so that anyone who is having the same problem can find it easier.

Taryn;
Sorry about the issue with VEP. If you're running the 1.1.8 release there was a bug in VEP running that got fixed in the latest development version (https://github.com/bcbio/bcbio-nextgen/commit/6bf4d3ff25771a7c5e503f2e7fa2e8fe1a5363df). If you update with bcbio_nextgen.py upgrade -u development hopefully it'll resolve the issues you're having.

Thanks, I was running 1.1.6, which was the version just after the "Java.lang.Exception: Problem retrieving reference variant..." error was occurring.  I've updated it and VEP seems to be running now, but I'm not longer getting my final gemini database again.  I checked my log and I had this warning:
[2019-12-08T13:51Z] multiprocessing: prep_gemini_db
[2019-12-08T13:51Z] Not running gemini, no samples with variants found: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008_posiSrt_markDup, 151002_7001448_0359_AC7F6GANXX_Sample_HG003-EEogPU_v02-KIT-Av5_TCTTCACA_L008_posiSrt_markDup, 151002_7001448_0359_AC7F6GANXX_Sample_HG004-EEogPU_v02-KIT-Av5_CCGAAGTA_L008_posiSrt_markDup
This was happening earlier, with the exact same warning, except before I wasn't getting any of the final db files and now it's only missing the ensemble.db file.
Last time I was able to fix it using:
bcbio_nextgen.py upgrade --datatarget gemini
When I went to run this line again it ran really quickly and the next run was still missing the ensemble.db file.
Any thoughts on why gemini isn't working?

Hi Taryn,
When you want to regenerate data, you need to take the follwing steps:

remove checkpoints_parallel
remove the geminidir

Bcbio checks if required files are present when rerunning, but it doesn't check the contents, so if an existing filename matches the required, the analysis step is skipped.
Hope this helps.
Cheers
M

Hi Matt,
Thanks for getting back to me so quickly.
Every time I run it I start from scratch, so this wouldn't be the problem.  I didn't realize that rerunning it from the same directory would skip steps I'd already done.  This will make re-running go a lot faster in the future.
Unfortunately, unless it checks the entire computer for the matching filename, this isn't the reason it's not running.

I've attached the log files here in case they help with the problem, since I have no idea why I'm not getting that final db file.  Let me know if there's anything else I can attach that might be useful.
bcbio-nextgen.log.txt
bcbio-nextgen-commands.log.txt
bcbio-nextgen-debug.log.txt
stdout_warnings.txt


Enable Coiled Analytics for Dask Gateway clusters

Context
We are using Dask heavily but don't have a lot of visibility into how exactly the clusters are being used. I'm sitting with @mrocklin at SciPy, and he just told me about Coiled Analytics:

Coiled Analytics lets you track Dask usage wherever Dask is run.
Motivation

When running computations we often ask ourselves questions like the following:
Did my computation finish?
Did any exceptions occur?
How much did that cost me?
What is taking most of the time?
Why is that cluster still running?

Experienced users know that Dask presents answers to these questions visually through the Dask dashboard. However, the Dask dashboard only tracks the real-time performance of a single Dask cluster. Coiled extends Dask by tracking many Dask clusters across many users and storing those results over time for later analysis. Coiled analytics provides a team-wide view of all clusters over time.

This would be super useful to all of the 2i2c hubs that run Dask and Dask Gateway
Proposal
We configure our Dask Gateway clusters to report their data to Coiled Analytics.
Updates and actions
No response

I'm aware of users who have asked for this level of transparency on costs. I agree it is worthy the time to explore it.

We are not planning on using coiled analytics on these clusters anytime soon. Closing, can be re-opened if things change!


[WIP] Use MMEval's coco metric

Thanks for your contribution and we appreciate it a lot. The following instructions would make your pull request more healthy and more easily get feedback. If you do not understand some items, don't worry, just make the pull request and seek help from maintainers.
Motivation

Use MMEval's CocoMetric, https://github.com/open-mmlab/mmeval/pull/9

Modification
Please briefly describe what modification is made in this PR.
BC-breaking (Optional)
Does the modification introduce changes that break the backward-compatibility of the downstream repos?
If so, please describe how it breaks the compatibility and how the downstream projects should modify their code to keep compatibility with this PR.
Use cases (Optional)
If this PR introduces a new feature, it is better to list some use cases here, and update the documentation.
Checklist

Pre-commit or other linting tools are used to fix the potential lint issues.
The modification is covered by complete unit tests. If not, please add more unit test to ensure the correctness.
If the modification has potential influence on downstream projects, this PR should be tested with downstream projects, like MMDet or MMCls.
The documentation has been modified accordingly, like docstring or example tutorials.

Move to https://github.com/open-mmlab/mmdetection/pull/9079


question: partial complete within a string based on a character/keyword

hi folks,
thanks for working on this project.
i have a more advanced need, and i'd like to know if i can somehow modify this component to make it work for me. basically, i have a textedit component in which i type free form strings, and i want the autocomplete to kick-in for a part of the string.
example:
let's say i type "good morning @vie" -> i'd like the autocomplete to start completing after i type '@' and therefore show "vietnam"
or if i type "talk to @david about blah" -> i'd like autocomplete to kick in after the '@d', allow me to choose 'david' and then let me continue typing the rest of the string.
is this doable in any way?
thanks in advance for your help!

Hey @shie-erlich, what you are describing is actually pretty different from what this component stands for (search box with a list under it).
I believe though, that you can fork this repo and make those changes (there should be a lot of changes, but you can deffinetly find some of  the code base useful).
I am closing this as this is not a plugin issue, please feel fee to consult me and continue this discussion.


STM32L151 I2C problems

I'm currently porting NuttX to a new (not publicly released yet) board. It uses STM32L151C8T6-A MCU.
However, I can't properly read data from I2C devices using the i2ctool.
I can list attached devices using i2c dev 00 7f, but dumping registers using i2c dump -b 1 -a <addr> 256 will return garbage data. Sometimes it returns all ff and sometimes it returns random values.
I tried messing with the menuconfig options: Alternate implementation, dynamic timeouts, huge timeout values, etc. And none of these worked.
These I2C devices work well with STM32 HAL APIs and a Raspberry Pi.
Please tell me how to solve this problem, thanks in advance.

Hi @ReimuNotMoe what device are you trying to dump? Do you have a Logic Analyzer to see the bus? Even a "cheaper" logic analyzer can do the trick: https://acassis.wordpress.com/2015/07/19/sigrok-and-a-cheap-saleae-clone-can-save-your-life-i-meant-your-time/

Hi @ReimuNotMoe what device are you trying to dump? Do you have a Logic Analyzer to see the bus? Even a "cheaper" logic analyzer can do the trick: https://acassis.wordpress.com/2015/07/19/sigrok-and-a-cheap-saleae-clone-can-save-your-life-i-meant-your-time/
This way you can compare the i2ctool command from NuttX against STM32 HAL and the Raspberry Pi i2ctool.

I bought a DSLogic Plus logic analyzer and used it to inspect the i2c lines.
It seems that there are only a bunch of STARTs and STOPs and there are no actual data transfers when running i2c dump -b 1 -a <addr> 256.

So after looking these screenshots again and again, I found the problem: the NuttX i2ctool isn't sending register addresses to the device? Is this intentional or standardized?

Hi @ReimuNotMoe I just ordered some MCP23017 modules to test. It is not clear what is the expected behavior of the i2ctool dump.

Hi @ReimuNotMoe I just ordered some MCP23017 modules to test. It is not clear for me what is the expected behavior of the i2ctool dump.

I mean the NuttX i2ctool isn't telling the device which register to read from. It didn't write register address to device before initializing incremental read.
Since NuttX is trying to be Linux-ish in all ways (AFAIK), it might be better to make the NuttX i2ctool behave like the one in Linux.

Yes, you are right @ReimuNotMoe the NuttX i2ctool needs to duplicate the Linux i2ctool. People can see NuttX as a Linux-like for microcontroler! ;-)

Let's close this issue now, @ReimuNotMoe you can provide a patch to make NuttX i2c-tools more compatible with Linux's version.


wrong amount of feathers for agro arrows

🐛 Bug Report
Write a description of the bug here, give all the information you can about what it is, how it happened.

Adding to this that OSB has the same issue. https://i.imgur.com/jao9VlU.png

Fixed in next update.


Bundling fail for windows (target OS) in Mac

I'm using MacOS (High Sierra) to bundle the app for windows.  I get this error
bundling failed: bundling for environment windows/amd64 failed: building failed: # runtime/cgo exec: "x86_64-w64-mingw32-gcc": executable file not found in $PATH
Should I be installing something to make this work?

@apnerve this is a golang error, not an astilectron specific one therefore I can point you in the right direction but there's nothing more I can do.
It seems you're using CGO and you're trying to cross compile. Therefore you need to set up the proper toolchains to make this work. I urge you to try to build your project manually for Windows without using the bundler to make sure your environment is properly set up.
Again, as it's a not an astilectron error there's nothing more I can do.
Cheers

This PR is that you are looking for. https://github.com/asticode/go-astilectron-bundler/pull/18
But unfortunately I have no time at the moment to work on it. If you have some time - you are welcome to finish it.

@apnerve did you manage to fix your problem?

@asticode Not yet. I decided to take a pure electron approach for now.

Also, looks like I need to build for windows on a windows machine. It doesn't have anything to do with astilectron and hence closing this issue.

Thanks for the update.
Cheers.


the influence of the patch size

hi,thanks for your work.I have some questions about the patch size.I use 32 patch size and i noticed that i can not learn the optical-flow.Can you share your insights .Thanks

Hi,
Thank you for your question. After some testing, I determined the billinear sampler for MC is faulty.
I have replaced the old billinear sampler with a working one from https://github.com/iwyoo/tf-bilinear_sampler . Mode 0 will now output the correctly warped frame along with the optical flow maps.
zhxl0903

Hi,thank you for your reply. I have another question about the weights.  I have noticed that you modify the weights from 0.01 to 1e-6.  When I test with this weights(1e-6) but I donot replace the bilinear sampler, it also has a better effect. So I have this question why you modify the weights.  In addition, I have another question why you use tf.nn.tanh after the t1_fine_warp. Thanks for your explanation.

Hi,
It looks like the weights are set too high which over penalised the huber loss, reducing the flow map gradients to zero. Hence, the flows become near constant 0. I have replaced reduce_sum in huber loss with reduce mean. Mode 0 now generates good flowmaps with a weight around 1e-3. tf.nn.tanh will work with normalised images in the range (-1, 1) or (0, 1), if we have MC loss term.
zhxl0903

Hi,
thanks for your reply. I gained good results for flowmaps with your weights. Thank you for your kindness help.

Hi, I have another question about the billinear sampler function that why you donot set the value of normalize parameter True. I think if we donot set, it is almost the same as original image. Thanks for your comments.

Hi,thanks for your work.
I have another question about the billinear sampler function that why you donot set the value of normalize parameter True.Thanks for your explanation.


Delete two same component and create one in the component folder

There are two same components name From, so delete them and create a new one in the components folder and use it in the contribute and sendFund page.
Close #592

Did not show the identity in contribute. fixed.


Internet connection crash fix from main branch

Explain your changes
"Fix" app crash issue while internet is offline during login/signup. I have added return while discoverConfiguration method called.
Checklist

[x] I have read the “Pull requests” section in the contributing guidelines.
[x] I agree to the terms within the code of conduct.

🛟 If you need help, consider asking for advice over in the Kinde community.

I tested the code before and after the fix, and I can confirm that the crash due to the "SWIFT TASK CONTINUATION MISUSE" error was indeed occurring. The fix you implemented by adding a return statement after resuming the continuation correctly resolves the crash by ensuring that the continuation is not resumed more than once.
This PR is approved


zh-trans: add translate-compose-kubernetes.md

zh-trans: add translate-compose-kubernetes.md

@AdamDang The preview of this work is at here: https://5c26f115ab4431000a07cc52--k8s-v1-12.netlify.com/zh/docs/tasks/configure-pod-container/translate-compose-kubernetes/
Please do a self-check and fix other issues shown in the preview.

/hold

@AdamDang Each time you push a new commit, the netlify task will be triggered automatically thus generating a new preview version.

@tengqm  How about the preview url? It's changed with new commit or keep the same ?

@AdamDang Not sure. You can check it before and after you pusing a commit. The comment left by the netlify bot changes when new commit is pushed, the hash code is always the latest one, e.g. d9dc870

@AdamDang Follow the link provided by netlify bot which will lead you to the preview.

@tengqm the URL is changed to:
https://5c27437b6cf67a00089b0d5f--k8s-v1-12.netlify.com/zh/docs/tasks/configure-pod-container/translate-compose-kubernetes/
Everything looks OK now!
Thanks a lot!

Translate construct kubernates


[main] Upgrade to latest dependencies

Cron -knative-prow-robot
/cc knative-extensions/serving-progressive-rollout-approvers
/assign knative-extensions/serving-progressive-rollout-approvers
Produced by: knative-extensions/knobots/actions/update-deps

/lgtm
/approve

/lgtm
/approve

/lgtm
/approve

/retest

/lgtm

/easycla

/lgtm

/easycla

/easycla

/easycla

/easycla


[TS Migration] Migrate PlaidLink directory to TypeScript

Details

Fixed Issues

$
https://github.com/Expensify/App/issues/25068
PROPOSAL: N/A
Tests

Log into the app
Navigate to the Settings page
Navigate to the Wallet page
Go through the Add bank account process and make sure it works correctly

[x] Verify that no errors appear in the JS console

Offline tests

N/A
QA Steps

Same as Tests section above

[x] Verify that no errors appear in the JS console

PR Author Checklist

[x] I linked the correct issue in the ### Fixed Issues section above
[x] I wrote clear testing steps that cover the changes made in this PR

[x] I added steps for local testing in the Tests section
[x] I added steps for the expected offline behavior in the Offline steps section
[x] I added steps for Staging and/or Production testing in the QA steps section
[x] I added steps to cover failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[x] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)
[x] I tested this PR with a High Traffic account against the staging or production API to ensure there are no regressions (e.g. long loading states that impact usability).

[x] I included screenshots or videos for tests on all platforms
[x] I ran the tests on all platforms & verified they passed on:

[x] Android: Native
[x] Android: mWeb Chrome
[x] iOS: Native
[x] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[x] MacOS: Desktop

[x] I verified there are no console errors (if there's a console error not related to the PR, report it or open an issue for it to be fixed)
[x] I followed proper code patterns (see Reviewing the code)

[x] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick)
[x] I verified that the left part of a conditional rendering a React component is a boolean and NOT a string, e.g. myBool && <MyComponent />.
[x] I verified that comments were added to code that is not self explanatory
[x] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[x] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method

[x] If any non-english text was added/modified, I verified the translation was requested/reviewed in #expensify-open-source and it was approved by an internal Expensify engineer. Link to Slack message:

[x] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[x] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is approved by marketing by adding the Waiting for Copy label for a copy review on the original GH to get the correct copy.
[x] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[x] I verified the JSDocs style guidelines (in STYLE.md) were followed

[x] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[x] I followed the guidelines as stated in the Review Guidelines
[x] I tested other components that can be impacted by my changes (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar are working as expected)
[x] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[x] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[x] I verified that if a function's arguments changed that all usages have also been updated correctly
[x] If a new component is created I verified that:

[x] A similar component doesn't exist in the codebase
[x] All props are defined accurately and each prop has a /** comment above it */
[x] The file is named correctly
[x] The component has a clear name that is non-ambiguous and the purpose of the component can be inferred from the name alone
[x] The only data being stored in the state is data necessary for rendering and nothing else
[x] If we are not using the full Onyx data that we loaded, I've added the proper selector in order to ensure the component only re-renders when the data it is using changes

[x] Any internal methods bound to this are necessary to be bound (i.e. avoid this.submit = this.submit.bind(this); if this.submit is never passed to a component event handler like onClick)

[x] All JSX used for rendering exists in the render method
[x] The component has the minimum amount of code necessary for its purpose, and it is broken down into smaller components in order to separate concerns and functions

[x] If any new file was added I verified that:

[x] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[x] If a new CSS style is added I verified that:

[x] A similar style doesn't already exist
[x] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(themeColors.componentBG))

[x] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[x] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[x] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[x] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[x] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[x] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.
[x] I have checked off every checkbox in the PR author checklist, including those that don't apply to this PR.

Screenshots/Videos

Android: Native

Android: mWeb Chrome

iOS: Native

iOS: mWeb Safari

MacOS: Chrome / Safari

MacOS: Desktop

Before making this PR ready for review please add QA steps!

@s77rt can you please do checklist on this PR?

@s77rt I applied the changes you suggested, thank you for thorough review!

@JKobrynski Thanks! Code looks good to me. Working on checklist / tests. I noticed the tests steps are not correct. I think we need to go through the Add bank process not the debit card process.

Reviewer Checklist

[X] I have verified the author checklist is complete (all boxes are checked off).
[X] I verified the correct issue is linked in the ### Fixed Issues section above
[ ] I verified testing steps are clear and they cover the changes made in this PR

[X] I verified the steps for local testing are in the Tests section
[X] I verified the steps for Staging and/or Production testing are in the QA steps section
[X] I verified the steps cover any possible failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[X] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)

[X] I checked that screenshots or videos are included for tests on all platforms
[X] I included screenshots or videos for tests on all platforms
[X] I verified tests pass on all platforms & I tested again on:

[X] Android: Native
[X] Android: mWeb Chrome
[X] iOS: Native
[X] iOS: mWeb Safari
[X] MacOS: Chrome / Safari
[X] MacOS: Desktop

[X] If there are any errors in the console that are unrelated to this PR, I either fixed them (preferred) or linked to where I reported them in Slack
[X] I verified proper code patterns were followed (see Reviewing the code)

[X] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick).
[X] I verified that the left part of a conditional rendering a React component is a boolean and NOT a string, e.g. myBool && <MyComponent />.
[X] I verified that comments were added to code that is not self explanatory
[X] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[X] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method
[X] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[X] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is approved by marketing by adding the Waiting for Copy label for a copy review on the original GH to get the correct copy.
[X] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[X] I verified the JSDocs style guidelines (in STYLE.md) were followed

[X] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[X] I verified that this PR follows the guidelines as stated in the Review Guidelines
[X] I verified other components that can be impacted by these changes have been tested, and I retested again (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar have been tested & I retested again)
[X] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[X] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[X] If a new component is created I verified that:

[X] A similar component doesn't exist in the codebase
[X] All props are defined accurately and each prop has a /** comment above it */
[X] The file is named correctly
[X] The component has a clear name that is non-ambiguous and the purpose of the component can be inferred from the name alone
[X] The only data being stored in the state is data necessary for rendering and nothing else
[X] For Class Components, any internal methods passed to components event handlers are bound to this properly so there are no scoping issues (i.e. for onClick={this.submit} the method this.submit should be bound to this in the constructor)
[X] Any internal methods bound to this are necessary to be bound (i.e. avoid this.submit = this.submit.bind(this); if this.submit is never passed to a component event handler like onClick)
[X] All JSX used for rendering exists in the render method
[X] The component has the minimum amount of code necessary for its purpose, and it is broken down into smaller components in order to separate concerns and functions

[X] If any new file was added I verified that:

[X] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[X] If a new CSS style is added I verified that:

[X] A similar style doesn't already exist
[X] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(themeColors.componentBG)

[X] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[X] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[X] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[X] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[X] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[X] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.
[ ] I have checked off every checkbox in the PR reviewer checklist, including those that don't apply to this PR.

Screenshots/Videos

Android: Native

https://github.com/Expensify/App/assets/16493223/f50be612-15cd-41f2-9c25-5c711204f724

Android: mWeb Chrome

https://github.com/Expensify/App/assets/16493223/1e156d92-a279-4a3f-afb5-6e4ff63759d6

iOS: Native

https://github.com/Expensify/App/assets/16493223/c5567a0d-7629-4b14-ab4b-eef8eafc11b3

iOS: mWeb Safari

https://github.com/Expensify/App/assets/16493223/3dfc82c9-d3f9-4485-9c7c-fa90cb202f88

MacOS: Chrome / Safari

https://github.com/Expensify/App/assets/16493223/0df52eec-86c2-4194-ae08-4bd21f704036

MacOS: Desktop

https://github.com/Expensify/App/assets/16493223/f22ab77d-4d0c-41cb-a647-3e1862fe713d

@s77rt bump on this one, thanks

@mountiny Was just waiting for the steps update 😅
@JKobrynski Sorry for the delay here. Next time please tag me otherwise I wouldn't know that a change was made

:hand: This PR was not deployed to staging yet because QA is ongoing. It will be automatically deployed to staging after the next production release.

Issue https://github.com/Expensify/App/issues/32079 repro when executing this PR

🚀 Deployed to production by https://github.com/mountiny in version: 1.4.5-7 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
success ✅

🕸 web 🕸
success ✅


[BUG] CLI cannot create/send multipart POST REST request (from file)

What is the bug?
My goal is to use opensearch-cli to import the /_dashboards/api/saved_objects/_import REST API
However, the API expects the POST request with content-type: multipart/form-data
See: https://github.com/opensearch-project/OpenSearch-Dashboards/blob/d7004dc5b0392477fdd54ac66b29d231975a173b/src/core/server/saved_objects/routes/import.ts
The Opensearch CLI only offers the possibility to specify a file with the --data flag. Native CURL commands offer the possibility to specify the file via --data-binary flag.
The CURL POST command generated by the Opensearch CLI cannot automatically set the multipart boundary, so the post command fails as follows:
I use the authenticated curl post command here as follows:
Without providing headers
opensearch-cli curl post --profile local  --path "/_dashboards/api/saved_objects/_import" --data @export.ndjson
Error:
{
  "error": "Unsupported Media Type",
  "message": "Unsupported Media Type",
  "statusCode": 415
}

Providing multipart-form-data header
opensearch-cli curl post --profile local --path "/_dashboards/api/saved_objects/_import" -H "content-type:multipart/form-data;"  --data @export.ndjson
Error:
{
  "error": "Bad Request",
  "message": "Invalid content-type header: multipart missing boundary",
  "statusCode": 400
}

Providing multipart-form-data header and any random boundary
opensearch-cli curl post --profile local --path "/_dashboards/api/saved_objects/_import" -H "content-type:multipart/form-data; boundary:something;"  --data @export.ndjson
Error:
{
  "error": "Bad Request",
  "message": "Invalid content-type header: multipart missing boundary",
  "statusCode": 400
}

How can one reproduce the bug?
Steps to reproduce the behavior:

Export any saved objects via Opensearch Web UI
Try to import these using the cli curl commands above

What is your host/environment?

OS: ubuntu
Version 20.04.5 LTS
Opensearch-cli version 1.1.0 linux/amd64
OpenSearch version 2.3.0

This looks worth fixing. Feel free to submit a PR.

@VachaShah would you be willing to do a release?

We have a release planned for today for 1.2.0.

We have the release process in progress but figuring out some issues along the way. Build release issue: https://github.com/opensearch-project/opensearch-build/issues/4185

Version 1.2.0 is released: https://github.com/opensearch-project/opensearch-cli/releases/tag/v1.2.0


Replace #fileID, #filePath, #line, and #column with a single macro.

We have a bunch of functions that take separate, defaulted arguments for file ID, column, etc. We'd like to normalize these functions to always take a single SourceLocation instance, but until now there hasn't been a way to express such a thing as a default argument without capturing the wrong source location.
This PR takes advantage of SE-0422 to create a new #_sourceLocation macro (name pending API review) that does what we want here. We can't use the obvious #sourceLocation because the language already reserves that macro name for an unrelated use.
Resolves rdar://121883259.
Checklist:

[x] Code and documentation should follow the style of the Style Guide.
[x] If public symbols are renamed or modified, DocC references should be updated.

@swift-ci please test

@swift-ci please test

@swift-ci please test Windows

@swift-ci please test

@swift-ci please test Linux


IsAlt() method returns false positives

It's time to revisit the IsAlt() logic for whosonfirst properties since it is causing things like Asia to be reported as an alt file.
https://github.com/whosonfirst/go-whosonfirst-geojson-v2/blob/master/properties/whosonfirst/whosonfirst.go#L276-L283
https://spelunker.whosonfirst.org/id/102191569/

Should be fixed as of 0.11.0 release.


Fixing invalid URL.

Was pointing to the SPS host instead of AEX.

@justmarks could you take a quick look.

Done ☺
From: Mitch Denny<EMAIL_ADDRESS>Sent: Tuesday, March 6, 2018 3:55 PM
To: Microsoft/vsts-auth-samples<EMAIL_ADDRESS>Cc: Justin Marks<EMAIL_ADDRESS>Mention<EMAIL_ADDRESS>Subject: Re: [Microsoft/vsts-auth-samples] Fixing invalid URL. (#17)
@justmarkshttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjustmarks&data=04|01|Justin.Marks%40microsoft.com|866fd9e7550649d54eae08d583bdb440|72f988bf86f141af91ab2d7cd011db47|1|0|636559773227087433|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwifQ%3D%3D|-2&sdata=lhwxlxhp1mqf44d3o0f%2Fr%2FD26dxZO1MFK73E0njl%2FCk%3D&reserved=0 could you take a quick look.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMicrosoft%2Fvsts-auth-samples%2Fpull%2F17%23issuecomment-370972260&data=04|01|Justin.Marks%40microsoft.com|866fd9e7550649d54eae08d583bdb440|72f988bf86f141af91ab2d7cd011db47|1|0|636559773227087433|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwifQ%3D%3D|-2&sdata=EnXoPjvfZhuVlDREXC6YGvapeQCFDjI%2Fn2%2FHf8yD4XQ%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABYJhQyfZG9acrttLwmixc11o3eIGe3Kks5tbyHggaJpZM4Sfow3&data=04|01|Justin.Marks%40microsoft.com|866fd9e7550649d54eae08d583bdb440|72f988bf86f141af91ab2d7cd011db47|1|0|636559773227087433|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwifQ%3D%3D|-2&sdata=%2Fs8MOJFu5ht1JGqHmJ2EwDgyrEN4F6LSMD%2BwwBE2mAY%3D&reserved=0.


Direct3DTexture:Load error

Getting Direct3DTextue:Load error "Incorrect parameter".
After closing the dialog window, the game is left in this state. No textures are loaded.

OS: Windows 10 21H1 (19043.906)
CPU: R5 3600X
GPU: RX 580 8 GB
AMD drivers: 21.4.1 (27.20.21002.112)

Looks like it has to do with enabling Hardware MIP Maping from the game's Hardware Only Video Options. Works as expected, when MIP Maping is disabled.

Looks like it has to do with enabling Hardware MIP Maping from the game's Hardware Only Video Options. Works as expected, when MIP Maping is disabled.

Hm, I think you really want mip-mapping enabled, so I don't think your workaround is a good idea.
Maybe it does not recognize that you are running XWA?
Try setting
XWAMode = 1
(i.e. change the -1 to 1) in ddraw.cfg


Piping data into the client results in a connection exception

I've installed ClickHouse on a fresh Ubuntu 14.04.3 LTS installation.
$ echo "deb http://repo.yandex.ru/clickhouse/trusty stable main" | \
    sudo tee -a /etc/apt/sources.list
$ sudo apt-key adv \
    --keyserver keyserver.ubuntu.com \
    --recv E0C56BD4
$ sudo apt-get update
$ sudo apt-get install \
    clickhouse-client \
    clickhouse-server-common
$ sudo service clickhouse-server start

The client version is showing as 1.1.54140.
$ clickhouse-client --version
ClickHouse client version 1.1.54140.

The client itself is working with a trivial select.
$ echo "select 1" | clickhouse-client --time

1
0.001

I'm able to create a table without issue but when I try to decompress gzip-compressed CSV data and pipe it in the following occurs:
$ time (gunzip -c trips_xaa.csv.gz | clickhouse-client --query="INSERT INTO trips FORMAT CSV")

Code: 210. DB::NetException: Connection reset by peer while writing to socket ([::1]:9000)

real    0m23.783s
user    0m11.264s
sys     0m5.000s

The trips_xaa.csv.gz file itself is around 1.9GB and contains 20M lines of CSV data.
Any idea why I'm getting the connection issues when I'm trying to pipe data in?

This amount of data shouldn't be a problem. Is there anything interesting in server logs (/var/log/clickhouse-server/clickhouse-server.log, /var/log/clickhouse-server/clickhouse-server.err.log)?

It looks like a memory allocation failure.
2017.01.25 00:41:55.513494 [ 3 ] <Error> executeQuery: Code: 173, e.displayText() = DB::Exception: Allocator: Cannot mmap., errno: 12, strerror: Cannot allocate                                                                 memory, e.what() = DB::Exception (from [::1]:48186) (in query: INSERT INTO trips FORMAT CSV), Stack trace:

0. clickhouse-server(StackTrace::StackTrace()+0x16) [0x1216d16]
1. clickhouse-server(DB::Exception::Exception(std::string const&, int)+0x1f) [0xf7c40f]
2. clickhouse-server(DB::throwFromErrno(std::string const&, int, int)+0x101) [0x1224821]
3. clickhouse-server(Allocator<false>::alloc(unsigned long, unsigned long)+0x14c) [0xf85a0c]
4. clickhouse-server() [0x11062fa]
5. clickhouse-server(DB::DataTypeString::deserializeBinaryBulk(DB::IColumn&, DB::ReadBuffer&, unsigned long, double) const+0x234) [0x1106f84]
6. clickhouse-server(DB::NativeBlockInputStream::readData(DB::IDataType const&, DB::IColumn&, DB::ReadBuffer&, unsigned long)+0x14c) [0x10c80fc]
7. clickhouse-server(DB::NativeBlockInputStream::readData(DB::IDataType const&, DB::IColumn&, DB::ReadBuffer&, unsigned long)+0x122) [0x10c80d2]
8. clickhouse-server(DB::NativeBlockInputStream::readImpl()+0x31e) [0x10c8a0e]
9. clickhouse-server(DB::IProfilingBlockInputStream::read()+0x2a0) [0x10c50b0]
10. clickhouse-server(DB::TCPHandler::receiveData()+0x62) [0xf8fb32]
11. clickhouse-server(DB::TCPHandler::receivePacket()+0x65) [0xf8ffe5]
12. clickhouse-server(DB::TCPHandler::readData(DB::Settings const&)+0x189) [0xf90499]
13. clickhouse-server(DB::TCPHandler::processInsertQuery(DB::Settings const&)+0x241) [0xf90791]
14. clickhouse-server(DB::TCPHandler::runImpl()+0xd7d) [0xf9166d]
15. clickhouse-server(DB::TCPHandler::run()+0x1c) [0xf9234c]
16. clickhouse-server(Poco::Net::TCPServerConnection::start()+0xf) [0x301d0af]
17. clickhouse-server(Poco::Net::TCPServerDispatcher::run()+0x10b) [0x303ac3b]
18. clickhouse-server(Poco::PooledThread::run()+0x87) [0x30b3b07]
19. clickhouse-server(Poco::ThreadImpl::runnableEntry(void*)+0x96) [0x3077486]
20. /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182) [0x7f8523c7d182]
21. /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7f852329847d]

For the record I'm running this on a VM with a GB of RAM and a 1 GB swap file. I'll ramp that up to 8 GB and see what happens.

I've bumped the VM up to 8 GB and the data imported without issue.

Good. See also tips for operating ClickHouse: https://github.com/yandex/ClickHouse/blob/master/doc/administration/tips.txt


Bug: General Ledger Entries - Export to Excel - Wrong data

The following data on General Leger Entries:

Go to Print & Send -> Microsoft Excel.
Excel with empty Source No. and Source Type fields generated.

(It always takes the first value and fills all columns with it on Source No. and Source Type fields)
Its works well with other actions (Microsoft Word, Print Page).
Platform: NAV 2018
Build: 48794
Localization: BE

As the template you used told you, this repo isn't for customer-support. As this isn't about the AL language or compiler, it's off-topic. It should be raised via Support.

Hi, this issue is out of scope of for this repository. You should do one of the following:
Open a support request to CSS through the PartnerSource portal
Open a bug in Collaborate
Contact your Service Account Manager (SAM) in your local subsidiary to understand what is included in your contract as of support incident and PAH (Partner Advisory Hours). Your SAM might also direct you "step by step" how to open a support request or how to get credentials, if this is the first time for you or your company
As a reminder, this repository only handles issues to do with the compiler or VSCode development experience for AL.
The reason why this is out of scope is because this is about the runtime behavior of the BC application and it should go to the team that handles the application.


Remove unused ArtFile variable from PaletteHeader constructor

Currenty two constructor overloads exist for PaletteHeader.
PaletteHeader::PaletteHeader() : remainingTagCount(0) {}
PaletteHeader::PaletteHeader(const ArtFile& artFile)  : remainingTagCount(1)

The first one allows initializing the struct with minimum work but still making it viable. The second one initializes the header with regular values (which oddly enough does not require any input from ArtFile).
Perhaps changing the second constructor into a static function that returns a populated PaletteHeader would be more appropriate. Then the dummy ArtFile variable would no longer be needed.

That sounds like a good plan.


feat: style footer block

Please always provide the GitHub issue(s) your PR is for, as well as test URLs where your change can be observed (before and after):
Fix #
Test URLs:

Before: https://main--basf-retailfirst--hlxsites.hlx.page/
After: https://issues-5--basf-retailfirst--hlxsites.hlx.page/


monitoring - grafana dashboard displays etcd db size of all nodes not per-node

What kind of request is this (question/bug/enhancement/feature request):
enhancement
Steps to reproduce (least amount of steps as possible):
user noticed etcd db size was listed as 3.2Gb+ while etcdctl command shows the db size as 703Mb.  User had five nodes.
Result:
dashboard reports sum() function of all nodes and not per-node db size, this can be misleading.
Environment information

Rancher version (rancher/rancher/rancher/server image tag or shown bottom left in the UI):
Rancher v2.3.5

Installation option (single install/HA):
etcd HA install

gz#10844

This same query is used for the "Database usage close to the quota 500M" alert that ships with Rancher, so can result in confusion.

The logic is most likely considering the entire db usage across the cluster, where a cluster is a single unit.  The total db usage is always a sum of the individual nodes.

To update the default etcd alert, please following this KB


Default Sql Server db functions to DBO schema

Set the the default schema for db functions in Sql Server to dbo.
Addresses #9214

Updated and unit tests added.

Can you add a functional test when default schema is specified which is different from dbo and function is defined on that schema and query picks up the schema from model correctly.

Let me make sure I am following what you are asking for.
You want the default schema set to "abc" and the function set to "xyz" and then make sure the sql uses "xyz"?  By functional test do you want it to actually hit a database and run a query?

Since the convention does not do anything if model has DefaultSchema set,
What if a function is defined with no schema & model has default schema, does it produce a valid SQL for it?
One of the easiest way to verify SQL validity is to actually hit the database and run the query.

I believe current functional tests covers when function is defined without schema and we use the "dbo"
We should have functional test for
function defined without schema & with model.defaultschema set and function uses that.
function defined with schema & with model.defaultschema set & function uses the schema from function only.
You can probably add new tests in QueryBugsSqlServerTest

If there is no schema set on the function but a default schema is set then the default schema is used.  If you don't want the default schema to be used at all then you need to set the schema on the function to an empty string.
For Sql Server that use case would only be for calling built in functions, all udf calls require a schema.
The logic order currently is

Use the schema set directly on the function.  This schema can be an empty string.
Use the default schema.
Use dbo

Any function test that hit the db need to be in UdfDbFunctionSqlServerTests.  That uses the Northwind database which has the setup script which we can use to create the functions in the database.

If there is no schema set on the function but a default schema is set then the default schema is used.

That's the scenario I want tested because I have doubts on that.
We added UdfDbFunctionSqlServerTests for UDF testing but we don't modify northwind.sql generally. At that time due to time restrictions we went that way. The issue is northwind is not re-created always.
For AppVeyor/Travis it works fine because we start with new VM which does not have any database at all so always northwind will be created from latest script.
For all local dev machines & CI machines which are not dropping database, this causes mismatch since there will be outdated northwind in sqlserver. And that leads to failure unless northwind database is manually dropped.

I don't see a QueryBugsSqlServerTest in the codebase.
Do you not want me to modify the northwind.sql and find a different approach for creating a new databsae and creating the function for each run?

Ah, its QueryBugsTest only.
Best would be to have UDF functions test class to use northwind model but use a different database which would get recreated every time so adding more testing around udf in future does not affect northwind database. But that may be more work. If you don't have enough time for it, feel free to put it in QueryBugsTest.

I actually have a big family wedding the rest of this week/weekend so I won't be able to get these changes in until early next week.

@pmiddleton - No rush, we have a lot of time before next release 😄

@smitpatel - I added the unit tests you were looking for.  Let me know what you think.

@pmiddleton - Thanks I was looking for precisely that test since I was not able to understand how the default model schema was set on function. After looking more in code today I found out the RelationalDbFunctionConvention which sets name & schema from attribute or defaults.
Should RelationalDbFunctionConvention be ModelBuiltConvention like above rather than annotation changed convention? (it is only applied when the annotation is created & not changed). Then we may override it in SqlServer, to suggest further default to be "dbo". The downside is name & schema will be plugged in once the model is built. Not sure if that is critical to have. Upside lesser convention invocations.
What do you think?
also cc: @AndriySvyryd , @anpete

It depends if we want the user to be able to read the name and schema, set via the attribute, during OnModelCreating.  As it stands now you can, if we switch to a ModelBuiltConvention you won't be able to.
That would also be a minor change to end user behavior from 2.0 to 2.1.

The test in QueryBugsTest fail if function is defined using Attribute without specifying schema. The RelationalDbFunctionConvention sets schema to model.DefaultSchema but if the function is found using attribute then at that time OnModelCreating hasn't run so we don't know default schema hence it fails to set any schema.
Further, if user set default schema then define function then set default schema to something else then we are not updating the schema in db function. This is because RelationalDbFunctionConvention would run only when adding annotation for DbFunction first time. Since we follow last one win strategy, all our metadata object goes to schema defined 2nd time but the function goes to first schema causing error. This kind of setting default schema again would be used in scenario like extensible class library using EF (like Identity), when final consumer would want to set default schema to something else)

Though above is in existing code and out of the scope of PR.
@pmiddleton - Can you rebase on latest dev?

filed #9360

Rebased.

Based on your findings I'm leaning towards just applying all of the defaults in a ModelBuiltConvention.
We can make RelationalDbFunctionConvention a ModelBuiltConvention and have it deal with attribute & default schema.  We can then have SqlServerDbFunctionConvention derive and override RelationalDbFunctionConvention to deal with dbo.
Thoughts?

@AndriySvyryd needs to approve it.

Instead of this being a convention you could put the check in DbFunction.Schema getter. This would also fix #9360

We would still need a SQL Server convention, but it would set a new property - DbFunction.DefaultSchema to "dbo" instead of DbFunction.Schema. And this convention needs only to run once, when the DbFunction is created.

I added a DbFunction.DefaultSchema and set that in the convention when the function is created.  I also added some new unit tests.  I think this gets us to where we want to be for #9360 and #9214

@AndriySvyryd  - Changes made

@smitpatel - switched to a helper method.

Merged via 7529563ec9136359a78a223f6e69441641a03924
Thanks for contribution @pmiddleton

Hey Paul et alia, reading the two issues on this, my understanding is that dbo is the conventional default schema. But (on EF Core 2.0.1) my queries using a function are failing (sql server returns function not found error) unless I explicitly set the schema to dbo in the function ala
 [DbFunction(Schema ="dbo")]
        public static string EarliestBattleFoughtBySamurai(int samuraiId)
        {
            throw new Exception();
        }

Am I misunderstanding something?
Thanks!

@julielerman - Yes, that would be expected behavior in 2.0.1. The issue is fixed in 2.1.0-preview1-final

yeah .just found the note in https://github.com/aspnet/EntityFrameworkCore/issues/9663 :)
thanks!

@julielerman  - Yup I missed that one in 2.0.

@julielerman - 2.1.0-preview1-final will also allow you to use instance methods as well as static methods for db functions.  See #9755


OpenAPI/Swagger spec

https://github.com/AI21Labs/studio-demos/issues/3

Where can I find the OpenAPI/Swagger spec you generated to create this SDK?

As I remember, I found this while trying to add openapi.yaml/openapi.json to their documentation and it worked. Here's the url: https://api.ai21.com/openapi.json


Access ImageMagick in laravel-horizon

Info:

Docker version: 19.03.1, build 74b1e89
Laradock commit: 818eb1f59d6830657c4318acc33a93ed812037ef
System info: Debian GNU/Linux 9

Issue:
We are using Spatie medialibrary. When uploading and processing images with a classical php artisan queue:work in the workspace, everything is fine. But when running laravel-horizon, jobs fail with this error:
ImageMagick module not available with this PHP installation.

or (when we change the driver)
GD Library extension not available with this PHP installation.

Is there a way to install the extensions in laravel-horizon container, or to make them accessible? Are we missing something?
WORKSPACE_INSTALL_IMAGEMAGICK=true
PHP_FPM_INSTALL_IMAGEMAGICK=true

Hello,
I have the same issue here, any help would be appreciated :)
Thanks

The same problem, how did you solve it?


[struct_pack] Bitfield support

Hey guys!
I just found that struct_pack can't handle one usefull trick for less memory usage - bitfield.
Example with game item object:
With bitfields will be just 4 bytes (without alignment - 30 bits):
struct Item {
  uint32_t Slot : 8;
  uint32_t Id : 14;
  uint32_t Level : 4;
  uint32_t Option1 : 1;
  uint32_t Option2 : 1;
  uint32_t Option3 : 1;
  uint32_t Option4 : 1;
};

Without bitfields will be 10 bytes (without alignment - 72 bits):
struct Item {
  uint8_t Slot;
  uint16_t Id;
  uint8_t Level;
  uint8_t Option1;
  uint8_t Option2;
  uint8_t Option3;
  uint8_t Option4;
};

Of course i understand that this is very specific feature, but maybe any chance to include it in todo list?

Here is a workaround:
#include<cstdint>
struct Item {
  uint32_t Slot : 8;
  uint32_t Id : 14;
  uint32_t Level : 4;
  uint32_t Option1 : 1;
  uint32_t Option2 : 1;
  uint32_t Option3 : 1;
  uint32_t Option4 : 1;
};

using wrapper_t=char[sizeof(Item)];
void serialize(const Item& item) {
    auto &wrapper=*(wrapper_t*)&item;
    struct_pack::serialize(wrapper);
}

Another better workaround. I believe that is what you want.
struct Item {
  uint32_t Slot : 8;
  uint32_t Id : 14;
  uint32_t Level : 4;
  uint32_t Option1 : 1;
  uint32_t Option2 : 1;
  uint32_t Option3 : 1;
  uint32_t Option4 : 1;
  auto& value();
  const auto& value() const;
};
using wrapper_t=char[sizeof(Item)];
auto& Item::value() { return *(wrapper_t*)this; }
const auto& Item::value() const { return *(const wrapper_t*)this; }
STRUCT_PACK_REFL(Item, value());
auto test() {
  Item it{};
  it.Slot = 1;
  it.Id = 14;
  it.Option3 = 1;
  auto buffer = struct_pack::serialize(it);
  auto res = struct_pack::deserialize<Item>(buffer);
  auto &it2 = res.value();
  assert(it2.Id == it.Id);
  assert(it2.Slot == it.Slot);
  assert(it2.Option3 == it.Option3);
}

Make sure your code in only work in little-endian.

I afraid the bitfield is hard for cross-platform. Make sure you only use it in the same endian.

For native support, during c++ don't have enough type traits util for bitfield, user have write some boiled code.
Maybe we can support it as:
struct Item {
  uint32_t Slot : 8;
  uint32_t Id : 14;
  uint32_t Level : 4;
  uint32_t Option1 : 1;
  uint32_t Option2 : 1;
  uint32_t Option3 : 1;
  uint32_t Option4 : 1;
};
void struct_pack_bitfield_decl(Item);
//OR: STRUCT_PACK_BITFIELD_DECL(Item);

But remember, bitfield is not cross-platform. There has no type check for each field. It can't work in opposite endian. It may have some problem when cross different platform/compiler.

Furthermore, a cross-platform way is to use std::bitset

Furthermore, a cross-platform way is to use std::bitset

All right, but seems it's cant resolve common target - compact size, as example:
struct Item {
  std::bitset<8> Slot;
  std::bitset<14> Id;
  std::bitset<4> Level;
  std::bitset<1> Option1;
  std::bitset<1> Option2;
  std::bitset<1> Option3;
  std::bitset<1> Option4;
};

Will be 28 bytes. Can't check which size will be after serialization becouse struct_pack invokes C1001 in reflection.hpp:

Furthermore, a cross-platform way is to use std::bitset

All right, but seems it's cant resolve common target - compact size, as example:
struct Item {
  std::bitset<8> Slot;
  std::bitset<14> Id;
  std::bitset<4> Level;
  std::bitset<1> Option1;
  std::bitset<1> Option2;
  std::bitset<1> Option3;
  std::bitset<1> Option4;
};

Will be 28 bytes. Can't check which size will be after serialization becouse struct_pack invokes C1001 in reflection.hpp:

I mean:
struct Item {
  std::bitset<32> data;
  uint8_t getSlot();
  void setSlot(uint8_t);
  uint16_t getID();
  void setID(uint16_t);
  //.....
};

Here is a workaround. I believe that is what you want.
struct Item {
  uint32_t Slot : 8;
  uint32_t Id : 14;
  uint32_t Level : 4;
  uint32_t Option1 : 1;
  uint32_t Option2 : 1;
  uint32_t Option3 : 1;
  uint32_t Option4 : 1;
  auto& value();
  const auto& value() const;
};
using wrapper_t=char[sizeof(Item)];
auto& Item::value() { return *(wrapper_t*)this; }
const auto& Item::value() const { return *(const wrapper_t*)this; }
STRUCT_PACK_REFL(Item, value());
// reflect Item as a char[4] in struct_pack type system.
auto test() {
  Item it{};
  it.Slot = 1;
  it.Id = 14;
  it.Option3 = 1;
  auto buffer = struct_pack::serialize(it);
  auto res = struct_pack::deserialize<Item>(buffer);
  auto &it2 = res.value();
  assert(it2.Id == it.Id);
  assert(it2.Slot == it.Slot);
  assert(it2.Option3 == it.Option3);
}

If you don't care for cross-platform, that is the workaround.

Will be 28 bytes. Can't check which size will be after serialization becouse struct_pack invokes C1001 in reflection.hpp:

Furthermore, a cross-platform way is to use std::bitset

All right, but seems it's cant resolve common target - compact size, as example:
struct Item {
  std::bitset<8> Slot;
  std::bitset<14> Id;
  std::bitset<4> Level;
  std::bitset<1> Option1;
  std::bitset<1> Option2;
  std::bitset<1> Option3;
  std::bitset<1> Option4;
};

Will be 28 bytes. Can't check which size will be after serialization becouse struct_pack invokes C1001 in reflection.hpp:

I mean:
struct Item {
  std::bitset<32> data;
  uint8_t getSlot();
  void setSlot(uint8_t);
  uint16_t getID();
  void setID(uint16_t);
  //.....
};

You need to write the store rule manually, but it's only way for cross-platform.

Oh, now get it, thank you!