Better way

Hello, i analysed the youtube code and what is triggering the popup is on this file
https://www.youtube.com/yts/jsbin/desktop_polymer_inlined_html_polymer_flags_v2-vflNwouvq/desktop_polymer_inlined_html_polymer_flags_v2.js
There are multiple ways the popup/pause is triggered,
first there is the checking of the variable window._lact which is the timestamp of the last action. Modifying it regularily will prevent some of the trigger, but there are triggers that are called via ajax.
On the polymer file, there is this function
function(k){if(1==k.nextAddress){a.reset();a.youThereData_=b.configData.youThereData;if(a.youThereData_.reason&&"YOU_THERE_TRIGGER_REASON_3"==a.youThereData_.reason&&!jU())return EP("YOU_THERE_EVENT_TYPE_RATE_LIMITED"),k.return();c=parseInt(a.youThereData_.lactThresholdMs,10);return!B("disable_youthere_lact_threshold_check")&&Sn()+1E3*a.youThereData_.promptDelaySec<c?(EP("YOU_THERE_EVENT_TYPE_BELOW_LACT_THRESHOLD",Ko()),k.return()):0>=a.youThereData_.playbackPauseDelayMs?(ZCa(a),k.return()):xa(k,
a.playerProvider_().getPlayerPromise(),2)}d=k.yieldResult;e=d.getCurrentTime();if(!a.youThereData_)return k.return();g=a.youThereData_.promptDelaySec;a.showWarningJob_=Gn(L,function(){return Ka(function(m){a.showWarningJob_=0;return xa(m,$Ca(a),0)})},1E3*Math.max(g-e,0));
ya(k)}

i think that if you replace it with
function(k){}
it will not be triggered.
However, i don't know how to modify on the fly the script, i tried with tampermonkey to intercept the script and put the script content from the external file to an inline script, but it doesn't work, the code is not executed. Maybe you know how to do that ?
edit: as the script is very big (6mb large), it is very difficult to put breakpoints or modify the script in real time as the browser is struggling a lot or even crashing. I tried the override functionnality in chrome but it make the page load during multiple minutes ...

actually i found a way that seems to works after multiple hours of test.
Simply do
window.addEventListener('load', function() {
document.querySelector('ytd-watch-flexy').youthereDataChanged_ = function() {};
}, false);
i put that into tampermonkey

i published a greasemonkey/tampermonkey script here https://greasyfork.org/fr/scripts/401348-yes-i-m-here-youtube

Nice, I think you are on to something there. From a quick test I did, it indeed does seem to work, if you put the code directly into the console but I tried it as an extension and from there it seems to not recognize these variables youthereDataChanged_, youThereManager_. I would have to look more into it.

follow my greasyfork link, i have published an updated version, but now it's my own code haha :)

Yeah I saw it, that's the code I tried. Don't worry, I'm not gonna use your code in any case :D
I don't really want to override any YouTube functions anyway, since I can't be sure what code they execute themselves and I don't want to break anything in the process.

on which browser did you tried

Chrome

did you tried with tampermonkey + install the script ?

i published a greasemonkey/tampermonkey script here https://greasyfork.org/fr/scripts/401348-yes-i-m-here-youtube

Thank you for your script! This addon is broken for a long time and the owner ignores my reports but your script works flawlessly so I just uninstalled the addon and use the script. Thanks again!

i published a greasemonkey/tampermonkey script here https://greasyfork.org/fr/scripts/401348-yes-i-m-here-youtube

Hey!!! Thanks worked for me

use my tampermonkey script it works better :)

how exactly does it work better? why is yours even doing so much stuff every second?
I really tested my way (_lact=timeNow every 15min) for hundreds of hours and it worked perfectly

what do you mean so much stuff every second ? The first timeout is only to wait that the player is loaded, then it remove a function and never execute later

it doesn't make sense to use setInterval that way... why not use setTimeout ?

No I'm only running it 100 times if the player have not been found. I've never had any problem on YouTube, but I didn't tested on YouTube music if that was your problem

No I'm only running it 100 times if the player have not been found.

and isn't it bad anyway...  and performance is not worse...

your solution have "worse performance" as you run it every 15 minutes while I run it only once or a few times until the player have been loaded and it never run after

30 or 100 times but every second, not every 15 minutes... it's worse performance... because these 100 iterations are done in 1 minute and 40 seconds, in which it makes amount of instructions, that solution with windows.__lact makes only after hours... so no, You solution doesn't have better performance, mainly in first minute and 40 seconds or maybe resp. in 30 seconds...

You forgot what I said about popup starting directly when loading a video. Modifying that variable after 15 minutes will not works. I wanted something that works for me in every case

Your solution didn't worked as well. At least on YT Music.

I never tested on music, the popup on start happened multiple times for me, and it happened a few times that the player wasn't loaded so I had to add a retry functionality but using timeout or interval doesn't make a big difference as I'm clearing the interval once the player is loaded. It's just a preference, but that doesn't make the code bad. I'm running every second as the popup that display on start was only a few seconds after loading so it was required for me.

@Araxeus  The code I proposed in https://github.com/lawfx/YoutubeNonStop/issues/25#issuecomment-954668455 and that you proposed in https://github.com/lawfx/YoutubeNonStop/pull/43#issuecomment-954702962 (which is Manifest v3) makes for some reason the extension stop working.
How do I know?
Because after youtube is loaded the extension just vanished in my browser task management (Shift+Esc).
I don't know if this could be the cause the extension not working.

@JohnyP36 This is https://github.com/BPower0036/YT-Nonstop still working

How can you add @momala454 's script into lawfx 's extension?

actually i found a way that seems to works after multiple hours of test. Simply do
window.addEventListener('load', function() { document.querySelector('ytd-watch-flexy').youthereDataChanged_ = function() {}; }, false);
i put that into tampermonkey

Do you have to change the autoconfirm.js to this:
const script = document.createElement('script');
script.textContent = window.addEventListener('load', function() { document.querySelector('ytd-watch-flexy').youthereDataChanged_ = function() {}; }, false);
script.onload = function () {
    this.remove();
};
(document.head || document.documentElement).appendChild(script);

or maybe this:
var ynsInjection =
  '(' +
  function () {
    const tag = '[YT Nonstop]';
    const isYoutubeMusic = window.location.hostname === 'music.youtube.com';
    function log(message) {
      console.log(`${tag}[${getTimestamp()}] ${message}`);
    }
    function getTimestamp() {
      let dt = new Date();
      let time = dt.getHours() + ':' + dt.getMinutes() + ':' + dt.getSeconds();
      return time;
    }
    window.addEventListener('load', function() { document.querySelector('ytd-watch-flexy').youthereDataChanged_ = function() {}; }, false);
  } +
  ')();';
console.log(`[Youtube NonStop v${chrome.runtime.getManifest().version}]`);
var script = document.createElement('script');
script.textContent = ynsInjection;
(document.head || document.documentElement).appendChild(script);
script.remove();

at least i can say that i do not like the mutation observer...
I rather much prefer a interval that changes last modified action timestamp on a global property
listening on all DOM changes are more costly i think

I must disagree with jimmy.
yes, listening to DOM changes is costly, but we don't need to listen to whole DOM. And actually if we listen to just specific part of DOM that doesn't change often, it's for sure better than interval, that would either execute too often unnecesary, or miss some change, as time of change is not known. Also cost of listener is actually not that big, as cost of whole logic, that is triggered by it. Ofc, for making it work efficiently, we shouldn't use mutation observer, but just inject listener on only that part of DOM, that has effect on video auto-pause.  So if specific elements internal attributes change, just rewrite them at that moment.


bcbio_setup_genome gff issue

Hi again
Thanks for fixing https://github.com/chapmanb/bcbio-nextgen/issues/1218 . Running the bcbio_setup_genome without a gff3 file now works fine.  A new problem however emerged when adding the gff3, it complains about duplicate IDs.
There may be a problem with the gff so I've emailed the NCBI about it:
"I'm having problems with gff file that does not seem to adhere to the gff3 specification (GCF_000008985.1_ASM898v1_genomic.gff).
The problem comes from that IDs are not unique. One case that I found is ID=cds2 but there might more.
This cds corresponds to a cds that undergoes programmed ribosomal frameshifting and is therefore added as two separate lines / reading frames in the gff but where the IDs are the same. Is this the correct way of representing this feature?"
So lets wait and see what they say.
Traceback:
$ bcbio_setup_genome.py -f GCF_000008985.1_ASM898v1_genomic.fna.gz --gff3 -g GCF_000008985.1_ASM898v1_genomic.gff -i bwa -n AJ749949.2 -b 2
Converting /home/parlar/Downloads/GCF_000008985.1_ASM898v1_genomic.gff to /home/parlar/Downloads/GCF_000008985.1_ASM898v1_genomic.gtf.
Traceback (most recent call last):
  File "/usr/local/bin/bcbio_setup_genome.py", line 191, in <module>
    args.gtf = gff3_to_gtf(args.gtf)
  File "/usr/local/bin/bcbio_setup_genome.py", line 50, in gff3_to_gtf
    db = gffutils.create_db(gff3_file, ":memory:")
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/create.py", line 1273, in create_db
    c.create()
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/create.py", line 488, in create
    self._populate_from_lines(self.iterator)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/create.py", line 571, in _populate_from_lines
    fixed, final_strategy = self._do_merge(f, self.merge_strategy)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/create.py", line 218, in _do_merge
    raise ValueError("Duplicate ID {0.id}".format(f))
ValueError: Duplicate ID cds2

Hi Pär,
We had the same general issus with NCBI's bacterial files so I have some "quick fix" scripts using gbk files to generate cleaned up files for a custom bacterial genome. You can find them in this github folder: https://github.com/druvus/hsph-scripts
The files you need are:

gb2gtf_bacteria.py
gb2ptt_bacteria.py
gb2rnt_bacteria.py

The scripts should be cleaned up and merged but it might help you get started with you bacterial  analysis.

Thanks, Andreas! Did you report the lack of adherence to the gff3 spec to the ncbi? Any comments from them?

Hi,
I had to change a few lines in the code to get the files compatible, I
was thinking to add it to bcbio scripts folder to make them available
for all people. But I will add them this afternoon. We changed a little
the code (mainly for QC figures) that affects GTF information.
All this thanks to @druvus.
On 02/10/2016 08:54 AM, Andreas Sjödin wrote:

Hi Pär,
We had the same general issus with NCBI's bacterial files so I have
some "quick fix" scripts using gbk files to generate cleaned up files
for a custom bacterial genome. You can find them in this github
folder: https://github.com/druvus/hsph-scripts
The files you need are:

gb2gtf_bacteria.py
gb2ptt_bacteria.py
gb2rnt_bacteria.py

The scripts should be cleaned up and merged but it might help you get
started with you bacterial analysis.
—
Reply to this email directly or view it on GitHub
https://github.com/chapmanb/bcbio-nextgen/issues/1220#issuecomment-182385520.

Brilliant! Thanks @lpantano .

Hi @parlar,
you can try this script and let me know if you get any error:
https://github.com/chapmanb/bcbio-nextgen/blob/master/scripts/utils/gb2genome.gtf
You can get the usage using -h flag, and you should use bcbio python to be sure all dependency are installed.
it should produce FASTA and GTF ready to pass to setup_genome script.
thanks @druvus for starting this.
cheers

Thanks @lpantano for fixing it.

Hi again,
I received this elaborate reply from Majda Valjavec-Gratian, NCBI:

Dear Colleague,
I have checked with the NCBI Reference Sequence staff and they stated that this is legal and expected for the GFF3 spec, which is documented here:
http://www.sequenceontology.org/gff3.shtml
In particular:
ID – Indicates the ID of the feature. IDs for each feature must be unique within the scope of the GFF file. In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations) the same ID may appear on multiple lines. All lines that share an ID collectively represent a single feature.
That is, a multi-interval CDS (a discontinuous feature, represented in the flatfilie view by JOIN or ORDER), whether from splicing (multiple exons) or an event such as ribosomal slippage, is expected to have multiple CDS rows in the GFF3 file. The shared ID indicates that they are part of a single feature.
It is most common to see IDs shared across multiple rows for CDS features, and some software expects it to only be true for CDS features, but the GFF3 specification allows this type of markup for any feature. Within NCBI's GFF3 files, it is also seen on some gene and tRNA features (in particular those that are trans-spliced), and it is also used for alignments that appear in eukaryotic annotations.
You may also want to refer to the example in the GFF3 specification under "Programmed frameshift", which has two CDS rows with "ID=cds01".
Majda
Best regards,
Majda Valjavec-Gratian, Ph.D.
NCBI User Services

So, distribution of features of multiple lines but with a single ID is in agreement with the gff3 specification. Should the setup_genome script itself be modified to handle this situation?

Thanks Pär and Andreas,
I'd like to be able to handle it if we can figure out a way to do it. Where did GCF_000008985.1_ASM898v1_genomic.gff come from so I can have something to look at?

The first example from the gffutils docs might be applicable:
https://pythonhosted.org/gffutils/examples.html#mouse-extra-comma-gff3

Hi Rory,
the file Pär is using can be downloaded from NCBI.
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000008985.1_ASM898v1/GCF_000008985.1_ASM898v1_genomic.gff.gz
It is the refseq version so it should be generic to all bacterial reference genomes.

Thanks @druvus, sorry about slow response

Oh sweet, I missed that you all fixed it already. Is running the separate script first workable or does it need to get integrated more?

The separate scripts works fine for RNA-seq but it is not optimal for WGS studies. It would be preferable to update the script to also use repeat information (rRNA copies and IS elements). I mainly use custom genomes in bcbio for RNA-seq studies so I haven't had time to look into how to improve conversion of  bacterial annotation in a more generic way.

hum, you mean that the current genome.fa that comes from the script has
not rRNA and repeat elements? Because I understand this happens when
creating the GTF file, what confused for the FASTA file.
Let me know where I can improve that, and happy to update.
On 02/19/2016 03:23 PM, Andreas Sjödin wrote:

The separate scripts works fine for RNA-seq but it is not optimal for
WGS studies. It would be preferable to update the script to also use
repeat information (rRNA copies and IS elements). I mainly use custom
genomes in bcbio for RNA-seq studies so I haven't had time to look
into how to improve conversion of bacterial annotation in a more
generic way.
—
Reply to this email directly or view it on GitHub
https://github.com/chapmanb/bcbio-nextgen/issues/1220#issuecomment-186390426.

My mistake, getting late over here. Took a closer look at original and generated files. I didn't realise that they had individual locus names for all genes inside IS elements in the genbank file. The output files should be ok to use in bcbio as the difference is minimal to the outer borders of TEs. @parlar have better knowledge about bacterial genomes than me so he could probably fill in here.
thanks @lpantano and @roryk

Hi,
I think this has been solved in the latest version, let us know if it happens again.
Thanks!

Dear all,
I am trying to add a custom genome to bcbio and I am getting the same error as @parlar:
$ bcbio_setup_genome.py --cores 30 --fasta GCF_000003205.7_Btau_5.0.1_genomic.fna.gz --gff3 --gtf GCF_000003205.7_Btau_5.0.1_genomic.gff.gz --name Btaurus --build Btau --buildversion 5.0.1
[...]
ValueError: Duplicate ID ATP5J

The problem seems to be that in the GFF some genes have several annotations:
NC_007299.6     Gnomon  gene    10101475        10102134        .       +       .       ID=gene103;Dbxref=BGD:BT20338,GeneID:282690;Name=ATP5J;gbkey=Gene;gene=ATP5J;gene_biotype=protein_coding
NC_007299.6     Gnomon  mRNA    10101475        10102134        .       +       .       ID=rna100;Parent=gene103;Dbxref=GeneID:282690,Genbank:XM_015461927.1,BGD:BT20338;Name=XM_015461927.1;gbkey=mRNA;gene=ATP5J;
NC_007299.6     Gnomon  exon    10101475        10101720        .       +       .       ID=id643;Parent=rna100;Dbxref=GeneID:282690,Genbank:XM_015461927.1,BGD:BT20338;gbkey=mRNA;gene=ATP5J;product=ATP synthase%2
NC_007299.6     Gnomon  exon    10101821        10102134        .       +       .       ID=id644;Parent=rna100;Dbxref=GeneID:282690,Genbank:XM_015461927.1,BGD:BT20338;gbkey=mRNA;gene=ATP5J;product=ATP synthase%2
NC_007299.6     Gnomon  CDS     10101490        10101720        .       +       0       ID=cds74;Parent=rna100;Dbxref=GeneID:282690,Genbank:XP_015317413.1,BGD:BT20338;Name=XP_015317413.1;gbkey=CDS;gene=ATP5J;pro
NC_007299.6     Gnomon  CDS     10101821        10102030        .       +       0       ID=cds74;Parent=rna100;Dbxref=GeneID:282690,Genbank:XP_015317413.1,BGD:BT20338;Name=XP_015317413.1;gbkey=CDS;gene=ATP5J;pro
NC_007299.6     BestRefSeq      gene    10102198        10109514        .       +       .       ID=gene104;Dbxref=BGD:BT20338,GeneID:282690;Name=ATP5J;description=ATP synthase%2C H+ transporting%2C mitochondrial
NC_007299.6     BestRefSeq      mRNA    10102198        10109514        .       +       .       ID=rna101;Parent=gene104;Dbxref=GeneID:282690,Genbank:NM_174717.3,BGD:BT20338;Name=NM_174717.3;gbkey=mRNA;gene=ATP5
NC_007299.6     BestRefSeq      exon    10102198        10102241        .       +       .       ID=id645;Parent=rna101;Dbxref=GeneID:282690,Genbank:NM_174717.3,BGD:BT20338;gbkey=mRNA;gene=ATP5J;product=ATP synth
NC_007299.6     BestRefSeq      exon    10105723        10105893        .       +       .       ID=id646;Parent=rna101;Dbxref=GeneID:282690,Genbank:NM_174717.3,BGD:BT20338;gbkey=mRNA;gene=ATP5J;product=ATP synth
NC_007299.6     BestRefSeq      exon    10108609        10108733        .       +       .       ID=id647;Parent=rna101;Dbxref=GeneID:282690,Genbank:NM_174717.3,BGD:BT20338;gbkey=mRNA;gene=ATP5J;product=ATP synth
NC_007299.6     BestRefSeq      exon    10109338        10109514        .       +       .       ID=id648;Parent=rna101;Dbxref=GeneID:282690,Genbank:NM_174717.3,BGD:BT20338;gbkey=mRNA;gene=ATP5J;product=ATP synth
NC_007299.6     BestRefSeq      CDS     10105730        10105893        .       +       0       ID=cds75;Parent=rna101;Dbxref=GeneID:282690,Genbank:NP_777142.1,BGD:BT20338;Name=NP_777142.1;gbkey=CDS;gene=ATP5J;p
NC_007299.6     BestRefSeq      CDS     10108609        10108733        .       +       1       ID=cds75;Parent=rna101;Dbxref=GeneID:282690,Genbank:NP_777142.1,BGD:BT20338;Name=NP_777142.1;gbkey=CDS;gene=ATP5J;p
NC_007299.6     BestRefSeq      CDS     10109338        10109375        .       +       2       ID=cds75;Parent=rna101;Dbxref=GeneID:282690,Genbank:NP_777142.1,BGD:BT20338;Name=NP_777142.1;gbkey=CDS;gene=ATP5J;p

or, in the case of tRNA, there are several copies throughout the genome:
NC_007299.6     tRNAscan-SE     gene    962925  962996  .       +       .       ID=gene19;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    962925  962996  .       +       .       ID=rna15;Parent=gene19;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:962958..962960);gbkey=tRNA
NC_007299.6     tRNAscan-SE     exon    962925  962996  .       +       .       ID=id88;Parent=rna15;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:962958..962960);gbkey=tRNA;g
NC_007299.6     tRNAscan-SE     gene    16358699        16358770        .       -       .       ID=gene114;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    16358699        16358770        .       -       .       ID=rna108;Parent=gene114;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:compleme
NC_007299.6     tRNAscan-SE     exon    16358699        16358770        .       -       .       ID=id697;Parent=rna108;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complement
NC_007299.6     tRNAscan-SE     gene    29254475        29254547        .       +       .       ID=gene151;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    29254475        29254547        .       +       .       ID=rna149;Parent=gene151;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:29254508
NC_007299.6     tRNAscan-SE     exon    29254475        29254547        .       +       .       ID=id1146;Parent=rna149;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:29254508.
NC_007299.6     tRNAscan-SE     gene    54292519        54292590        .       +       .       ID=gene292;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    54292519        54292590        .       +       .       ID=rna327;Parent=gene292;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:54292552
NC_007299.6     tRNAscan-SE     exon    54292519        54292590        .       +       .       ID=id3895;Parent=rna327;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:54292552.
NC_007299.6     tRNAscan-SE     gene    57198824        57198895        .       -       .       ID=gene309;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    57198824        57198895        .       -       .       ID=rna341;Parent=gene309;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:compleme
NC_007299.6     tRNAscan-SE     exon    57198824        57198895        .       -       .       ID=id3986;Parent=rna341;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complemen
NC_007299.6     tRNAscan-SE     gene    62038577        62038648        .       -       .       ID=gene354;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    62038577        62038648        .       -       .       ID=rna416;Parent=gene354;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:compleme
NC_007299.6     tRNAscan-SE     exon    62038577        62038648        .       -       .       ID=id4728;Parent=rna416;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complemen
NC_007299.6     tRNAscan-SE     gene    78062025        78062096        .       +       .       ID=gene536;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    78062025        78062096        .       +       .       ID=rna642;Parent=gene536;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:78062058
NC_007299.6     tRNAscan-SE     exon    78062025        78062096        .       +       .       ID=id6836;Parent=rna642;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:78062058.
NC_007299.6     tRNAscan-SE     gene    114504033       114504104       .       -       .       ID=gene843;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    114504033       114504104       .       -       .       ID=rna1003;Parent=gene843;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
NC_007299.6     tRNAscan-SE     exon    114504033       114504104       .       -       .       ID=id10379;Parent=rna1003;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
NC_007299.6     tRNAscan-SE     gene    131426903       131426975       .       -       .       ID=gene983;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    131426903       131426975       .       -       .       ID=rna1165;Parent=gene983;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
NC_007299.6     tRNAscan-SE     exon    131426903       131426975       .       -       .       ID=id11583;Parent=rna1165;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
NC_007299.6     tRNAscan-SE     gene    132739512       132739583       .       +       .       ID=gene1013;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007299.6     tRNAscan-SE     tRNA    132739512       132739583       .       +       .       ID=rna1196;Parent=gene1013;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:132739
NC_007299.6     tRNAscan-SE     exon    132739512       132739583       .       +       .       ID=id11882;Parent=rna1196;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:1327395
NC_007300.6     tRNAscan-SE     gene    13453842        13453913        .       -       .       ID=gene1378;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    13453842        13453913        .       -       .       ID=rna1657;Parent=gene1378;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:comple
NC_007300.6     tRNAscan-SE     exon    13453842        13453913        .       -       .       ID=id17310;Parent=rna1657;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
NC_007300.6     tRNAscan-SE     gene    15487091        15487162        .       +       .       ID=gene1396;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    15487091        15487162        .       +       .       ID=rna1676;Parent=gene1396;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:154871
NC_007300.6     tRNAscan-SE     exon    15487091        15487162        .       +       .       ID=id17504;Parent=rna1676;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:1548712
NC_007300.6     tRNAscan-SE     gene    32900832        32900904        .       +       .       ID=gene1565;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    32900832        32900904        .       +       .       ID=rna1886;Parent=gene1565;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:329008
NC_007300.6     tRNAscan-SE     exon    32900832        32900904        .       +       .       ID=id20201;Parent=rna1886;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:3290086
NC_007300.6     tRNAscan-SE     gene    37767686        37767757        .       -       .       ID=gene1600;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    37767686        37767757        .       -       .       ID=rna1928;Parent=gene1600;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:comple
NC_007300.6     tRNAscan-SE     exon    37767686        37767757        .       -       .       ID=id20793;Parent=rna1928;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
NC_007300.6     tRNAscan-SE     gene    39204474        39204545        .       +       .       ID=gene1610;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    39204474        39204545        .       +       .       ID=rna1937;Parent=gene1610;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:392045
NC_007300.6     tRNAscan-SE     exon    39204474        39204545        .       +       .       ID=id20874;Parent=rna1937;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:3920450
NC_007300.6     tRNAscan-SE     gene    56244673        56244744        .       -       .       ID=gene1692;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    56244673        56244744        .       -       .       ID=rna2028;Parent=gene1692;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:comple
NC_007300.6     tRNAscan-SE     exon    56244673        56244744        .       -       .       ID=id21917;Parent=rna2028;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
NC_007300.6     tRNAscan-SE     gene    61262230        61262301        .       +       .       ID=gene1711;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    61262230        61262301        .       +       .       ID=rna2047;Parent=gene1711;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:612622
NC_007300.6     tRNAscan-SE     exon    61262230        61262301        .       +       .       ID=id22076;Parent=rna2047;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:6126226
NC_007300.6     tRNAscan-SE     gene    72086669        72086740        .       -       .       ID=gene1775;Dbxref=GeneID:100170902;Name=TRNAC-GCA;gbkey=Gene;gene=TRNAC-GCA;gene_biotype=tRNA
NC_007300.6     tRNAscan-SE     tRNA    72086669        72086740        .       -       .       ID=rna2119;Parent=gene1775;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:comple
NC_007300.6     tRNAscan-SE     exon    72086669        72086740        .       -       .       ID=id22734;Parent=rna2119;Dbxref=GeneID:100170902;Note=transfer RNA cysteine (anticodon GCA);anticodon=(pos:complem
[...]

As I see it, and according to a previous reply from @parlar, it seems that none of them is in agreement with gff3 specifications.
How should I deal with these cases?
thanks,


fix typo

"You his" should be "Use this"
Summarize the change in the pull request title
Describe your change, specifically why you think it's needed.
Fixes #Issue_Number (if necessary)
@Article_Author please review (look at the author metadata tag)

@jocasti : Thanks for your contribution! The author, @aczechowski, has been notified to review your proposed change.

Reviewed editorial correction.


Upload observations mgmt command: prepend timeout to ltfp call to prevent endless retries on failure.

This change is

Reviewed 1 of 1 files at r1.
Review status: all files reviewed at latest revision, all discussions resolved.

Comments from Reviewable


Restore HTMLDocument constructable value in DOM

Don't touch anything else in the DOM. Less consistent with @types/web than #45553, but safer to ship late in 4.4's release.

I’m assuming the https://github.com/microsoft/TypeScript/pull/45554/files#diff-649a115a1a1a9a6c5eeefa536f5e12d3ef96bfc1c9ea437c42aa28f685ad6960 diff made sense when you viewed it locally; it references DOM types in it so I guess line numbers just changed on super long lines?

Yep, it's just a dump of most of the DOM types, and Window lost its HTMLDocument member, replaced by the global declare var HTMLDocument

@typescript-bot cherry-pick this to release-4.4


KITTI Dataset

Hi  @TixiaoShan , I  noticed that you update KITTI data several days ago. And I tried new KITTI data. Lidar and IMU data are ok. But GPS data seems to have some problems.You can see below picture. The red path is the result of lio sam and another one is gps path tranformed to local cartesian coordinate.
Another question is lio sam will drift a lot without loop closure. Does IMU noises cause that ?

@LeisureLei Hi, I suspense you are set gpsTopic as "odometry/gpsz". Did you tried "odometry/gps"?

@LeisureLei Hi, I suspense you are set gpsTopic as "odometry/gpsz". Did you tried "odometry/gps"?

Yse, I set gpsTopic as "odometry/gps",  but I get nothing from this topic. Also, I have already install robot localization package. Thus I use geographic package to tranform the message from "/gps/fix" to UTM coordinate(The result is shown above). Have you already tried new KITTI data with gps ? Is there anything OK ?

@LeisureLei I am not sure you are taking about kitti_2011_09_30_drive_0028_synced.bag. But I did't get any issue run this dataset.

@LeisureLei I am not sure you are taking about kitti_2011_09_30_drive_0028_synced.bag. But I did't get any issue run this dataset.

Yse, when I was using kitti_2011_09_30_drive_0028_synced.bag to try lio sam, I found that lio sam has an obvious difference with grountTruth like below picture. Thus I tried to add GPS to constraint trajetory， but I got a bad result, which made me to check the GPS message.

@LeisureLei Sorry I did not get your point which the lio-sam is obvious difference with ground truth. It is really close to ground truth as I saw it :). By the way could you tell me where you got the ground truth data? Is that from the same rosbag?

@LeisureLei Sorry I did not get your point which the lio-sam is obvious difference with ground truth. It is really close to ground truth as I saw it :). By the way could you tell me where you got the ground truth data? Is that from the same rosbag?

The diffence is mainly on z-axis.
The groundtruth data is from KITTI website——08.txt file.(The gps data from kitti_2011_09_30_drive_0028_synced.bag seems not to be used as groundtruth )

@LeisureLei Looking at the navsat launch file it appears that the gps odometry topic is called odometry/navsat (source), have you tried using that instead of odometry/gps?

@LeisureLei could you give me the link of kitti_2011_09_30_drive_0028_synced.bag ? thank you.

@px4Li  hi, could you show me that how you compare the lio-sam result with groundtruth ? evo_ape only supports three formats , kitti,tum&euroc. kitti format requires same poses size , tum requies simliar timestamps...i am confused about it. thanks.

@px4Li hi, could you show me that how you compare the lio-sam result with groundtruth ? evo_ape only supports three formats , kitti,tum&euroc. kitti format requires same poses size , tum requies simliar timestamps...i am confused about it. thanks.

I use tum format.The groundtruth may have no timestamp.Thus I add timestamp manually.The real timestamp can get form bag.

@px4Li hi, could you show me that how you compare the lio-sam result with groundtruth ? evo_ape only supports three formats , kitti,tum&euroc. kitti format requires same poses size , tum requies simliar timestamps...i am confused about it. thanks.

I use tum format.The groundtruth may have no timestamp.Thus I add timestamp manually.The real timestamp can get form bag.

would you mean that you transform the groundtruth(kitti format) to tum format, then compare?

@px4Li hi, could you show me that how you compare the lio-sam result with groundtruth ? evo_ape only supports three formats , kitti,tum&euroc. kitti format requires same poses size , tum requies simliar timestamps...i am confused about it. thanks.

I use tum format.The groundtruth may have no timestamp.Thus I add timestamp manually.The real timestamp can get form bag.

would you mean that you transform the groundtruth(kitti format) to tum format, then compare?

Yes, you can also compare trajectory using kitti format.Just saving lio-sam results as kitti format and changing absolute time into relative time

@px4Li hi, could you show me that how you compare the lio-sam result with groundtruth ? evo_ape only supports three formats , kitti,tum&euroc. kitti format requires same poses size , tum requies simliar timestamps...i am confused about it. thanks.

I use tum format.The groundtruth may have no timestamp.Thus I add timestamp manually.The real timestamp can get form bag.

would you mean that you transform the groundtruth(kitti format) to tum format, then compare?

Yes, you can also compare trajectory using kitti format.Just saving lio-sam results as kitti format and changing absolute time into relative time

i am still confused about it. would you add my qq(744895490) . thank you .

@LeisureLei Where precisely did you find the ground truth for sequence 2011_09_30_drive_0028_sync in KITTI's website? You mentioned something like ——08.txt file but I can't find it anywhere.

@LeisureLei I am not sure you are taking about kitti_2011_09_30_drive_0028_synced.bag. But I did't get any issue run this dataset.

Yse, when I was using kitti_2011_09_30_drive_0028_synced.bag to try lio sam, I found that lio sam has an obvious difference with grountTruth like below picture. Thus I tried to add GPS to constraint trajetory， but I got a bad result, which made me to check the GPS message.

@LeisureLei I also used using kitti_2011_09_30_drive_0028_synced.bag for evaluation but it seems that my results are very misaligned in comparison with the ground truth. Have you experienced something similar in the beginning or do you have any idea on how to solve this issue?

Hi @LeisureLei I managed to align the results with the ground truth. But, there are still large differences (image below). I see that your results using the same dataset are quite good. Did you change anything else, like for example the IMU intrinsics?

Hi @LeisureLei I managed to align the results with the ground truth. But, there are still large differences (image below). I see that your results using the same dataset are quite good. Did you change anything else, like for example the IMU intrinsics?

I haven't modefied IMU intrinsics. I use evo tools to align traj but with tum format, like "evo_traj tum groungTruth.txt test_traj.txt -va -p"

Hi @LeisureLei I managed to align the results with the ground truth. But, there are still large differences (image below). I see that your results using the same dataset are quite good. Did you change anything else, like for example the IMU intrinsics?

I haven't modefied IMU intrinsics. I use evo tools to align traj but with tum format, like "evo_traj tum groungTruth.txt test_traj.txt -va -p"

Yes, I also did exactly the same as you say, but the results I got are the ones shown in the image. As you can see, they are quite different from the ones you obtained before, while they should be the same as we are using the same input (I only changed the extrinsic IMU-LiDAR as recommended). I can't think of something altering the results.

Hi @LeisureLei I managed to align the results with the ground truth. But, there are still large differences (image below). I see that your results using the same dataset are quite good. Did you change anything else, like for example the IMU intrinsics?

I haven't modefied IMU intrinsics. I use evo tools to align traj but with tum format, like "evo_traj tum groungTruth.txt test_traj.txt -va -p"

Hi @LeisureLei, could you please share with me the final TXT file you used when comparing the LIO-SAM results in evo with KITTI's ground truth? Or send it through email to<EMAIL_ADDRESS>I just need this to show as sample results obtained with this algorithm for my thesis. I tried a lot but couldn't solve/fix it myself, so I would really appreciate your help.

Hi @LeisureLei I managed to align the results with the ground truth. But, there are still large differences (image below). I see that your results using the same dataset are quite good. Did you change anything else, like for example the IMU intrinsics?

I haven't modefied IMU intrinsics. I use evo tools to align traj but with tum format, like "evo_traj tum groungTruth.txt test_traj.txt -va -p"

Hi @LeisureLei, could you please share with me the final TXT file you used when comparing the LIO-SAM results in evo with KITTI's ground truth? Or send it through email to<EMAIL_ADDRESS>I just need this to show as sample results obtained with this algorithm for my thesis. I tried a lot but couldn't solve/fix it myself, so I would really appreciate your help.

kitti-loop.txt
Sorry for reply late. I just noticed your message. Here is the txt file. But I am not sure whether it will satisfy you.

@px4Li hi, could you show me that how you compare the lio-sam result with groundtruth ? evo_ape only supports three formats , kitti,tum&euroc. kitti format requires same poses size , tum requies simliar timestamps...i am confused about it. thanks.

I use tum format.The groundtruth may have no timestamp.Thus I add timestamp manually.The real timestamp can get form bag.

hi！can you tell me how to add the timestamp? if possible could u send to me the gt file with<EMAIL_ADDRESS>

Hi @LeisureLei I managed to align the results with the ground truth. But, there are still large differences (image below). I see that your results using the same dataset are quite good. Did you change anything else, like for example the IMU intrinsics?

I haven't modefied IMU intrinsics. I use evo tools to align traj but with tum format, like "evo_traj tum groungTruth.txt test_traj.txt -va -p"

Hi @LeisureLei, could you please share with me the final TXT file you used when comparing the LIO-SAM results in evo with KITTI's ground truth? Or send it through email to<EMAIL_ADDRESS>I just need this to show as sample results obtained with this algorithm for my thesis. I tried a lot but couldn't solve/fix it myself, so I would really appreciate your help.

kitti-loop.txt Sorry for reply late. I just noticed your message. Here is the txt file. But I am not sure whether it will satisfy you.

Hello, is the txt you provided groundtruth?

Hi @TixiaoShan , I noticed that you update KITTI data several days ago. And I tried new KITTI data. Lidar and IMU data are ok. But GPS data seems to have some problems.You can see below picture. The red path is the result of lio sam and another one is gps path tranformed to local cartesian coordinate. Another question is lio sam will drift a lot without loop closure. Does IMU noises cause that ?

can you share me ground truth files.
<EMAIL_ADDRESS>

Hey guys! @LeisureLei , @px4Li @yxallnyy @tigerschweiger Apologies...i am a bit late to the party..and i need some help regarding misalignment of imu preintegration based trajectory and GPS trajectory. This is the satellite view of both trajectories:

(if you are somehow not able to see the uploaded img then) Actually imu based trajectory is slightly off the road like tilted anticlockwise slightly wrt gps trajectory (ground truth). So can you tell me what changes i need to make in params.yaml file? One idea i got is to change the imu intrinsics (modify bias noises etc) but i want to know would that help?
Also one more thing, there are two trajectory topics published as a result of liosam /lio_sam/imu/path (Pubisher: imuPreintegraton module) and /lio_sam/mapping/path (Publisher: mapOptimization module), I want to know what is the actual; output trajectory of liosam? Apparently both trajectories overlap but are off-road wrt gps trajectory but still I need clarification.

Hey @ataparlar I found its workaround not by tweaking parameters of LIO-SAM params.yaml but relocalized the output trajectory by integrating robot_localization package of ROS on output liosam trajectory and the gps sensor data. That was months ago but the output trajectory was much aligned with ground truth!. Hope that helps!

Just wanted to enquire, what can be done about this warning message (except ignoring) to enable the deskew function:
"Point cloud timestamp not available, deskew function disabled, system will drift significantly!" i get while running LIO-SAM?

Also while running with another rosbag I got from kitti raw say sequence 0027 and launching the lio sam launch file, I get this error message:
"[ERROR] [1730802813.546919026]: Point cloud is not in dense format, please remove NaN points first!"
how to fix this?

Hi @ashwinjoseph95

Just wanted to enquire, what can be done about this warning message (except ignoring) to enable the deskew function: "Point cloud timestamp not available, deskew function disabled, system will drift significantly!" i get while running LIO-SAM?

You need to change the quote in this line with the timestamp field of your cloud.

Also while running with another rosbag I got from kitti raw say sequence 0027 and launching the lio sam launch file, I get this error message: "[ERROR] [1730802813.546919026]: Point cloud is not in dense format, please remove NaN points first!" how to fix this?

And for this, you should check this comment.

Hi @harisbinyousaf24

Hey guys! @LeisureLei , @px4Li @yxallnyy @tigerschweiger Apologies...i am a bit late to the party..and i need some help regarding misalignment of imu preintegration based trajectory and GPS trajectory. This is the satellite view of both trajectories:  (if you are somehow not able to see the uploaded img then) Actually imu based trajectory is slightly off the road like tilted anticlockwise slightly wrt gps trajectory (ground truth). So can you tell me what changes i need to make in params.yaml file? One idea i got is to change the imu intrinsics (modify bias noises etc) but i want to know would that help? Also one more thing, there are two trajectory topics published as a result of liosam /lio_sam/imu/path (Pubisher: imuPreintegraton module) and /lio_sam/mapping/path (Publisher: mapOptimization module), I want to know what is the actual; output trajectory of liosam? Apparently both trajectories overlap but are off-road wrt gps trajectory but still I need clarification.

Hi, have you solved this problem? I am facing with a similar thing right now.

I found out that this problem is related to the coordinate conversion methods. If you are giving your GNSS sensor's output Odometry msg as the LIO-SAM's input Odometry (gpsTopic in the param file), there most likely be a rotation difference between the paths. Because sensors usually use GeographicLib::LocalCartesian::Forward for converting (lat, lon, alt) to (x, y, z).  You should use `GeographicLib::UTMUPS::Forward' instead as a position source.


Bug/sprite sheet image

imageResourceName is now the actual path of the loaded image
This means it site in the pixi cache correctly now and will not get loaded /prepared twice.

@GoodBoyDigital I'm not sure this is a good idea after working on it for awhile. Basically, if there's an error with the image loading, it's easy to check *_image.error in the resources. In your implementation here, you only get the resource by full path. We could add both or leave it how it is. Either way, you should add a test which demonstrates the use-case you described.


AMBARI-23343. Server should acknowledge agent about received reports

What changes were proposed in this pull request?
Now server sends OK response to agent report message.
How was this patch tested?
Manual testing.

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/Ambari-Github-PullRequest-Builder/1381/
Test FAILed.
Test FAILured.


Ember Canary - Property state is undefined on renderNode cause of deprecation

I'm getting an error in ember-internals when running ember#canary.
TypeError: undefined is not an object (evaluating 'renderNode.state.stream')

I'm guessing that the state property has been fully removed now following the deprecation warning to start using _state. Is there any reason for continuing to use state? Those properties were deprecated sometime in v1.8.0.
Could check if it exists first and fallback to using _state.

This is a different state. It's part of the private streams API.
We need to switch to getState.
On Sep 13, 2015 5:40 PM, "Matt Grannary"<EMAIL_ADDRESS>wrote:

I'm getting an error in ember-internals when running ember#canary.
TypeError: undefined is not an object (evaluating 'renderNode.state.stream')
I'm guessing that the state property has been fully removed now following
the deprecation warning to start using _state. Is there any reason for
continuing to use state? Those properties were deprecated sometime in
v1.8.0.
Could check if it exists first and fallback to using _state.
—
Reply to this email directly or view it on GitHub
https://github.com/ef4/liquid-fire/issues/362.

I see. Ya that worked for getting the right state property and accessing the stream. Getting another error now though. Not sure if it's in relation to this stream.
Error: Stream error: compute not implemented

Does that ring a bell?

Yes. We need to import a different thing from the stream module now. We're
getting BasicStream when we want Stream.
I expect to publish a fix shortly, I just got detoured fixing ember-qunit
too, because that was messing up LF's test suite under canary.
On Sep 13, 2015 6:27 PM, "Matt Grannary"<EMAIL_ADDRESS>wrote:

I see. Ya that worked for getting the right state property and accessing
the stream. Getting another error now though. Not sure if it's in relation
to this stream.
Error: Stream error: compute not implemented
Does that ring a bell?
—
Reply to this email directly or view it on GitHub
https://github.com/ef4/liquid-fire/issues/362#issuecomment-139923942.

No worries. Thanks!

Perfect. That did the trick. Changed the require to get Stream instead of default and all is well. Do you need help getting this patch in?

Sure, happy to take a PR, as long as it's also backward-compat.
On Sep 13, 2015 7:12 PM, "Matt Grannary"<EMAIL_ADDRESS>wrote:

Perfect. That did the trick. Changed the require to get Stream instead of
default and all is well. Do you need help getting this patch in?
—
Reply to this email directly or view it on GitHub
https://github.com/ef4/liquid-fire/issues/362#issuecomment-139927623.

@ef4 any chance we could get a release with this fix in place?

Released 0.21.3


Toggle documentation only works to open  the documentation, not to close it

I use 1.21.1 on Windows 10.
When I  toggle documentation  for a function, a  "panel" with the documentation opens  below. There does not appear to be any way of getting rid of it, in particular "toggle documentation"  command does not get rid of this  "panel".

See my comment in #15903.


Updated README.md file

This PR attempts to update the README.md file with some additional content:

Adding Badges with Insights from VS Code Marketplace.
License section at the end of the file
Applying some Markdown rules (see: markdownlint)

btw: feel free to close this PR if this is too much or not in your interest 🦦

What do you think about using this background image (https://pbs.twimg.com/media/FTBJk7NWIAAe-WT?format=jpg&name=small) as a logo for this package? Or putting it at the top of the README.md file.

What do you mean?  "Performance Profiling" doesn't really have anything to do with this ;-)

What do you mean? "Performance Profiling" doesn't really have anything to do with this ;-)

Without that specific title. I like the background image with the clouds. It adds that little something to this repo because of "Cloud.Ready." - just a thought. It would replace the simple logo provided in this PR on top of the README.md.
What do you think about the changes in this PR so far - yay or nay?

Rest of the changes - yay!
shall I merge?

got it
feel free to merge if the changes would fit into this repo


Can't change the ID/name of routes with type kameletBinding and Integration, and Kamelet adds "-action" to new name

Describe the Bug
When users try to change the integration and kameletBinding name (or id), the old name and ID stays displayed in the dropdown and also after sync - the old name reappears. For Camel Route the name change works as expected.
A bit different situation is for Kamelet type - after the name change, there is suffix "-action" added to the new Kamelet name, so instead of "test" there is "test-action"
Steps to Reproduce the Bug or Issue

create a route of type Integration, KameletBinding or Kamelet
try to change the ID or name

Screenshots or Videos

Platform

OS: [e.g. macOS, Windows, Linux]
Browser: [e.g. Chrome, Safari, Firefox]
Version: [latest]

This was fixed, the pending part is the Kamelet action suffix. I'm moving the issue to the backend


Improve travis caching

This updates pip on travis to (re)enable binary wheel caching.  It looks like it brings the pip install step down from 6 minutes to 10 seconds.
I also went ahead and cached the installs of cmake and mongo using the scripts girder uses, and I added similar scripts for spark and scala.

6 minutes to 10 seconds

This is awesome! :+1: :+1:

Great, thanks @jbeezley .
LGTM, merging.


Clean up Item Types

Item mapping spreadsheet
We have identified roughly 75 Item Types to be cleaned up before migration. Areas include

[ ] 3D items
[ ] Haithi Trust
[ ] Archives
[ ] Collection Management
[ ] Gov Docs
[ ] Reserves
[ ] Map Library
[ ] Music
[ ] Special Collections
[ ] Artworks

@katallm - I looked at the Item mapping spreadsheet and identified some item codes that will/may affect ILL or Prospector. Let me know when you're ready to go forward on this. We will have to decide some of these in conjunction with whomever is hired in Coll. Couriers to run that section since Prospector and Mobius resides mostly with that section rather than mine.

[ ] 73 | 1034 | ILL Borrowed Materials - Already Resolved on spreadsheet under Notes
[ ] 100 | #N/A | No Prospector No ILL
[ ] 102 | 2499 | Book, no Prospector
[ ] 94 | 161466 | Ebooks, Prospector
[ ] 95 | 6376 | SILLVR streaming videos
[ ] 200 | #N/A | Prospector-Requestable
[ ] 201 | 840 | Prospector NonRequestable
[ ] 202 | #N/A | MOBIUS AV Circ
[ ] 203 | #N/A | MOBIUS TEST
[ ] 205 | #N/A | Prospector Media
[ ] 206 | #N/A | Prospector PASCAL journals
[ ] 207 | #N/A | Prospector CRL Items
[ ] 209 | #N/A | MOBIUS GENERAL CIRC
[ ] 210 | #N/A | MOBIUS NON-CIRC
[ ] 211 | #N/A | MOBIUS Audiobook
[ ] 220 | #N/A | Marmot monograph

@libraryfemme Are the locations in https://github.com/culibraries/folio/issues/40#issuecomment-963639517 ones that you want to keep or cleanup?

@jwfuller - I don't actually know, because Prospector and Mobius are not under my section. We only handle a few short routines for Prospector. The Prospector position is interviewing right now, so depending on who ends up as head of Collection Courier and Caretakers, it will have to be decided in conjunction with that person. Maybe Claire Hoag. I also think we should include Lisa Tatum in this discussion.
We definitely want to keep 73.


How to instrument with afl-gcc?

when i want to instrument elfutils(libelf), i found that there are lots of nested function definitions, which are not supported by clang, so i want to use afl-gcc to generate CGs.
But it turns out that afl-gcc doesn't support "-targets=$TMP_DIR/BBtargets.txt" and "-outdir=$TMP_DIR" options. it said "configure: error: C compiler cannot create executables"
is there any solutions? what compile options should be applied?
thx very much.

Hi. You can take a look into afl-as.h to see how AFL instruments the basic block ID. Then, the distance of each basic block to predefined targets could be instrumented in the same way. Note that you need to accumulate the total distance values and the number of exercised basic block at runtime in order to calculate the seed distance of the current input. AFLGo currently supports only llvm-mode. Best.


WIP Add migration docs for 2.2 and 3.0

Fixes #14218
Fixes #9259
Creating the skeleton for the two topics. Need more information to finish this.

Here is DOTNET_SKIP_FIRST_TIME_EXPERIENCE related change. cc @KathleenDollard
DOTNET_SKIP_FIRST_TIME_EXPERIENCE used to control many things including extracting package cache, disabling telemetry, disabling printing of welcome message, disabling aspnet certificate configuration, disabling global tools PATH configuration.
Started from 3.0.100 we separated the functionality of this flag to many smaller flag and stopped honoring it. The setup of extracting package cache is no longer needed. Disable telemetry is solely controlled by the existing flag DOTNET_CLI_TELEMETRY_OPTOUT=1. We shortened the welcome message and it will always shows the first time. Aspnet certificate configuration can be disabled by DOTNET_GENERATE_ASPNET_CERTIFICATE=0. Global tools PATH configuration can be disabled by DOTNET_ADD_GLOBAL_TOOLS_TO_PATH=0

Maira, what Will said is correct and is the right info for docs. Here are a couple of edits and can you align the grammar in the bullets and anything else you see:
Prior to .NET Core 3.0.100, the .NET Core SDK used the DOTNET_SKIP_FIRST_TIME_EXPERIENCE environmental variable to control many things including extracting package cache, disabling telemetry, disabling printing of welcome message, disabling aspnet certificate configuration, disabling global tools PATH configuration.
Started from 3.0.100 we separated the functionality of this flag to many smaller flag and stopped using the DOTNET_SKIP_FIRST_TIME_EXPERIENCE variable:

The setup of extracting package cache is no longer needed.
Disable telemetry is solely controlled by the existing flag DOTNET_CLI_TELEMETRY_OPTOUT=1.
We shortened the welcome message and it will always shows the first time.
Aspnet certificate configuration can be disabled by DOTNET_GENERATE_ASPNET_CERTIFICATE=0.
Global tools PATH configuration can be disabled by DOTNET_ADD_GLOBAL_TOOLS_TO_PATH=0

Thanks, I'll add that info. Sorry I missed this earlier somehow.

Closing this one since all I had was the skeleton topics. Someone will need to pick this up.


get_ssm_parameter_tags  errors

2024-04-11T20:47:24.391Z	9b0519f7-f889-4173-9887-278e5d233921	ERROR	Invoke Error 	{
"errorType": "ValidationException",
"errorMessage": "The parameter doesn't meet the parameter name requirements. The parameter name must begin with a forward slash "/". It can't be prefixed with \"aws\" or \"ssm\" (case-insensitive). It must use only letters, numbers, or the following symbols: . (period), - (hyphen), _ (underscore). Special characters are not allowed. All sub-paths, if specified, must use the forward slash symbol "/". Valid example: /get/parameters2-/by1./path0_.",
"name": "ValidationException",
"$fault": "client",
"$metadata": {
"httpStatusCode": 400,
"requestId": "856ee638-b920-457d-b2ee-ab9848f0a830",
"attempts": 1,
"totalRetryDelay": 0
},
"type": "ValidationException",
"message": "The parameter doesn't meet the parameter name requirements. The parameter name must begin with a forward slash "/". It can't be prefixed with \"aws\" or \"ssm\" (case-insensitive). It must use only letters, numbers, or the following symbols: . (period), - (hyphen), _ (underscore). Special characters are not allowed. All sub-paths, if specified, must use the forward slash symbol "/". Valid example: /get/parameters2-/by1./path0.",
"stack": [
"ValidationException: The parameter doesn't meet the parameter name requirements. The parameter name must begin with a forward slash "/". It can't be prefixed with \"aws\" or \"ssm\" (case-insensitive). It must use only letters, numbers, or the following symbols: . (period), - (hyphen), _ (underscore). Special characters are not allowed. All sub-paths, if specified, must use the forward slash symbol "/". Valid example: /get/parameters2-/by1./path0.",
"    at throwDefaultError (/var/runtime/node_modules/@aws-sdk/node_modules/@smithy/smithy-client/dist-cjs/index.js:838:20)",
"    at /var/runtime/node_modules/@aws-sdk/node_modules/@smithy/smithy-client/dist-cjs/index.js:847:5",
"    at de_CommandError (/var/runtime/node_modules/@aws-sdk/client-ssm/dist-cjs/index.js:6875:14)",
"    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)",
"    at async /var/runtime/node_modules/@aws-sdk/node_modules/@smithy/middleware-serde/dist-cjs/index.js:35:20",
"    at async /var/runtime/node_modules/@aws-sdk/node_modules/@smithy/core/dist-cjs/index.js:165:18",
"    at async /var/runtime/node_modules/@aws-sdk/node_modules/@smithy/middleware-retry/dist-cjs/index.js:320:38",
"    at async /var/runtime/node_modules/@aws-sdk/middleware-logger/dist-cjs/index.js:33:22",
"    at async get_ssm_parameter_tags (file:///var/task/index.mjs:186:36)",
"    at async generateTaggingFromCloudTrail (file:///var/task/index.mjs:246:37)"
]
}

It was caused by the letter @ in the role. I replaced it with _.


Please invite me to the community

Name
Airaki Willsman
Additional Context
I would like to be part of this community and contribute here.

Invitation sent to join the GitHub Organization. Welcome to Infraform 🎉Please check your mail to accept the invitation sent by GitHub! 🤖About usInfraform is an open source solution for serverless platforms, it is designed for developing solutions and enhancing creators to create their infrastructure 💻 Great to have you in our community ✨ Looking forward to your valuable contributions! 🤓 You can also check our community ✨ Github ✨ LinkedIn 💜 You can also share our community with other folks who want to learn about development, DevOps, tech, and contribute together and with us 👉💜👈


Not work in virtualenv

Traceback (most recent call last):
File "/home/dos/.virtualenvs/accommodirect/bin/ptpython", line 5, in
from pkg_resources import load_entry_point
File "/home/dos/.virtualenvs/accommodirect/lib/python2.7/site-packages/pkg_resources/init.py", line 3018, in
working_set = WorkingSet._build_master()
File "/home/dos/.virtualenvs/accommodirect/lib/python2.7/site-packages/pkg_resources/init.py", line 614, in _build_master
return cls._build_from_requirements(requires)
File "/home/dos/.virtualenvs/accommodirect/lib/python2.7/site-packages/pkg_resources/init.py", line 627, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/home/dos/.virtualenvs/accommodirect/lib/python2.7/site-packages/pkg_resources/init.py", line 805, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: jedi>=0.8.1
pip freeze | grep jedi
jedi==0.8.1-final0

its a pip bug, update pip


Add a few tests for Functional Components

I think we are lacking tests for functional components. Those types of components resemble allot more statefull components now.
A functional component signature is now - https://github.com/vuejs/rfcs/blob/master/active-rfcs/0031-attr-fallthrough.md#functional-components
const Component = (props, { slots, attrs, emit }) => h('div', { class: ['a'] }, slots)

Component.props = { /*...*/ }
Component.inheritAttrs = false
Component.displayName = 'FunctionalComponent'

I can take this over and try to add test cases on as many places as I can.
We also need to test asyncFunctionalComponents - https://github.com/vuejs/rfcs/blob/async-component/active-rfcs/0026-async-component-api.md

We also haven't got anything for defineAsyncComponent, either. IIRC this had some weird bugs in beta, we should test it. One common case is loading routes/pages async.

We have #187 and #158 relating to bugs in functional components, so I will close this.


list->array conversion does not compile on macos

This simple function
import numpy as np
#pythran export func()
def func():
    a = [1, 2, 3, 4]
    return (np.array(a))

Does not compile on macos (but it does in linux).

Version 0.8.5 does not fix this issue.

If this is useful:
import numpy as np
#pythran export func()
def func():
    a = [1, 2, 3, 4]
    return np.array(a) # <- does not compile
    # return np.array(a,dtype=int) # <- does not compile
    # return np.array(a,dtype=float) # does compile

In other words, if the returned array is float  things are OK.
Error log:
error.txt

Confirmed this is fixed on mac os and linux at https://github.com/serge-sans-paille/pythran/commit/c3dd1ef72aa7de51d84ab25ea4d936101d8a5802


add topics

I suggesting adding the topics matrix-multiplication, benchmark in the About section at https://github.com/certik/matmul

Thanks @Beliavsky. Let me know if the tags look good now.

They do -- closing this issue.


Labeling and search update

What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)
Labels now for Analysis objects not only FW-files
working search function in report dashboard
What is the current behavior? (You can also link to an open issue here)
limited label function
What is the new behavior (if this is a feature change)? If possible add a screenshot.

Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)
no - just model changes

very cool new feature!


"Ghost" Kodi platform

Home Assistant release with the issue:
0.91.0
Last working Home Assistant release (if known):
unknown
Operating environment (Hass.io/Docker/Windows/etc.):
Hass.io vm in HyperV
Component/platform:
https://www.home-assistant.io/components/media_player.kodi/
Description of problem:
At one point I had a Kodi player in my setup, but this has been removed. Ever since I get these in my log:
Updating kodi media_player took longer than the scheduled update interval 0:00:10
Update of media_player.kodi_digihome_local is taking over 10 seconds

Problem-relevant configuration.yaml entries and (fill out even if it seems unimportant):
There is no specific Yaml, Kodi was added through discovery. I have searched all config files (including hidden) for any reference to Kodi, none was found. I also deleted the database to remove any leftover references.
Traceback (if applicable):
n/a
Additional information:

Is the kodi player still in operation?
Unless you exclude it from discovery if the player is still on the network it will be re-added

Is the kodi player still in operation?
Unless you exclude it from discovery if the player is still on the network it will be re-added

Thank you for this hint, it helped me resolve the issue. I used an upnp scanner on my network and it still showed my pc which had Kodi on it advertising, but there was no xml schema attached.
I did uninstall Kodi on this server, but as it was never restarted it apparently was still advertising the service (with an empty xml schema). This is probably why Home Assistant had trouble. A full server reboot seems to have resolved the issue.


Very slow plotting and drawing (> 5 hrs)

Hi all,
I am trying to create a subplot (square grid) of out of a large DataFrame object (8016878, 29). It took more than 5 hrs (!) to make the plot and another 3.5+ hrs to draw it !
I wanted to ask why is there such a huge performance hit. Is there something I am doing wrong in my code below ?
I saw (via the linux Top command) that julia has allocated ~ 20 GB of data to VIRT memory and 0.016 terabyte to RES. This seems unusually high.
The command I am using to make the subplot is as follows:
set_default_plot_size( 9inch, 3.6inch)

myplot =plot(Results,x="Escape_Vinf",y="TOF", color="NumFlyby", xgroup="KBO", Geom.subplot_grid(Geom.point), Guide.colorkey("# Flybys "),  Guide.xlabel("Escape Velocity (au/yr.)"),Guide.ylabel("TOF (yrs.)"),Theme(default_point_size=0.3mm,highlight_width=0.01mm, minor_label_font_size=11pt, background_color=color("white"), colorkey_swatch_shape=:circle, guide_title_position=:left ))

draw(PNG("Output.png",  9inch, 3.6inch, dpi=300),myplot);

I would really appreciate any advice on speeding up the plotting or if there is any clever way to improve it ?
I am on Julia 0.3.xx and latest stable version of Gadfly.
thanks a lot.

Others who know Gadfly better than I may have specific suggestions, but in general I'd suggest profiling any time you have performance questions. ProfileView.jl gives you a nice way of viewing the results, and you can even post the results as an SVG file or IJulia notebook so that others (who might know more about Gadfly's internals) can browse the results.
It will take a few minutes to learn how to use these tools, but my experience has been that learning to use the profiler is the fastest route to learning how to write efficient julia code (i.e., it will have long-lasting benefits for you).
I'd recommend profiling on a small subset of your DataFrame; if you really have to do the full 5 hours, then you should definitely set Profile.init(delay=0.1,n=10^7) or something (otherwise you will fill up the profiling buffer in the first 20s or so).

The call the plot took 5 hours? That's really peculiar. I tried to reproduce it by generating 8 million rows of random data. The plot call took 0.85 seconds and draw took about 9 minutes. That's still quite slow, but nothing like what you got.
What are the types of the columns, and how many unique values are there in KBO? Also, is it possible that you're out of memory and it's swapping? It does allocate a lot.

Same here, i tried to plot 10mio data and had similar times like Daniel.
@GravityAssisted, can you somehow tell us more about the data and your computer. Even 20G for holding the data is strange.

Thanks all for the replies.
My computer is a very capable machine with 12 cores, 32 GB of RAM and 512GB SSD. I don't think I am running out of memory or RAM.
The original Dataframe is a huge one with 8016878 rows and 29 columns. Some of the columns have text (long ASCII strings) and some are floating point (Float64) numbers. The Dataframe itself in .csv format takes couple+ of gigabytes of storage space.
I didn't had the chance to profile (maybe tonight I will) but I did notice a little improvement by removing the columns I don't need in my dataframe (I only need like 10, with only 2 of them being strings). I am also currently trying to move to Julia-0.4 and it does seem to give me a performance boost. Its running as we speak so lets see how fast it can be. I will update again.
Finally in Julia-0.4 Gadfly is having another issue of drawing to PNG back end as it complains about installation of Cairo (which I already have). I was able to overcome this by drawing to SVG and converting using Imagmagick.
thanks


Fix: ssm prefix custom cdk policy

Feature or Bugfix

Bugfix

Detail
As part of the environment stack we deploy some SSM parameters prefixed with dataall prefix in all cases. The custom DataallCustomCDKPolicy provided to use in the cdk bootstrap command restricts SSM permissions to resource-prefixed parameters. As a result, when using an environment with a resource prefix different from the default dataall the stack fails to create and to delete because it cannot create or delete those SSM parameters.

The first commit adds the generic dataall SSM permisssions to the custom policy. It open the permissions slightly
The second and third commits rename the SSM parameters to use the resource prefix

Each commit would solve the issue on its own, so we don't really need both. However, there are arguments to keep both. Having generic permissions to dataall-SSM parameters is restrictive and might be useful for other cases when the toolkit is used. It is good to keep all created resources prefixed with the same prefix, so that users can easily track which resources belong to a data.all environment.
The only issue is that for number 2, we need users to update the environment stacks before creating more datasets (add in release notes)
Relates

v2.1 release

Security
Please answer the questions below briefly where applicable, or write N/A. Based on
OWASP 10.

Does this PR introduce or modify any input fields or queries - this includes
fetching data from storage outside the application (e.g. a database, an S3 bucket)?

Is the input sanitized?
What precautions are you taking before deserializing the data you consume?
Is injection prevented by parametrizing queries?
Have you ensured no eval or similar functions are used?

Does this PR introduce any functionality or component that requires authorization?

How have you ensured it respects the existing AuthN/AuthZ mechanisms?
Are you logging failed auth attempts?

Are you using or adding any cryptographic features?

Do you use a standard proven implementations?
Are the used keys controlled by the customer? Where are they stored?

Are you introducing any new policies/roles/users?

Have you used the least-privilege principle? How?

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Tested on AWS deployment. I wanted to know your opinion @noah-paige:

Should we remove the permission to dataall- SSM params?
Should we go ahead with the renaming? or is it an unnecessary change?
I do not have an strong opinion (only slight opinions) on it :)

Re-tested with the latest changes


How cython memoryview accept input of various dimensions

Hi everyone. I'm using cython to speed up my code, and use memoryview to let functions defined in cython accept array input. Eventually, I would like my function to be able to accept 3-D, 2-D, 1-D and even scalar input. However, it seems that I have to specify the dimension when I typed the memoryview of the arguments. Then how can I enable both 3-D, 2-D and 1-D input? One way I can imagine is define several functions doing the same thing but accepting input of different dimensions, and then write another caller function with a check of the input dimension to call specific processing function. But, is there any other more elegant way of doing this?
Thanks!

Please ask support questions on the Cython-users mailing list, not the bug tracker.
The purpose of memoryviews is pretty much to enable fast indexing, so a memoryview with an unknown number of indexes isn't really a meaningful concept.

Please ask support questions on the Cython-users mailing list, not the bug tracker.
The purpose of memoryviews is pretty much to enable fast indexing, so a memoryview with an unknown number of indexes isn't really a meaningful concept.


OMP Error #15: Multiple OpenMP Runtime Instances Detected

OMP: Error #15: Initializing libiomp5md.dll, but found libiomp5md.dll already initialized.
OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://www.intel.com/software/products/support/.
system:windows11
Python:3.12.2

I recommend creating a new conda environment to help avoid library conflicts.


Width & Height attributes didn’t work with viewBox

🐛 Bug Report
width & height attributes didn’t work with viewBox.
I need to be able to keep the width & height + viewBox but it didn't work.
To Reproduce
Steps to reproduce the behavior:

Add  all dimensions options in configuration https://react-svgr.com/docs/options/#dimensions
Width & Height attributes didn’t work with viewBox

Expected behavior
Width & Height attributes work with viewBox
Link to repl or repo (highly encouraged)
Please provide a minimal repository on GitHub.
Issues without a reproduction link are likely to stall.
Run npx envinfo --system --binaries --npmPackages @svgr/core,@svgr/cli,@svgr/webpack,@svgr/rollup --markdown --clipboard
Paste the results here:

I'm also noticing this, after updating all my viewboxes have been removed

any fix for this?

???

This may help.
https://react-svgr.com/docs/migrate/#svgo


Add timeout parameter to Client::sync method

Adds a timeout parameter to the Client::sync method, that is just passed directly into the Request object as one of the parameters.

I pushed a PR to master fixing CI, please rebase.

The type of the duration parameter has now changed, I'll implement this separately from this PR.


Add BackendEstimatorV2

Summary
This PR adds BackendEstimatorV2 as a BaseEstimatorV2 implementation using a backend.
This is another approach to #11899.
This PR provides an implementation that directly relies on backend.run while #11899 provides a converter from EstimatorV1 to EstimatorV2.
This PR can do qubit-wise grouping taking into account broadcasting, e.g., estimator.run([(circuit, ["IX", "YI"])]) -> run 1 circuit.
I made tests based on those for StatevectorEstimator.
Notes (same as #11928)

I intentionally specified only BackendV2 as backend option though it still supports BackendV1 because I think we need to support only the latest version of backends. If requested, I can add BackendV1.

I added BackendV1 support as well as BackendV2

I didn't add transpile feature because Runtime Primitives V2 do not support transpile during execution. Users need to transform input circuits into ISA format beforehand.

Details and comments

Pull Request Test Coverage Report for Build<PHONE_NUMBER>
Details

130 of 135 (96.3%)  changed or added relevant lines in 3 files are covered.
4 unchanged lines in 1 file lost coverage.
Overall coverage increased (+0.04%) to 89.323%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

qiskit/primitives/backend_estimator_v2.py
126
131
96.18%

Files with Coverage Reduction
New Missed Lines
%

crates/qasm2/src/lex.rs
4
91.94%

Totals

Change from base Build<PHONE_NUMBER>:
0.04%

Covered Lines:
59255

Relevant Lines:
66338

💛  - Coveralls

The following example with Aer:
import numpy as np
from qiskit.circuit.library import IQP
from qiskit import transpile
from qiskit.quantum_info import SparsePauliOp, random_hermitian
from qiskit.primitives import BackendEstimatorV2
from qiskit_aer import Aer

qasm_simulator = Aer.get_backend('qasm_simulator')
qasm_simulator_estimator = BackendEstimatorV2(backend=qasm_simulator, default_precision=0.1)

n_qubits = 12

mat = np.real(random_hermitian(n_qubits, seed=1234))
circuit = IQP(mat)
observable = SparsePauliOp("Z" * n_qubits)

isa_circuit = transpile(circuit, backend=qasm_simulator, optimization_level=1)
isa_observable = observable.apply_layout(isa_circuit.layout)

job = qasm_simulator_estimator.run([(isa_circuit, isa_observable)])
result = job.result()

print(f" > Expectation value: {result[0].data.evs}")
print(f" > Metadata: {result[0].metadata}")

 > Expectation value: -0.025
 > Metadata: {'precision': 0.1}

Here an example with FakeBackend:
import numpy as np
from qiskit.circuit.library import IQP
from qiskit import transpile
from qiskit.quantum_info import SparsePauliOp, random_hermitian
from qiskit.primitives import BackendEstimatorV2
from qiskit_ibm_runtime.fake_provider import FakeAlmadenV2

fake_almaden = FakeAlmadenV2()
fake_almaden_estimator = BackendEstimatorV2(backend=fake_almaden)

n_qubits = 12

mat = np.real(random_hermitian(n_qubits, seed=1234))
circuit = IQP(mat)
observable = SparsePauliOp("Z" * n_qubits)

isa_circuit = transpile(circuit, backend=fake_almaden, optimization_level=1)
isa_observable = observable.apply_layout(isa_circuit.layout)

job = fake_almaden_estimator.run([(isa_circuit, isa_observable)], precision=0.01)
result = job.result()

print(f" > Expectation value: {result[0].data.evs}")
print(f" > Metadata: {result[0].metadata}")

 > Expectation value: -0.00575
 > Metadata: {'precision': 0.01}

I added BackendV1 support and tests with Fake7QPulseV1.

I'm wondering how to add seed.

add seed parameter to the constructor, i.e., BackendEstimator(self, *, backend, default_precision, seed).
add seed parameter to run method, i.e., BackendEstimator.run(self, pubs, *, default_precision, seed).
We will pass seed to a simulator via _run_circuit. Then, we can set a random seed number though some simulator behavior might be deterministic.

I made a PoC to add seed_simulator option torun method. I confirmed that it fixes deviation of expectation values of the unit tests.
If it looks good, I will merge the branch to this PR.
https://github.com/t-imamichi/qiskit-terra/compare/backend-estimator-v2...t-imamichi:qiskit-terra:backend-estimator-v2-seed

I made a PoC to add seed_simulator option torun method and constructor.

@t-imamichi We had said in the options RFC that we didn't want to pass options to run() (except those that are required, i.e. shots and precision) anymore. The primitive should instead have an options attribute, preferably a dataclass, e.g.
estimator = BackendEstimatorV2(...)
estimator.options.seed_simulator = 42

This would also be more consistent with what qiskit-ibm-runtime has.

@t-imamichi thanks for the update! I'd prefer having default_precision in options as well, since unlike precision, default_precision is not defined in the base interface. I think it's nicer to have all options not defined in the base to live together in options.

Some non-blocking comments. It they can be addressed in this PR, great. Otherwise, in a follow up. The comment in https://github.com/Qiskit/qiskit/pull/11931#issuecomment-1997497967 seems to be the only blocking issue on this PR.

I moved default_precision to Options and update reno to include an example.
I have a question. I used dataclass to define Options instead of using qiskit.providers.Options to allow autocompletion and expect a validation of a wrong option name. If qiskit.providers.Options is preferable, I would update the options.

On my side, LGTM and this can be merged.

I have a question. I used dataclass to define Options instead of using qiskit.providers.Options to allow autocompletion and expect a validation of a wrong option name. If qiskit.providers.Options is preferable, I would update the options.

I don't think it matters. @jyu00 ?

I have a question. I used dataclass to define Options instead of using qiskit.providers.Options to allow autocompletion and expect a validation of a wrong option name. If qiskit.providers.Options is preferable, I would update the options.

Dataclass is actually more preferable than qiskit.providers.Options, so this looks good to me!


Update manage to stop on agent failure

When running a set of tests, and the start routine fails to communicate to one of the designated agents, the execution of the tests would continue. Of course this would cause some or all of the tests to fail. This PR changes that logic and when the test harness does not get a successful startup of an agent, will let the user know there was an issue, skip the running of the tests, and stop any running test harness services. This should end the interop results getting complete failures in the reports when it was just an agent startup issue.

There is an issue with the credo agent I've been working on for a few days now. So this PR stopped the running of tests last night. However the job to push results to Allure ran and it shows empty in the report. Do you think this is ok, or should we skip the results push if tests don't run. It is an indicator that something went wrong and no tests were executed I suppose. I'm leaning to avoiding a results push if tests are skipped. Agreed?


RPI support for selenium

Hi Team,
I tried a new solution for arm/v7 since the selenium for RPI is still unstable, I downloaded the jar file and run in the background, but idk on how it works or I'm in a correct way on how to use it.
The Selenium Grid 4 does not have /wd/hub but tried with and without and still not working, can someone help me out?

closing - duplicate https://github.com/dgtlmoon/changedetection.io/discussions/455

Another solution should be using an API like imgbb.com


Add Pingdom to Hub

Migrated from GitLab: https://gitlab.com/meltano/hub/-/issues/231
Originally created by @pnadolny13 on 2022-04-07 20:25:21

Now that we're moving to rely more on the hub API as part of https://gitlab.com/meltano/meltano/-/issues/3283, we should add Pingdom to notify us when the Hub is down.
This might be covered by another gitlab pages notification that we already have set up but wanted to log it just in case its not covered.
cc @aaronsteers @pandemicsyn

View 2 previous comments from the original issue on GitLab


Printing Tables Issues in Beta 2

There is a serious bug when attempting to print in Beta 2. Yes, I know you're on Beta 3, but I've already reported the serious CSS breakage issues with that release, so such it is unusable.
I am trying to create a printer-friendly means of for our students to print a hard-copy of their personal information on file with our university.
The  section of the page's HTML is as follows:
`

PERSONAL INFORMATION

CAMPUS INFORMATION

				<button id="PRINT" type="button" class="btn btn-default float-end" tabindex="32765"><?php insertSvgSprite( PRINT_ICON,  BUTTON_CLASS ); ?>Print</button>
				<button id="CLOSE" type="button" class="btn btn-link    float-end" tabindex="32766"><?php insertSvgSprite( CANCEL_ICON, BUTTON_CLASS ); ?>Close</button>

The screen-only CSS is as follows:
body {
background-image:  none;
}
#HEADER {
display: 			block;
margin-bottom: 	18pt;
}
#HEADER img {
display: 			block;
width: 			100%;
margin: 			12pt auto 	!important;
}
#HEADER h2 {
display: 			block;
text-align: 		center 		!important;
color: 			#000000 	!important;
font-weight: 		700;
font-size: 		24pt;
margin-bottom: 	12pt;
}
#PERSON {
margin-bottom: 	36pt 			  !important;
}
table {
border: 			3pt solid #000000 !important;
}
tr {
border-bottom: 	2pt solid #000000 !important;
}
th {
padding-right: 	 9pt				  !important;
border-right: 		 2pt solid #000000 !important;
background-color:  #DDDDDD		  !important;
}
td {
padding-left: 		9pt !important;
}
caption {
caption-side: 	top;
padding-bottom: 	14pt;
padding-bottom: 	9pt;
font-size:		18pt;
font-weight: 		700;
text-align: 		center;
color: 			#000000;
}
tr {
border-top: 		1.5pt solid #000000;
border-bottom: 	1.5pt solid #000000;
}
.btn {
margin: 			0			!important;
}
#BUTTONS {
padding-top: 		12pt		!important;
}
footer {
border: 			none;
height: 			48pt;
}
`
The print-only CSS is identical except for the following 3 rules:
`body {
width:				8.5in;
height:				11in;
margin:				.5in 1in 1in 1in;
background-image: 	none;
}	/* end body rule */
#PERSON {
margin-bottom: 		36pt 	!important;
page-break-after: 		always 	!important;
}
#BUTTONS, footer {
display: 				none;
}
`
It's rendered output in the browser window is as shown in this screenshot:

However, whenever I try to print this page to a printer and/or save it as a PDF, I get the following (the attached is a JPG of the PDF output:

Thanks!

After successfully getting Beta 3 running, the symptoms are identical

v5 dropped support for print styles since the very first alpha. If you want specific styles for print, you'll have to implement them by yourself.


Simple WebAPI clients get booted out of Consul due to lack of health check

This is more to ask for guidance than a bug report. I made a very simple WebAPI service and registered it using Nanophone, which succeeded, but Consul booted it out of the cluster, I think because it did not implement any sort of health check.
It's probably a good idea to have a health check of course, but I was wondering if you had any thoughts on this? Microphone seems to register a default health check. This is all new to me so I don't know what best practice is yet, but the "getting started" story needs to be as simple as possible.
Here is the consul log FWIW
2016/07/20 11:19:31 [INFO] agent: Synced service 'consul'

==> Failed to check for updates: Get https://checkpoint-api.hashicorp.com/v1/check/consul?arch=amd64&os=windows&signature=&version=0.6.4: dial tcp <IP_ADDRESS>:443: connectex: No connection could be made because the target machine actively refused it.
2016/07/20 11:21:02 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:25 [WARN] Service tag "version-1.0" will not be discoverable via DNS due to invalid characters. Valid characters include all alpha-numerics and dashes.
2016/07/20 11:22:25 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:25 [INFO] agent: Synced service 'case-id_localhost_9000'
2016/07/20 11:22:25 [DEBUG] agent: Check 'service:case-id_localhost_9000' in sync
2016/07/20 11:22:25 [DEBUG] http: Request PUT /v1/agent/service/register (2ms) from=<IP_ADDRESS>:56229
2016/07/20 11:22:25 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:25 [DEBUG] agent: Service 'case-id_localhost_9000' in sync
2016/07/20 11:22:25 [DEBUG] agent: Check 'service:case-id_localhost_9000' in sync
2016/07/20 11:22:25 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:25 [DEBUG] agent: Service 'case-id_localhost_9000' in sync
2016/07/20 11:22:25 [DEBUG] agent: Check 'service:case-id_localhost_9000' in sync
2016/07/20 11:22:25 [DEBUG] agent: pausing 273.409331ms before first HTTP request of http://localhost:9000//status
2016/07/20 11:22:27 [WARN] agent: http request failed 'http://localhost:9000//status': Get http://localhost:9000//status: net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers)
2016/07/20 11:22:28 [WARN] agent: check 'service:case-id_localhost_9000' is now critical
2016/07/20 11:22:29 [WARN] agent: check 'service:case-id_localhost_9000' is now critical
2016/07/20 11:22:30 [WARN] agent: check 'service:case-id_localhost_9000' is now critical
2016/07/20 11:22:31 [WARN] agent: check 'service:case-id_localhost_9000' is now critical
2016/07/20 11:22:32 [WARN] agent: check 'service:case-id_localhost_9000' is now critical
2016/07/20 11:22:33 [WARN] agent: check 'service:case-id_localhost_9000' is now critical
2016/07/20 11:22:34 [WARN] agent: check 'service:case-id_localhost_9000' is now critical
2016/07/20 11:22:35 [DEBUG] http: Request GET /v1/health/state/critical (0) from=<IP_ADDRESS>:56229
2016/07/20 11:22:35 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:35 [INFO] agent: Deregistered service 'case-id_localhost_9000'
2016/07/20 11:22:35 [INFO] agent: Deregistered check 'service:case-id_localhost_9000'
2016/07/20 11:22:35 [DEBUG] http: Request PUT /v1/agent/service/deregister/case-id_localhost_9000 (999.2µs) from=<IP_ADDRESS>:56229
2016/07/20 11:22:35 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:35 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:37 [DEBUG] agent: Service 'consul' in sync
2016/07/20 11:22:40 [DEBUG] http: Request GET /v1/health/state/critical (0) from=<IP_ADDRESS>:56229

@PhilipDaniels A health check is definitely registered - maybe Consul is kicking it out before it came up? Try ignoring critical services in your ConsulRegistryHostConfiguration and see what happens. Did you start with your own project, or with the sample projects in the Nanophone repo? If the former, I suggest you clone the repo and take a look at the samples.


[W4.4b][W14-A1]Mukesh Gadupudi

Added new classes for Block, PostalCode, Street and Unit. Updated the expected output too.

@shanmu9898
Some comments added. Please ack & close the PR after reading comments.

Yeap! Noted. Thank you sir

On 11-Feb-2018, at 6:32 PM, Akshay Narayan<EMAIL_ADDRESS>wrote:
@shanmu9898 https://github.com/shanmu9898
Some comments added. Please ack & close the PR after reading comments.
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I026 i044 i048 pro ventilation equipment

can you merge from master and resolve the conflicts?
also, can you please not close issues (like #44) until the pull-request has been merged? The issue should still be open until it is in master.


registration not working

I've created a new upload template that appears to be working, but when I click 'upload' nothing happens.
I'm on Win 10, working thru Chrom browser.  The test data created registrations as expeceted. I'm attaching the mapping.js and the demo/test data I'm using.   Are there logs somewhere that can be used to debug these kind of problems?
the mapping file is in the zip archive so GitHbe will take it.
thanks
steve
LacCore_Holes_test2.csv.txt
LaCoreHoleTemplate.zip

I got the same problem when I tried to upload the samples. For debugging in the Chrome browser, I used the "inspect" on the page and opened the "console" tab. When I tried to upload, I got a the following error:
POST https://sesardev.geosamples.org/webservices/upload.php 400 (Bad Request)
I retrieved the XML that MARS generates, and I attached it. LaCoreHole.xml.txt
I tried to upload the samples through SESAR's web services by pasting the XML at https://sesardev.geosamples.org/webservices/upload.php. The "sample_type" field occurs twice because MARS hard codes the sample_type to be "Individual Sample," which is a problem within MARS if the sample type is Core like with this data. So this definitely something that needs to be fixed within MARS.
To try to get the samples to upload, I removed the "sample_type" map from the file LaCoreHoleTemplate.js. When I retrieved the XML and uploaded through SESAR's web services again, I got some errors with what SESAR accepts as values. I also attached the errors that SESAR returned.
SESARError.xml.txt
Right now, MARS doesn't give the user any meaningful errors or warnings, which is something that should be addressed. In addition, it should notify the user of what values SESAR permits and allow the user to edit the data within the application. I'm interested in getting these samples to work, and so I will keep working on it and see what I find.
Thanks!
Tia

Thanks for looking into the problem. I didn't realize those validation rules were there. It would be great if the app could check before uploading and let the user know up front.  I'll look into where the rules are enumerated.

I was able to get the samples to register after modifying the mapping file a bit, and I have attached it below.
LaCoreHoleTemplate.js.txt
It was just a quick fix to get it working as soon as possible, and I would like to refine MARS a lot more to accommodate sample metadata more readily.
I didn't map a few fields because they were throwing errors.
For the "Original ID" field, I will need to modify MARS's toXML() function to accommodate nested XML tags.
For the "DepthTop" and "DepthBottom" fields to be included, there needs to be a Depth Scale, such as Meters Below Seafloor or Meters Composite Depth. I wasn't sure if either of those values were acceptable for this set of metadata, so I left out the mapping for those fields.
This was an excellent way to help me understand how MARS needs to be more modular and accepting of different styles of data, and I'm still working on allowing the "Original ID" and "Sample Type" fields to be mapped.
Thanks!

Thanks Tia, your updates will help me understand how it works better. I hope to loop back to this soon...
:)

Hmm, I"m back,tried running MARs again (windows 10, Chrome,localhost:8080, start with $npm run start-dev-watch
load mapping file from Tia, and sample data from Anders, app goes quied, never comes back from click on 'proceed' button.  Eventually Chrome stops with an 'Aw Snap' error message.  Am I missing something?  what should happen if the run is successful?
thanks


Dashboards as consumers of notebook artifacts

Description:
Easy export and/or store the contents of a notebook into an Observable artifacts repository.
Why:
Notebooks are valuable because they are quick ways to explore data. The user can quickly iterate and filter data through a DTC, create a helper function to create an SVG, and share contents of notebooks with a team member who also has Observable.
Notebooks are good for content creation but not necessarily content presentation. Notebooks can provide the building blocks for dashboards and already have permissions baked into a particular view. Artifacts derived from a notebook should have the same permissions as the notebook themselves unless granted otherwise.
Details:
Have a button or some UI in for a single cell that publishes to the Observable artifacts repository. Expose extra scopes as part of the observable login command and a new set of APIs to fetch/download the artifacts. Users of the CLI can call these Observable endpoints within a data loader given that they've authenticated via observable login.
Why Part 2:
Notebooks are constantly changing but artifacts are version-controlled. The act of promoting parts of a notebook to an artifact means the user/team is "locking in" the changes and having it be ready for production. We can also think about the possibilities of having a scheduled run with new artifacts posted on a dedicated time interval.
Inspiration:

JFrog Artifactory
JFrog REST APIs

closing as not planned; but it's a good idea to simplifying making artifacts from a project (e.g. with playwright).


Unexpected behavior with ucp

Using uuu version 1.5.21, but the issue exists on 1.4.139 as well. Haven't tried any other versions.
Copying a file and then copying again with a truncated version of the same file results in extra characters added to the resulting file on the device.
Steps to reproduce
On the PC running uuu, with the device in FBK mode, run
$ echo abcd > /tmp/test.txt
$ uuu FBK: ucp /tmp/test.txt T:/tmp/test.txt
$ echo ab > /tmp/test.txt
$ uuu FBK: ucp /tmp/test.txt T:/tmp/test.txt

Expected contents of /tmp/test.txt on the device:
ab

Actual contents of /tmp/test.txt on the device:
ab
d

Is this a known issue?

Possible it is bugs.
Can you try
diff --git a/libuuu/buffer.cpp b/libuuu/buffer.cpp
index 7e32a06..0500d6e 100644
--- a/libuuu/buffer.cpp
+++ b/libuuu/buffer.cpp
@@ -239,7 +239,7 @@ public:
                if (p->mapfile(backfile.substr(1), st.st_size))
                        return -1;

-               p->m_available_size = st.st_size;
+               p->m_DataSize = p->m_available_size = st.st_size;

                atomic_fetch_or(&p->m_dataflags, FILEBUFFER_FLAG_LOADED | FILEBUFFER_FLAG_NEVER_FREE);
                p->m_request_cv.notify_all();

@nxpfrankli Thank you for the quick response! I added that change on top of the most recent master commit and built, still seeing the issue.


[WFLY-16387] Convert the test resources to use Jakarta REST 3.1. Also…

… disable the deployment transformer.
The test renames are required to ensure the tests run.
https://issues.redhat.com/browse/WFLY-16387

The security manager failures are legitimate. I've got most of a fix, but struggling with one of the permissions still being denied.

If anyone is reviewing this, there's a discussion at https://wildfly.zulipchat.com/#narrow/stream/174184-wildfly-developers/topic/ControllerPermission