Added epistemic_reasoning_json_task for review

A task that tests inferences involving reasoning about the epistemic states (like knowledge and belief) of multiple agents.

@googlebot I signed it!

@michaelcohen-dev Thank you for submitting your task! We are in the process of pairing submissions with task reviewers and will be in touch soon.

I'm one of the reviewers for this task.
Correctness and Formatting: The task is presented in JSON form and seems to be formatted correctly.
Specificity: The task aims are probing the theory of the mind ability of models to reason about someone else's epistemic state. The metric chosen is appropriate for the task and is likely the capture the intended performance when averaged over the 2000 included test instances.
Thoroughness: While tasks are encouraged to target a single capability or flaw of large language models, they should attempt to quantify their target in a robust way. Tasks should attempt to control for, or average over, potential confounders and nuisance variables. The author uses the SNLI dataset to build their task using templates. While not necessary, I would recommend using MNLI (or a subset) given that it is multi-genre and that it obviates some of the biases present in the SNLI dataset. Further, given the templatic nature of the task, a few examples feel a bit odd/unnatural (e.g., "Isabella believes that Charlotte assumes that a group of kids play on a colorful structure."). but is unlikely to be fixed with simple filtering?
Difficulty: The task is constructed using templates on SNLI data. The author lists performance of a RoBERTa model trained on MNLI on this dataset (which seems like an appropriate choice given the task). Some of the templates have 100% (or near 100%) accuracy while others have poor performance. The fact that the performance is low on a strong baseline and that there is a gradation in the task are good attributes.
Not solvable by memorizing the Internet: Unlikely to be an issue given that the task is logical in nature.
Novelty: The task is based on the author's earlier course project. The author lists some relevant past work both from the cognitive sciences community and the NLP community. From my standpoint, the task is quite related to some of the logical reasoning/NLI-based tasks in BIG-Bench but is sufficiently different to warrant inclusion.
Justification: The README.md file contains the relevant information including what the task is attempting to measure, and the background and motivation, and why this is an important capability of large language models to quantify.
Size: The task JSON file is created using templates on the SNLI dataset. There are 2000 examples with 10 templates which seem sufficient to probe the LLMs for the intended task.
Compute resources: The JSON file is of modest size. This won't be an issue.

@michaelcohen-dev We are now requesting that task authors please include an explicit section in the README.md file called "data source", listing exactly where you got your data from (or explicitly state that you made it up yourself). Many thanks!

@mathopus are one of the assigned reviewers for this task.  Please provide feedback and be sure to notify me with a formal accept or does not meet criteria by Tuesday June 22 (if you have not already done so).

@keskarnitish are one of the assigned reviewers for this task.  Please provide feedback and be sure to notify me with a formal accept or does not meet criteria by Tuesday June 22 (if you have not already done so).

@chiafullo, is the June 22 deadline for the reviewers to review to submission, or is it the deadline for the submitters to revise their task according to the reviews? In other words, can submitters revise their task (in order to respond to the reviewers) after June 22 ?

@chiafullo I already provided the feedback earlier this week.
I advocate for accepting this task.

This task looks interesting, although at a certain level it is a fairly straight forward entailment test. The fact that are only ten templates is also a bit of a downside, as it limits the generalization of the test. Overall though I agree with the other reviewer that there is probably still room for improvement on this test even for the larger models and the questions are phrased in a novel way.
@chiafullo I accept.

@michaelcohen-dev We will be extending the review period so you will have time to revise if need be. We will also assign a meta-reviewer to your task to view before merging. Comms will be sent out shortly outlining the review extension.
Thanks for your submission :)

The amount of tasks we received this round is tremendous.  With so many tasks to review we have decided to extend the review period to Tuesday, June 29.
Reviewers: if the submitter has made revisions please be sure to notify me with a formal ”accept” or ”does not meet criteria” by Tuesday, June 29  (if you haven't already done so).
this is an automated message

@keskarnitish, Thank you for your review and for the accept decision. Regarding your suggestion:

While not necessary, I would recommend using MNLI (or a subset) given that it is multi-genre and that it obviates some of the biases present in the SNLI dataset. Further, given the templatic nature of the task, a few examples feel a bit odd/unnatural (e.g., "Isabella believes that Charlotte assumes that a group of kids play on a colorful structure."). but is unlikely to be fixed with simple filtering?>

I have thought about using (a subset of) MNLI instead of SNLI in the task. Technically, making the change is very easy;  the change would also avoid the known biases of SNLI. However, I decided to keep using SNLI, for the following two reasons:

First, the license agreement of SNLI is in  general more permissive than that of MNLI. SNLI is distributed under creative common 4.0. The FICTION genre of MNLI is more restrictive (needs "the explicit permission of the author") , and since I am not a legal expert on these matters, I would avoid using that MNLI genre.

The second reason is related to the issue you raised about examples being odd/unnatural. I agree that some of my examples have this property. I also don't have a simple filter to fix it entirely (filtering out examples that are not S-rooted, which I implemented, does help avoiding odd constructions). From my own experience going over generated examples, I believe that using SNLI rather than MNLI results (on average) in more natural sentences. Many sentences from the TELEPHONE and FACE-TO-FACE genres of  MNLI are not suitable for embedding in mental predicates like "thinks that" or "knows that", due to their conversational nature. For example, it is unnatural to have sentences with discourse markers (which are common in the conversational genres) embedded in a mental predicate. Consider appending "Isabella believes that" to the MNLI TELEPHONE example "i think it's real good anyway it's it's been it was nice meeting you". My (anecdotal) experience also shows that the TRAVEL genre tends to contain advice and suggestions in the form of imperative sentences (e.g. "Visit at sundown or out of season to get the full flavor of the setting."). My task requires declarative sentences.
SNLI examples, on the other hand, although less diverse, seem to interact more naturally with my epistemic reasoning templates. SNLI examples were exclusively generated from image captions, and so they tend to result in declarative sentences that describe concrete visual scenes. Such descriptions tend to embed naturally under mental states predicates like to know and to believe (it is natural to consider mental states whose content involve concrete visual scenes).

For these reasons, I have chosen to use SNLI over MNLI. If you think that these reasons should be reflected in the README file, let me know! Thanks again for your comments.

Thanks for the clarification @michaelcohen-dev. Having glanced at the MNLI examples myself, I agree with your assessment that that might make the sentences more unnatural.

Your task has been accepted in the initial review stage.  The next stage of this process is for us to assign your task a meta-reviewer for final review and merge.  An assigned meta-reviewer will follow-up by commenting on the PR should it need further revisions.

Thank you for the submission, and for the reviews! LGTM and merging!


"update file information failed" when trying to list a file shared with user in question.

I was using the following line of code to access a certain spreadsheet, shared with the user used in the request below. After updating to DSM 7, and updating this python module to latest version, it suddenly stopped working:
with SynologyDrive(os.environ.get('SYNO_USER'), os.environ.get('SYNO_PASS'), os.environ.get('SYNO_HOST'), dsm_version='7') as synd:
    sheet_file = synd.download_file("543138139674295052")

Returns the following error:
Traceback (most recent call last):
  File "./test.py", line 18, in <module>
    sheet_file = synd.download_file("543138139674295052")
  File "/Users/jonas/Library/Python/3.8/lib/python/site-packages/synology_drive_api/files.py", line 151, in download_file
    ret = self.get_file_or_folder_info(file_path)
  File "/Users/jonas/Library/Python/3.8/lib/python/site-packages/synology_drive_api/files.py", line 126, in get_file_or_folder_info
    return self.session.http_post(endpoint, data=urlencoded_data)
  File "/Users/jonas/Library/Python/3.8/lib/python/site-packages/synology_drive_api/base.py", line 220, in http_post
    return self._request('post', endpoint, **kwargs)
  File "/Users/jonas/Library/Python/3.8/lib/python/site-packages/synology_drive_api/base.py", line 210, in _request
    raise_synology_exception(res, bio_exist=bio_flag)
  File "/Users/jonas/Library/Python/3.8/lib/python/site-packages/synology_drive_api/base.py", line 132, in raise_synology_exception
    raise SynologyException(
synology_drive_api.base.SynologyException: {"error":{"code":1003,"errors":{"line":172,"message":"update file information failed"}},"success":false}

Any ideas why this is suddenly happening?

Manged to fix it like this:
https://github.com/zbjdonald/synology-drive-api/compare/master...frdmn:fix/get_shared_file?expand=1
Didn't open a PR since I'm not sure if that's the best way to go here nor if it's needed at other places as well. At least now I can access the spread sheet this way again...

Thanks for using this api. I just came to a new company without dsm 7. Would you be open to a PR if other requests are compatible?

haha, there are no test cases, you can test some api manually.

@frdmn Hi, in 1.0.11, I changed get_file_or_folder_info(). Could you test it in your case?


Initialize gpc test code closer to the real thing

Reviewer:

Description:

Steps to test this PR:

Automated tests:

[ ] Unit tests
[ ] Integration tests

Reviewer Checklist:

[ ] Ensure the PR solves the problem
[ ] Review every line of code
[ ] Ensure the PR does no harm by testing the changes thoroughly
[ ] Get help if you're uncomfortable with any of the above!
[ ] Determine if there are any quick wins that improve the implementation

PR Author Checklist:

[ ] Get advice or leverage existing code
[ ] Agree on technical approach with reviewer (if the changes are nuanced)
[ ] Ensure that there is a testing strategy (and documented non-automated tests)
[ ] Ensure there is a documented monitoring strategy (if necessary)
[ ] Consider systems implications

Moved into: https://github.com/duckduckgo/duckduckgo-privacy-extension/pull/2341


Unclear how a pod failed alert would be generated

One of the recommended prometheus alerts is
                   {
                        "alert": "Number of pods in failed state are greater than 0.",
                        "expression": "sum by (cluster, namespace, controller) (kube_pod_status_phase{phase=\"failed\"} * on(namespace, pod, cluster) group_left(controller) label_replace(kube_pod_owner, \"controller\", \"$1\", \"owner_name\", \"(.*)\"))  > 0",
                        "for": "PT5M",
                        "annotations": {
                            "description": "Number of pods in failed state are greater than 0"
                        },
                        "enabled": true,
                        "severity": 4,
                        "resolveConfiguration": {
                            "autoResolved": true,
                            "timeToResolve": "PT15M"
                        },
                        "actions": [
                            {
                                "actionGroupId": "[parameters('actionGroupResourceId')]"
                            }
                        ]
                    }

However, since k8s doesn't support a restart policy of never (it is always by default)(https://kubernetes.io/docs/concepts/workloads/controllers/deployment/#pod-template), it isn't clear how a pod enters a failed state. I had no success generating this alert.

Document Details
⚠ Do not edit this section. It is required for learn.microsoft.com ➟ GitHub issue linking.

ID: f09aeae6-06a7-d9e6-36ed-f26b91ef4df8
Version Independent ID: 786ddb6f-70a2-2c9c-37b9-21cfeaf3a22e
Content: Create metric alert rules in Container insights (preview) - Azure Monitor
Content Source: articles/azure-monitor/containers/container-insights-metric-alerts.md
Service: azure-monitor
Sub-service: containers
GitHub Login: @bwren
Microsoft Alias: bwren

@chitturs Thanks for your comment! We will review and provide an update as appropriate.


Clarify db user

A user pointed out the original text was a bit unclear. Updating to user PostgreSQL specific terms.

Copying in the user's message here:
"""
On this point - in the setup documentation, there is this line:
"This assumes your current OS user ($USER) is a db superuser of the same name, and that you are able to log in without a password."
What does "log in without a password" mean? That this user can log in to the machine without a password? As in passwordless ssh? Or that the user can log into the DB without a password? Which doesn't make a lot of sense, because we haven't created the DB yet.
"""

Thanks @bcipriano and @sharifsalah. I've pushed the update and it is staged here:
Creating the Database
PTAL.


VPN - prevention

Perhaps adding a secondary client-sided ban, could help people from switching to a different VPN - Exitnode from entering the chat.

also see #83

Looks good. I'll try to remember to merge this before the weekend.

AndrewBelt on Jun 9

kek


The start_interface_nonce is not handled correctly.

https://github.com/DMTF/spdm-emu/blob/f7a644cb3aed29f9ccbb3091d787bd555fb014ca/library/pci_tdisp_device_lib_sample/pci_tdisp_device_lock_interface.c#L45
https://github.com/DMTF/spdm-emu/blob/f7a644cb3aed29f9ccbb3091d787bd555fb014ca/library/pci_tdisp_device_lib_sample/pci_tdisp_device_lock_interface.c#L62
https://github.com/DMTF/spdm-emu/blob/f7a644cb3aed29f9ccbb3091d787bd555fb014ca/library/pci_tdisp_device_lib_sample/pci_tdisp_device_lock_interface.c#L67-L71
sizeof(*start_interface_nonce) equals to sizeof(uint8_t) which is 1, so currently, only the first byte is randomized, the left bytes are kept as is.

same issue found at https://github.com/DMTF/spdm-emu/blob/f7a644cb3aed29f9ccbb3091d787bd555fb014ca/spdm-device-sample/spdm_device_sample/library/pci_tdisp_device_lib/pci_tdisp_device_lock_interface.c#L62


testing

Overview

PR Checklist

[ ] Related to designs:
[ ] Related to JIRA ticket: [ABC-123]
[ ] I have run this code to verify it works
[ ] This PR includes unit tests for the code change
[ ] This PR includes testing instructions tests for the code change
[ ] The alpha package of this PR is passing end-to-end tests in all relevant Codecademy repositories

Testing Instructions

Don't make me tap the sign.
PR Links and Envs

Repository
PR Link
PR Env

Monolith
Monolith PR
Monolith Env

Portal
Portal Link
Portal Env

Another Repo
Another Link
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📬Published Alpha Packages:@codecademy/gamut-kit@0.6.218-alpha.7415b0.0@codecademy/gamut-labs@33.6.9-alpha.7415b0.0@codecademy/gamut@51.0.1-alpha.7415b0.0@codecademy/monaco@0.6.96-alpha.7415b0.0<EMAIL_ADDRESS>
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Fix the embargoed landing page

Test example on dev.
It was barfing out errors because someone used the wrong field name in the template.  See https://github.com/CDL-Dryad/dryad-product-roadmap/issues/409

Hi Ryan, I'm going to merge this in since it doesn't affect the main code directly (just migration) since I'm going to tag and deploy for end of sprint.  I'd welcome feedback, though.

Yes, this looks good. Thanks for fixing it!


Global namespaces from script files and module files via declare global considered different

Search Terms
declaration merging declare global script module
Problem
(Yeah, I know, globals again. I would also like to use modules, but that's hard to impossible for large existing projects. primefaces/primefaces#12717)
When you have a global script file (without import / export) and a module file that both amend a namspace in the global scope, typedoc seems to consider these as different.
When using the plugin typedoc-plugin-merge-modules, that results in the namespaces not getting merged. But I think the issue is not with the plugin, as it seems to happen even without the plugin. For example:
// base.ts
namespace PrimeFaces {
  export interface WindowExtensions{}
}
interface Window extends PrimeFaces.WindowExtensions {}

// src/a.ts
import "./module.js"; // make this a module file
declare global {
  namespace PrimeFaces {
    export interface WindowExtensions{
      a: string;
    }
  }
}

// src/b.ts
// similar a.ts

// src/c.ts
namespace PrimeFaces {
  export interface WindowExtensions{
    c: string;
  }
}

// src/d.ts
// similar to c.ts

// index.ts
console.log(window.a, window.b, window.c, window.d);

Now when generate docs from that, d/PrimeFaces is marked as a re-export of c/PrimeFaces. But a/PrimeFaces and b/PrimeFaces are not and contain only a and b, respectively. Interestingly enough though, c/PrimeFaces contains all of a, b, c and d.

With typedoc-plugin-merge-modules, that then results in duplicates:

Repro
git clone https://github.com/blutorange/primefaces-js-refactor-test.git
cd primefaces-js-refactor-test/
git checkout demo-typedoc-merge-script-module
yarn install
yarn tsc # note that this compiles, so all interfaces point to the same thing
yarn typedoc  --out docs src/index.ts src/a.ts src/b.ts src/c.ts src/d.ts src/module.ts
open docs/index.html

Just to let you know, I Just checked out your commit, seems to be working nicely in our case. :+1:
Before there were multiple namespaces

Now they're replaced with nice references:


Flaky test: ExtHostDocumentSaveParticipant event delivery, overall timeout:

Seen in https://travis-ci.org/Microsoft/vscode/jobs/172315446#L6894

https://github.com/Microsoft/vscode/issues/13148


⚠ ClamAV has degraded performance

In 4d9540c, ClamAV (https://spamassassin.apache.org/) experienced degraded performance:

HTTP code: 200
Response time: 516 ms

Resolved: ClamAV performance has improved in 34efecf.


fix outputs of WER/CER

WER and CER still return floats instead of dictionaries. This PR fixes it so it's consistent with the other metrics and allows usage e.g. in combine or Evaluator (see #378).
However, this will break one example in transformers and the Whisper blog would need an update. Do you think we could update this if I simultaneously with the evaluate release open a PR on transformers and add a note to the blog? cc @LysandreJik @sgugger

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint.


Step label indicator error: Cannot read property 'querySelector' of null

model.labelIndicator = model.label.querySelector('.' + this.CssClasses_.STEP_LABEL_INDICATOR);
inside stepper.js
This is the error:
stepper.js:281 : Uncaught TypeError: Cannot read property 'querySelector' of null

Following docs:

All step has a label. Label includes a title with text and optionally the supporting message (e.g. Optional).

      Name of step 1
      Summarize if needed

You coded the label element into step? If yes then post a codepen or jsfiddle with your full markup here.

OK Thanks - I confirmed the DOM element was on the page yet the error still appeared. However, I took the code from your samples and inserted them into my page and everything works.


Set up an SSL cert for httparchive.org

I hear that HTTPS thing is getting popular.

I've set up lets-encrypt on WPT and it should be easy enough to do on HA with the nginx support.  Only complication is the nginx server reverse-proxies the HA requests to an apache server so not sure if the webroot will "just work" or if it will need a few tweaks.

I just gave certbot a whirl and it failed to download a bunch of dependencies, which I think is a symptom of our version of Ubuntu being old.
The beta site is hosted on App Engine and the current site will become old.httparchive.org or something, so maybe it makes more sense to wait for the musical subdomains to settle down before setting up certs.

Yeah, I'd focus on HTTPS for the new (GAE-powered) site, with a view that we want to sunset current site asap -- lack of HTTPS being one of many reasons.

TODO:

[ ] migrate the beta site from its own GAE project to the primary httparchive project
[ ] set up a wildcard cert for GAE-hosted sites, to support the beta site in both dev (beta.httparchive.org) and prod (httparchive.org) stages

The legacy server is https now (httparchive.org, www, dev, desktop, mobile, chrome)

Pat, I set up a new A record for legacy.httparchive.org. Is the https cert a wildcard?

No.  Should be able to be added with certbot (I'll do it on Monday)

Cert has been expanded


hmr死循环渲染

Describe the bug
父组件注入响应式数据到子组件，子组件修改响应式数据，父组件展示此响应式数据，子组件修改时触发渲染，由于slot中存在子组件，造成子组件又渲染，子组件又修改了响应式数据，使得死循环。不知道算不算问题，不算的话直接关掉了
Reproduction
https://stackblitz.com/edit/vitejs-vite-tu3tor?file=src%2FComp.vue,src%2FComp1.vue&terminal=dev
Steps to reproduce
开发模式下修改Comp1.vue的all.value.push("1")的push值即可，可以看到多了很多一样的数据
修改可以把Comp.vue的{{all}}注释掉
System Info
System:
    OS: Linux 5.0 undefined
    CPU: (8) x64 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
    Memory: 0 Bytes / 0 Bytes
    Shell: 1.0 - /bin/jsh
  Binaries:
    Node: 16.14.2 - /usr/local/bin/node
    Yarn: 1.22.19 - /usr/local/bin/yarn
    npm: 7.17.0 - /usr/local/bin/npm
  npmPackages:
    @vitejs/plugin-vue: ^4.1.0 => 4.1.0
    vite: ^4.2.1 => 4.2.1

Used Package Manager
npm
Logs
No response
Validations

[X] Follow our Code of Conduct
[X] Read the Contributing Guidelines.
[X] Read the docs.
[X] Check that there isn't already an issue that reports the same bug to avoid creating a duplicate.
[X] Make sure this is a Vite issue and not a framework-specific issue. For example, if it's a Vue SFC related bug, it should likely be reported to vuejs/core instead.
[X] Check that this is a concrete bug. For Q&A open a GitHub Discussion or join our Discord Chat Server.
[X] The provided reproduction is a minimal reproducible example of the bug.

使用如下版本，将不再触发死循环，只会多一条数据。
  "dependencies": {
    "vue": "3.5.10"
  },
  "devDependencies": {
    "@vitejs/plugin-vue": "5.1.4",
    "vite": "5.4.8",
  }


Example build failed due to missing package

Well, _example/iris.go has some problem now. I can no long build or test it.
➜  _examples git:(master) go test ./...
iris.go:9:2: cannot find package "github.com/iris-contrib/middleware/basicauth" in any of:
	/usr/local/go/src/github.com/iris-contrib/middleware/basicauth (from $GOROOT)
	/root/GOPATH/src/github.com/iris-contrib/middleware/basicauth (from $GOPATH)

And go get github.com/iris-contrib/middleware/basicauth failed, because package github.com/iris-contrib/middleware/basicauth no longer exist in iris-contrib/middleware.
➜  _examples git:(master) go get github.com/iris-contrib/middleware/basicauth
package github.com/iris-contrib/middleware/basicauth: cannot find package "github.com/iris-contrib/middleware/basicauth" in any of:
	/usr/local/go/src/github.com/iris-contrib/middleware/basicauth (from $GOROOT)
	/root/GOPATH/src/github.com/iris-contrib/middleware/basicauth (from $GOPATH)

So, would you please check and take time to fix this?  @kataras
BTW, I run on Linux with go1.8
➜  _examples git:(master) go env
GOARCH="amd64"
GOBIN="/usr/local/go/bin"
GOEXE=""
GOHOSTARCH="amd64"
GOHOSTOS="linux"
GOOS="linux"
GOPATH="/root/GOPATH"
GORACE=""
GOROOT="/usr/local/go"
GOTOOLDIR="/usr/local/go/pkg/tool/linux_amd64"
GCCGO="gccgo"
CC="gcc"
GOGCCFLAGS="-fPIC -m64 -pthread -fmessage-length=0 -fdebug-prefix-map=/tmp/go-build282780244=/tmp/go-build -gno-record-gcc-switches"
CXX="g++"
CGO_ENABLED="1"
PKG_CONFIG="pkg-config"
CGO_CFLAGS="-g -O2"
CGO_CPPFLAGS=""
CGO_CXXFLAGS="-g -O2"
CGO_FFLAGS="-g -O2"
CGO_LDFLAGS="-g -O2"

Oh yes, I have forked it and fix it but didn't push the PR, wait for fix in the next minutes please

Done, https://github.com/gavv/httpexpect/pull/39

Thanks for reporting and sorry for delay. Fixed.


Create alphaday.md

Hi, Michael. Thank you for your interest in our project.
Unfortunately, the grant program has now been put on hold. We will let you know as soon as we get back to it.

Hello Ivan, thank you for informing me.
On Sat, May 27, 2023 at 12:50 PM Ivan Berman @.***>
wrote:

Hi, Michael. Thank you for your interest in our project.
Unfortunately, the grant program has now been put on hold. We will let you
know as soon as we get back to it.
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Reply to this email directly, view it on GitHub
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or unsubscribe
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Add support for searching for symbol characters like [ , ] , + , – , ^ , etc.

This would be useful for searching bookmark items whose name or URL have symbols on them.
The workflow here (https://github.com/manifestinteractive/alfred-workflows/tree/master/Chrome History) seems to have some support for this.

The reason this is broken is because we make a regex from the characters entered. I'll guess it's not being escaped correctly.
https://github.com/blainesch/alfred-chrome-bookmarks/blob/master/src/alfmarks.php#L97

Using something like preg_quote could potentially fix this issue. I'll play with something later.

Nice, that does enable some special characters to be searchable. Although, replacing the old bookmarks.php with the new alfmarks.php only worked when I added this to the bottom of alfmarks.php:
echo BookmarkModel::find($_SERVER['argv'][1])->sort()->to_xml();
Also, some of my bookmarks have the following characters, which the implementation in v1.1 does not yet support:

# (number sign)
& (ampersand)
* (asterisk) — seems to take a lot longer to search (and then fail) than other unsupported characters
_ (underscore)
| (vertical bar)
' (apostrophe)
< (less than sign)
> (greater than sign
/ (forward slash)
~ (tilde)

I got this by limiting the bookmarks search to 1 bookmark item containing all common symbols that are printed on the Apple keyboards (excluding the command symbol), and then typing the following characters, one at a time:
! @ # $ % ^ & * ( ) - – — _ = + [ { ] } \ | ; : ' " , < . > / ? ` ~

Items such as the number sign and greater then sign cannot be used at the beginning of the first argument as a restriction from alfred. They work if they are not the first character, as far as I have tested using this new code.

Number sign does seem to work when not at the beginning of the first argument, but greater sign doesn't.
What about the other characters?


customize: how to change colors

closes https://github.com/inveniosoftware/docs-invenio-rdm/issues/9
closes https://github.com/inveniosoftware/docs-invenio-rdm/issues/10

@zzacharo you need to rebase on master tho :)


[RPC] Added two RPC methods for listing transactions

Added implementation for
listtransactions
listsinceblock
RPC methods

Closing this one and moving it to https://github.com/stratisproject/StratisFullNode/pull/764 as it requires <IP_ADDRESS>


[HELP] Unable to start bigchaindb on UBUNTU

BigchainDB version: Latest
Operating System: ubuntu 16.4
Deployment Type: [Docker|Host|IPDB|Other] Cluster

If you are using IPDB, please specify your network type [test, prod]
and the bdb_url(BigchainDB URL) you are using.
For every other type of deployment, please specify the documentation/instructions
you are following.

BigchainDB driver: [yes|no] yes

If using a driver please specify, driver type [python|js|java]
and version. python

Description
I have started mongodb using a replSet command, but bigchaindb doesnt start because it seems to suggest mongodb wasn't started with replSet
Steps to Reproduce
alka@mixorg:~$ bigchaindb start
INFO:bigchaindb.config_utils:Configuration loaded from `/home/alka/.bigchaindb`
[2017-11-13 09:23:50] [INFO] (bigchaindb.commands.bigchaindb) BigchainDB Version 1.2.0.dev (MainProcess - pid: 5117)
[2017-11-13 09:23:50] [INFO] (bigchaindb.commands.bigchaindb) Starting BigchainDB main process with public key 64PfNxKSnnKsP3uEzfTsx1QxTBbaBMEkmC8uv2C2fuRD (MainProcess - pid: 5117)
[2017-11-13 09:23:50] [INFO] (bigchaindb.processes) Initializing BigchainDB... (MainProcess - pid: 5117)
[2017-11-13 09:23:50] [INFO] (bigchaindb.processes) Starting block (MainProcess - pid: 5117)
Process Process-10:
[2017-11-13 09:23:50] [INFO] (bigchaindb.processes) Starting voter (MainProcess - pid: 5117)
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 235, in _check_replica_set
    repl_opts = options['parsed']['replication']
KeyError: 'replication'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/bigchaindb", line 11, in <module>
    load_entry_point('BigchainDB==1.2.0.dev0', 'console_scripts', 'bigchaindb')()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/bigchaindb.py", line 355, in main
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 235, in _check_replica_set
    repl_opts = options['parsed']['replication']
KeyError: 'replication'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
    utils.start(create_parser(), sys.argv[1:], globals())
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/utils.py", line 206, in start
  File "/usr/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap
    self.run()
  File "/usr/lib/python3.5/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/lib/python3.5/dist-packages/multipipes/pipeline.py", line 67, in safe_run_forever
    self.run_forever()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/changefeed.py", line 35, in run_forever
    .next()['ts'])
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 62, in run
    return query.run(self.conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 122, in conn
    self.connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 153, in connect
    self._conn = self._connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 101, in _connect
    self.crlfile)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 198, in initialize_replica_set
    _check_replica_set(conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 238, in _check_replica_set
    raise ConfigurationError('mongod was not started with'
bigchaindb.common.exceptions.ConfigurationError: mongod was not started with the replSet option.
    return func(args)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/utils.py", line 51, in configure
    command(args)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/utils.py", line 78, in start_logging
    command(args)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/bigchaindb.py", line 209, in run_start
    processes.start()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/processes.py", line 57, in start
    vote.start()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/pipelines/vote.py", line 183, in start
    pipeline = create_pipeline()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/pipelines/vote.py", line 160, in create_pipeline
    voter = Vote()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/pipelines/vote.py", line 39, in __init__
    self.last_voted_id = Bigchain().get_last_voted_block().id
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/core.py", line 596, in get_last_voted_block
    self.me)
  File "/usr/lib/python3.5/functools.py", line 743, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/query.py", line 312, in get_last_voted_block_id
    sort=[('vote.timestamp', -1)]))
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 62, in run
    return query.run(self.conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 122, in conn
    self.connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 153, in connect
    self._conn = self._connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 101, in _connect
    self.crlfile)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 198, in initialize_replica_set
    _check_replica_set(conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 238, in _check_replica_set
    raise ConfigurationError('mongod was not started with'
bigchaindb.common.exceptions.ConfigurationError: mongod was not started with the replSet option.

Mongodb terminal
alka@mixorg:~$ bigchaindb start
INFO:bigchaindb.config_utils:Configuration loaded from `/home/alka/.bigchaindb`
[2017-11-13 09:23:50] [INFO] (bigchaindb.commands.bigchaindb) BigchainDB Version 1.2.0.dev (MainProcess - pid: 5117)
[2017-11-13 09:23:50] [INFO] (bigchaindb.commands.bigchaindb) Starting BigchainDB main process with public key 64PfNxKSnnKsP3uEzfTsx1QxTBbaBMEkmC8uv2C2fuRD (MainProcess - pid: 5117)
[2017-11-13 09:23:50] [INFO] (bigchaindb.processes) Initializing BigchainDB... (MainProcess - pid: 5117)
[2017-11-13 09:23:50] [INFO] (bigchaindb.processes) Starting block (MainProcess - pid: 5117)
Process Process-10:
[2017-11-13 09:23:50] [INFO] (bigchaindb.processes) Starting voter (MainProcess - pid: 5117)
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 235, in _check_replica_set
    repl_opts = options['parsed']['replication']
KeyError: 'replication'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/bigchaindb", line 11, in <module>
    load_entry_point('BigchainDB==1.2.0.dev0', 'console_scripts', 'bigchaindb')()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/bigchaindb.py", line 355, in main
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 235, in _check_replica_set
    repl_opts = options['parsed']['replication']
KeyError: 'replication'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
    utils.start(create_parser(), sys.argv[1:], globals())
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/utils.py", line 206, in start
  File "/usr/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap
    self.run()
  File "/usr/lib/python3.5/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/lib/python3.5/dist-packages/multipipes/pipeline.py", line 67, in safe_run_forever
    self.run_forever()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/changefeed.py", line 35, in run_forever
    .next()['ts'])
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 62, in run
    return query.run(self.conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 122, in conn
    self.connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 153, in connect
    self._conn = self._connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 101, in _connect
    self.crlfile)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 198, in initialize_replica_set
    _check_replica_set(conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 238, in _check_replica_set
    raise ConfigurationError('mongod was not started with'
bigchaindb.common.exceptions.ConfigurationError: mongod was not started with the replSet option.
    return func(args)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/utils.py", line 51, in configure
    command(args)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/utils.py", line 78, in start_logging
    command(args)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/commands/bigchaindb.py", line 209, in run_start
    processes.start()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/processes.py", line 57, in start
    vote.start()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/pipelines/vote.py", line 183, in start
    pipeline = create_pipeline()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/pipelines/vote.py", line 160, in create_pipeline
    voter = Vote()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/pipelines/vote.py", line 39, in __init__
    self.last_voted_id = Bigchain().get_last_voted_block().id
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/core.py", line 596, in get_last_voted_block
    self.me)
  File "/usr/lib/python3.5/functools.py", line 743, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/query.py", line 312, in get_last_voted_block_id
    sort=[('vote.timestamp', -1)]))
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 62, in run
    return query.run(self.conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 122, in conn
    self.connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/connection.py", line 153, in connect
    self._conn = self._connect()
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 101, in _connect
    self.crlfile)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 198, in initialize_replica_set
    _check_replica_set(conn)
  File "/usr/local/lib/python3.5/dist-packages/BigchainDB-1.2.0.dev0-py3.5.egg/bigchaindb/backend/mongodb/connection.py", line 238, in _check_replica_set
    raise ConfigurationError('mongod was not started with'
bigchaindb.common.exceptions.ConfigurationError: mongod was not started with the replSet option.

alka@mixorg:~$ sudo mongod --replSet bigchain-rs --port 27027
sudo: unable to resolve host mixorg
[sudo] password for alka:
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] MongoDB starting : pid=5488 port=27027 dbpath=/data/db 64-bit host=mixorg
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] db version v3.4.9
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] git version: 876ebee8c7dd0e2d992f36a848ff4dc50ee6603e
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2g  1 Mar 2016
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] allocator: tcmalloc
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] modules: none
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] build environment:
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten]     distmod: ubuntu1604
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten]     distarch: x86_64
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten]     target_arch: x86_64
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] options: { net: { port: 27027 }, replication: { replSet: "bigchain-rs" } }
2017-11-13T09:28:23.673+0530 I -        [initandlisten] Detected data files in /data/db created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten]
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten] **          See http://dochub.mongodb.org/core/prodnotes-filesystem
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten] wiredtiger_open config: create,cache_size=1396M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),
2017-11-13T09:28:24.305+0530 I STORAGE  [initandlisten] Starting WiredTigerRecordStoreThread local.oplog.rs
2017-11-13T09:28:24.305+0530 I STORAGE  [initandlisten] The size storer reports that the oplog contains 1817 records totaling to 177140 bytes
2017-11-13T09:28:24.305+0530 I STORAGE  [initandlisten] Scanning the oplog to determine where to place markers for truncation
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: Access control is not enabled for the database.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] **          Read and write access to data and configuration is unrestricted.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: You are running this process as the root user, which is not recommended.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/enabled is 'always'.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/defrag is 'always'.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.382+0530 I FTDC     [initandlisten] Initializing full-time diagnostic data capture with directory '/data/db/diagnostic.data'
2017-11-13T09:28:24.383+0530 I NETWORK  [thread1] waiting for connections on port 27027
2017-11-13T09:28:24.383+0530 W REPL     [replExecDBWorker-0] Locally stored replica set configuration does not have a valid entry for the current node; waiting for reconfig or remote heartbeat; Got "NodeNotFound: No host described in new configuration 1 for replica set bigchain-rs maps to this node" while validating { _id: "bigchain-rs", version: 1, protocolVersion: 1, members: [ { _id: 0, host: "localhost:27017", arbiterOnly: false, buildIndexes: true, hidden: false, priority: 1.0, tags: {}, slaveDelay: 0, votes: 1 } ], settings: { chainingAllowed: true, heartbeatIntervalMillis: 2000, heartbeatTimeoutSecs: 10, electionTimeoutMillis: 10000, catchUpTimeoutMillis: 60000, getLastErrorModes: {}, getLastErrorDefaults: { w: 1, wtimeout: 0 }, replicaSetId: ObjectId('59e5a85e7ff0e2721751f08c') } }
2017-11-13T09:28:24.383+0530 I REPL     [replExecDBWorker-0] New replica set config in use: { _id: "bigchain-rs", version: 1, protocolVersion: 1, members: [ { _id: 0, host: "localhost:27017", arbiterOnly: false, buildIndexes: true, hidden: false, priority: 1.0, tags: {}, slaveDelay: 0, votes: 1 } ], settings: { chainingAllowed: true, heartbeatIntervalMillis: 2000, heartbeatTimeoutSecs: 10, electionTimeoutMillis: 10000, catchUpTimeoutMillis: 60000, getLastErrorModes: {}, getLastErrorDefaults: { w: 1, wtimeout: 0 }, replicaSetId: ObjectId('59e5a85e7ff0e2721751f08c') } }
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] This node is not a member of the config
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] transition to REMOVED
2017-11-13T09:28:24.384+0530 I NETWORK  [replExecDBWorker-0] legacy transport layer closing all connections
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication storage threads
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication fetcher thread
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication applier thread
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication reporter thread

What I Did
Followed steps to set up a cluster according to docs.
Paste the command(s) you ran and the output.
If there was a crash, please include the traceback/error message here.

Hi,

We need more information. In particular, we need to know what you did before you did bigchaindb start. Saying "I followed the instructions" is not enough. Please show us what you did. Walk us through.
We will be merging some new instructions and automation tools for deploying a cluster. Those are in pull request https://github.com/bigchaindb/bigchaindb/pull/1790

Sorry.
First things first , I installed mongodb community edition on the system.
it is working as expected and have been able to execute to some queries too!
Then, I upgraded my pip and ran sudo apt-get install python3-pip
pip3 install --upgrade pip setuptools
pip3 install bigchaindb
git clone git@github.com:bigchaindb/bigchaindb.git
cd bigchaindb
python setup.py install
bigchaindb -y configure mongodb
I edited the config files as described by you folks.
Next, as this was going to be my first node, I ran the bigchaindb start command.
it hit me up with an error that mongodb needs to be working
So , I ran sudo service mongodb start in a different terminal..
then I ran ' bigchaindb start' it yielded the same error.
So, I went to the quickstart page,
created data/db  while being the super user on the system,
ran $ sudo chmod -R 700 /data/db
and
$ sudo mongod --replSet=bigchain-rs
The above command gave the error that the port was already in use.
(seems to be the issue everytime)
so, I executed mongod --replSet bigchain-rs --port 27027
which yielded,
alka@mixorg:~$ sudo mongod --replSet bigchain-rs --port 27027
sudo: unable to resolve host mixorg
[sudo] password for alka:
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] MongoDB starting : pid=5488 port=27027 dbpath=/data/db 64-bit host=mixorg
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] db version v3.4.9
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] git version: 876ebee8c7dd0e2d992f36a848ff4dc50ee6603e
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2g  1 Mar 2016
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] allocator: tcmalloc
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] modules: none
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] build environment:
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten]     distmod: ubuntu1604
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten]     distarch: x86_64
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten]     target_arch: x86_64
2017-11-13T09:28:23.652+0530 I CONTROL  [initandlisten] options: { net: { port: 27027 }, replication: { replSet: "bigchain-rs" } }
2017-11-13T09:28:23.673+0530 I -        [initandlisten] Detected data files in /data/db created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten]
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten] **          See http://dochub.mongodb.org/core/prodnotes-filesystem
2017-11-13T09:28:23.673+0530 I STORAGE  [initandlisten] wiredtiger_open config: create,cache_size=1396M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),
2017-11-13T09:28:24.305+0530 I STORAGE  [initandlisten] Starting WiredTigerRecordStoreThread local.oplog.rs
2017-11-13T09:28:24.305+0530 I STORAGE  [initandlisten] The size storer reports that the oplog contains 1817 records totaling to 177140 bytes
2017-11-13T09:28:24.305+0530 I STORAGE  [initandlisten] Scanning the oplog to determine where to place markers for truncation
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: Access control is not enabled for the database.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] **          Read and write access to data and configuration is unrestricted.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: You are running this process as the root user, which is not recommended.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/enabled is 'always'.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/defrag is 'always'.
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2017-11-13T09:28:24.373+0530 I CONTROL  [initandlisten]
2017-11-13T09:28:24.382+0530 I FTDC     [initandlisten] Initializing full-time diagnostic data capture with directory '/data/db/diagnostic.data'
2017-11-13T09:28:24.383+0530 I NETWORK  [thread1] waiting for connections on port 27027
2017-11-13T09:28:24.383+0530 W REPL     [replExecDBWorker-0] Locally stored replica set configuration does not have a valid entry for the current node; waiting for reconfig or remote heartbeat; Got "NodeNotFound: No host described in new configuration 1 for replica set bigchain-rs maps to this node" while validating { _id: "bigchain-rs", version: 1, protocolVersion: 1, members: [ { _id: 0, host: "localhost:27017", arbiterOnly: false, buildIndexes: true, hidden: false, priority: 1.0, tags: {}, slaveDelay: 0, votes: 1 } ], settings: { chainingAllowed: true, heartbeatIntervalMillis: 2000, heartbeatTimeoutSecs: 10, electionTimeoutMillis: 10000, catchUpTimeoutMillis: 60000, getLastErrorModes: {}, getLastErrorDefaults: { w: 1, wtimeout: 0 }, replicaSetId: ObjectId('59e5a85e7ff0e2721751f08c') } }
2017-11-13T09:28:24.383+0530 I REPL     [replExecDBWorker-0] New replica set config in use: { _id: "bigchain-rs", version: 1, protocolVersion: 1, members: [ { _id: 0, host: "localhost:27017", arbiterOnly: false, buildIndexes: true, hidden: false, priority: 1.0, tags: {}, slaveDelay: 0, votes: 1 } ], settings: { chainingAllowed: true, heartbeatIntervalMillis: 2000, heartbeatTimeoutSecs: 10, electionTimeoutMillis: 10000, catchUpTimeoutMillis: 60000, getLastErrorModes: {}, getLastErrorDefaults: { w: 1, wtimeout: 0 }, replicaSetId: ObjectId('59e5a85e7ff0e2721751f08c') } }
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] This node is not a member of the config
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] transition to REMOVED
2017-11-13T09:28:24.384+0530 I NETWORK  [replExecDBWorker-0] legacy transport layer closing all connections
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication storage threads
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication fetcher thread
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication applier thread
2017-11-13T09:28:24.384+0530 I REPL     [replExecDBWorker-0] Starting replication reporter thread
then, I ran 'bigchaindb start'
which led to the terminal responding, bigchaindb.common.exceptions.ConfigurationError: mongod was not started with the replSet option.

I think you need to shut down all MongoDB processes and services and try again. See:
https://docs.mongodb.com/manual/tutorial/manage-mongodb-processes/
and
https://stackoverflow.com/questions/11774887/how-to-stop-mongo-db-in-one-command

It's working now w/o changing ports. Thanks Troy ! :)
When can I expect the updated documentation on deploying a cluster?

When can I expect the updated documentation on deploying a cluster?

Soon. Just follow pull request https://github.com/bigchaindb/bigchaindb/pull/1790
Once it's merged, you'll be able to find the updated docs in:
https://docs.bigchaindb.com/projects/server/en/master/appendices/run-with-vagrant.html
and
https://docs.bigchaindb.com/projects/server/en/master/appendices/run-with-ansible.html

Hello, I still cannot run the $ bigchaindb start with the same error above. I did try stop mongodb but still error. I did start mongodb with flag --replSet but still error. Can you please help me some idea? I'm runing Ubuntu 17.10 on VMWare. Is it a problem?

Hi, @nguyenthuymo
I created a video which contains the step by step installation of bigchaindb.
https://www.youtube.com/watch?v=tB8Nbu_l_NA
Sorry for the late reply, hope this helps you :)


fix: add height: 100% to fix overflow

testing
this isn't happening on the stacked tabs example in the demo. the easiest way to test this is just to add this line of CSS manually to the tab panel on the live site where the issue is happening
https://docs.newrelic.com/docs/synthetics/synthetic-monitoring/getting-started/get-started-synthetic-monitoring/
in the inspector, add height: 100% to the div with the class css-id30ng (it has role="tabpanel")

i cannot reproduce this on the site.

i cannot reproduce this on the site.

whoops, sorry, that's my bad. i didn't realize there was a different class on tabpanels that were opened than ones that are closed. the class is actually css-id30ng

I think the problem here is, we're expecting the overall tabs component to be the height of the largest page up to 500px.  The content causing the issue here is going to 500px and can still scroll, but the Tabs aren't compensating for it.  Maybe we just pass the height all the way back to the Tabs component and set the overall height there?

i've followed the steps twice and im still getting this


Windows GitHub Actions Build Fails

See here
Looks to be a problem with matplotlib. A similar issue can be found here

https://github.com/ryansurf/cli-surf/pull/119


APPS-1159 Use unsigned Integer to store backup and restore statistics

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 76.26%. Comparing base (fd99b7c) to head (aa0cec2).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #155   +/-   ##
=======================================
  Coverage   76.26%   76.26%
=======================================
  Files          13       13
  Lines         552      552
=======================================
  Hits          421      421
  Misses        109      109
  Partials       22       22

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

I've updated automation too (to use Long in Java, not Integer), test run
http://<IP_ADDRESS>:8080/ui/#pitr/launches/all/5357


Seems to fail on nox

I was using your Pokemon Go Xposed app in the past. I followed the instructions here, disabled your old app, rebooted, entered credentials, but it connects to the official servers.
Im using latest Nox Player, with ssid wired connection

on it, its a weird issue that the configuration isn't read - investigating! thanks for noticing!

located, try updating to the newest version


Convert "associate_mesh/field..." subroutine to function

To mimic C++ down casting, it is convenient to transform auxiliary subroutine like this to function returning the correct pointer.

Agree. Something like
mesh_cur => associate_mesh_FD_1D(mesh)
and with optional error message e.g.
mesh_cur => associate_mesh_FD_1D(mesh, "Error casting mesh to mesh_FD_1D")
would be good IMO.

@francescosalvadore LGTM!
Can I go to implement this change or you are doing something big?

working on new files, no problem :)

@francescosalvadore
Done in the last commit pushed to master branch.
Note that I have adopted the following API:
mesh_cur => associate_mesh_FD_1D(mesh_input=mymesh, emsg='calling proc blabla')

where emsg is an optional auxiliary message: even if not passed, the associate function print a meaningful error message to stderr before quitting. Passing also emsg results into a message like
error: cast mesh to mesh_FD_1D
calling procedure blabla

I hope you like, but the messages can be easily changed.


itorch_launcher: portable test for existence of luajit

The itorch launcher tests the existences of luajit. If luajit
does not exist, lua is launched instead. The test does not work
on debian bash. I made a standard portable file existance test.

Thank you for your pull request and welcome to our community. We require contributors to sign our Contributor License Agreement, and we don't seem to have you on file. In order for us to review and merge your code, please sign up at https://code.facebook.com/cla - and if you have received this in error or have any questions, please drop us a line at<EMAIL_ADDRESS>Thanks!

Thank you for signing our Contributor License Agreement. We can now accept your code for this (and any) Facebook open source project. Thanks!

Thank you!


accessing windows filerequesters to select a file is very slow

Whenever I need to open a file using the windows filerequester, It is very slow.
winappdriver:{'build': {'revision': '8001', 'time': 'Sat Mar  9 00:12:56 2019', 'version': '1.1.1903'}, 'os': {'arch': 'amd64', 'name': 'windows', 'version': '10.0.18362'}}
driver:<appium.webdriver.webdriver.WebDriver (session="0C2C444F-EB36-4FDD-8FBC-B41BBB48D5B3")>

el = WebDriverWait(self.driver, args.timeout).until(EC.element_to_be_clickable((By.NAME, "Open...")))
el.click()
t0 = time()
el = WebDriverWait(self.driver, args.timeout).until(EC.element_to_be_clickable((By.XPATH, "//ComboBox/Edit[@Name='File name:']")))
print(f"found filename in {time()-t0:.02f}sec")
xmlwrite(self.driver.page_source, "./filerequester.xml")
t0 = time()
el.send_keys(config['local'])
print(f"entering filename in {time()-t0:.02f}sec")
t0 = time()
el = WebDriverWait(self.driver, args.timeout).until(EC.element_to_be_clickable((By.XPATH, "//Button[@AccessKey='Alt+o']")))
print(f"find open in {time()-t0:.02f}sec")
el.click()

The timings:
found filename in 6.35sec
written page_source to file:./filerequester.xml in 0.06sec
entering filename in 0.84sec
find open in 4.55sec

The requester file is 128K
Mode                LastWriteTime         Length Name
----                -------------         ------ ----
-a----       10/14/2019   9:00 AM         128141 filerequester.xml

The more files and directories will severely affect performance, but there should be shortcuts to the file name combobox and the open button.
The filerequester xml generated:
filerequester.zip
I'm also using smartbears testcomplete where this almost instant.

What version of WinAppDriver are you using? Can you try the latest v1.2 release with the following capability:
C#: appCapabilities.SetCapability("ms:experimental-webdriver", true);

I tried the latest release, and I added the caps to my unittest driver setup, but unfortuinately I did not see any improvement:
    @classmethod
    def setUpClass(self):
        assert winapptools.winappdriver_ready(winapp_driver_socket + "/status"), "winappdriver not running"
        self.app = config['config']
        desired_caps = {}
        desired_caps['app'] = self.app
        desired_caps['ms:experimental-webdriver'] = True
        desired_caps['platformName'] = "Windows"
        desired_caps['deviceName'] = "win10lap"
        try:
            self.driver = webdriver.Remote(
                command_executor=winapp_driver_socket,
                desired_capabilities= desired_caps
            )
        except urllib3.exceptions.MaxRetryError as e:
            print(f"Error: please make sure winappdriver is started in another powershell powershell - {e}")
            sys.exit(-1)
        except selenium.common.exceptions.WebDriverException as e:
            print(f"Error: {desired_caps['app']} - {e}")
            sys.exit(-1)

winappdriver:{'build': {'revision': '2002', 'time': 'Wed Oct  2 21:08:40 2019', 'version': '1.2.1910'}, 'os': {'arch': 'amd64', 'name': 'windows', 'version': '10.0.18362'}}
driver:<appium.webdriver.webdriver.WebDriver (session="78B63DE5-2D34-4645-A01B-02D5EDF22C8F")>
found filename in 6.88sec
entering filename in 0.98sec
find open in 5.21sec
written page_source to file:./cardreaders.xml in 0.00sec

I'd recommend switching out the XPath queries for Name or Automation/AccessibilityID. If they don't have those values, then try using an absolute XPath query from UI Recorder for the desired element.


S3DirectoryInfo.GetFiles returns exception "key is a directory name"

The following simple test returns the above exception:
S3DirectoryInfo test = new S3DirectoryInfo(client, "bucketname", "testdir/test");
test.Create();
var files = test.GetFiles("*", SearchOption.AllDirectories);
The reason is that S3DirectoryInfo.Create is creating an object called "testdir/test/" (note the trailing slash).
S3DirectoryInfo.EnumerateFiles checks each returned s3Object, skipping those that EndsWith("") - I'm taking a guess here, but perhaps the s3Object key is returned with a "/" slash, which doesn't satisfy this check?
The end result is passing an object key with a trailing slash to the S3FileInfo constructor, which then throws the exception.

I tested, all was working fine if change '/' to ''.


Investigate removing dnsmasq and use consul dns directly

Instead of going through <IP_ADDRESS>:53 -> consul:8600, let's have consul listen on port 53 and have the resolv.conf point to consul systems:
Tasks:

[x] update consul role to listen on host port 53 vs. 8600
[ ] update NetworkManager configuration to use consul servers before dhcp provided servers (/etc/NetworkManager/dhclient.d?)
[ ] remove dns settings from docker role (file: /etc/default/docker-network)
[ ] remove dnsmasq from zookeeper systemd dependency roles/zookeeper/templates/zookeeper-service.j2
[ ] remove dnsmasq role from site.yml
[ ] remove dnsmasq role from vagrant.yml
[ ] remove roles/dnsmasq
[ ] test: Build
[ ] test: Reboot
[ ] test: Vagrant
[ ] test: Single-DC
[ ] test: Multi-DC

Moving this to low priority.

Closing this issue for now. We can reopen it in the future.


How to use git account in spyder

Description
What steps will reproduce the problem?

What is the expected output? What do you see instead?
Please provide any additional information below
File "/Users/dainping/anaconda/lib/python2.7/site-packages/spyder/plugins/projects.py", line 234, in _create_project
self.open_project(path=path)
File "/Users/dainping/anaconda/lib/python2.7/site-packages/spyder/plugins/projects.py", line 261, in open_project
self.set_project_filenames(self.editor.get_open_filenames())
File "/Users/dainping/anaconda/lib/python2.7/site-packages/spyder/plugins/projects.py", line 325, in set_project_filenames
self.current_active_project.set_recent_files(recent_files)
File "/Users/dainping/anaconda/lib/python2.7/site-packages/spyder/widgets/projects/type/init.py", line 74, in set_recent_files
list(OrderedDict.fromkeys(recent_files)))
File "/Users/dainping/anaconda/lib/python2.7/site-packages/spyder/config/user.py", line 448, in set
self._save()
File "/Users/dainping/anaconda/lib/python2.7/site-packages/spyder/config/user.py", line 124, in _save
raise(e)
IOError: [Errno 2] No such file or directory: u'/Users/dainping/Documents/GitCode/platform-data/.spyproject/workspace.ini'
Version and main components

Spyder Version: 3.2.4
Python Version: 2.7.10
Qt Versions: 5.6.2, PyQt5 5.6 on Darwin

Dependencies
pyflakes >=0.5.0  :  1.5.0 (OK)
pycodestyle >=2.3 :  2.3.1 (OK)
pygments >=2.0    :  2.1.3 (OK)
pandas >=0.13.1   :  0.20.2 (OK)
numpy >=1.7       :  1.13.1 (OK)
sphinx >=0.6.6    :  1.5.1 (OK)
rope >=0.9.4      :  0.9.4 (OK)
jedi >=0.9.0      :  0.9.0 (OK)
psutil >=0.3      :  5.0.1 (OK)
nbconvert >=4.0   :  4.2.0 (OK)
sympy >=0.7.3     :  1.0 (OK)
cython >=0.21     :  0.25.2 (OK)
qtconsole >=4.2.0 :  4.2.1 (OK)
IPython >=4.0;<6.0:  5.1.0 (OK)
pylint >=0.25     :  1.6.4 (OK)

Please describe step by step how you got this error so we can reproduce it in our side. If you fail to do that, we'll close this issue in a week from now.

Appears to be a duplicate of #5934 ; not sure if it has anything to do with git. Probably a user install issue unless it only appears in specific situations; please see that issue and the potential fixes suggested there to see if that resolves your issue. If this can be isolated to something specific in Spyder, there is a chance it can get fixed from this end, but you'll need to provide more specific information first. Thanks.

Closed due to lack of response.


Is layout animation supported?

I was trying to get some animations working, LayoutAnimation is the easiest way for a lot of this stuff, but it does not seem to be working

No, layout animations have not been implemented for macOS.    It is tracked by https://github.com/microsoft/react-native-macos/issues/277 but is not currently funded.

thanks


Add file path in the crc error log for given store key

Summary
Adding the file path in the crc error log so we can easily identify the disk. CRC error can be caused by failed disk. This log message make identity the disk easier.

Codecov Report
Attention: 4 lines in your changes are missing coverage. Please review.

Comparison is base (2b96c58) 53.19% compared to head (c5c8392) 32.46%.

Files
Patch %
Lines

.../github/ambry/messageformat/MessageFormatSend.java
0.00%
2 Missing :warning:

...in/java/com/github/ambry/store/MessageReadSet.java
0.00%
1 Missing :warning:

...va/com/github/ambry/store/StoreMessageReadSet.java
0.00%
1 Missing :warning:

Additional details and impacted files
@@              Coverage Diff              @@
##             master    #2671       +/-   ##
=============================================
- Coverage     53.19%   32.46%   -20.74%
+ Complexity     7809     4476     -3333
=============================================
  Files           809      810        +1
  Lines         65637    65640        +3
  Branches       8018     8018
=============================================
- Hits          34917    21308    -13609
- Misses        27704    42097    +14393
+ Partials       3016     2235      -781

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


Fix error in LHASH documentation

[x] documentation is added or updated
[ ] tests are added or updated

This pull request is ready to merge

Merged to master, 3.0 and 1.1.1. Thank you.


Accuracy calculation is incorrect?

Hi,
I have been experimenting with using model.predict() to run some predictions manually rather than evaluating them directly with model.evaluate() because I need the predicted values and not just the overall accuracy.
When computing the accuracy manually I noticed that the accuracy keras' calculates in evaluate() is not correct. Is there a bug in the accuracy calculation?
Below a self-contained runnable minimal example that shows the difference (the example tests on the training data):
import numpy as np
from keras.preprocessing import sequence
from keras.models import Sequential
from keras.layers import Dense, Activation, Embedding, TimeDistributed, Bidirectional
from keras.layers import LSTM
import json
from keras.utils import np_utils

np.set_printoptions(threshold=np.nan)

def mapWords2Integer(input, startIdx=0):
    map = {}
    for s in input:
        for w in s:
            if w not in map:
               map[w]=startIdx
               startIdx+=1

    out = []
    for s in input:
        out_s = []
        for w in s:
            out_s.append(map[w])
        out.append(out_s)
    return map, out

tokens = [
    ['Great', 'Western', 'said', 'it', 'had', 'a', 'sharp', 'increase', 'in', 'margins', 'in', 'the', 'recent', 'third', 'quarter', '.'],
    ['Margins', 'are', 'the', 'difference', 'between', 'the', 'yield', 'on', 'the', 'company', 's', 'earning', 'assets', 'and', 'its', 'own', 'cost', 'of', 'funds', '.'],
    ['But', 'a', 'reduction', 'in', 'one-time', 'gains', 'on', 'the', 'sale', 'of', 'various', 'assets', 'and', 'an', 'increase', 'in', 'the', 'company', 's', 'provision', 'for ', 'loan', 'losses', 'held', 'down', 'the', 'earnings', 'gain', ', ', 'the', 'company', 'said', '.']
]

labels = [
    ['NNP', 'NNP', 'VBD', 'PRP', 'VBD', 'DT', 'JJ', 'NN', 'IN', 'NNS', 'IN', 'DT', 'JJ', 'JJ', 'NN', '.'],
    ['NNS', 'VBP', 'DT', 'NN', 'IN', 'DT', 'NN', 'IN', 'DT', 'NN', 'POS', 'VBG', 'NNS', 'CC', 'PRP$', 'JJ', 'NN', 'IN', 'NNS', '.'],
    ['CC', 'DT', 'NN', 'IN', 'JJ', 'NNS', 'IN', 'DT', 'NN', 'IN', 'JJ', 'NNS', 'CC', 'DT', 'NN', 'IN', 'DT', 'NN', 'POS', 'NN', 'IN', 'NN', 'NNS', 'VBD', 'RP', 'DT', 'NNS', 'NN', ',', 'DT', 'NN', 'VBD', '.']
]

longest_sequence = max(len(s) for s in (tokens))

valMap, valInt = mapWords2Integer(tokens,1)
labMap, labelInt = mapWords2Integer(labels,1)

vocabSize=len(valMap)

padValInt = sequence.pad_sequences(valInt, maxlen=longest_sequence)
padLabInt = sequence.pad_sequences(labelInt, maxlen=longest_sequence)

maximal_value = max([ys for sent in padLabInt for ys in sent])+1

train_label = np.array([np_utils.to_categorical(seq, maximal_value) for seq in padLabInt])

EMBEDDING_DIM=100

model = Sequential()
model.add(Embedding(vocabSize+1, EMBEDDING_DIM,mask_zero=True))
model.add(Bidirectional(LSTM(EMBEDDING_DIM, return_sequences=True)))
model.add(TimeDistributed(Dense(maximal_value)))
model.add(Activation('relu'))

# try using different optimizers and different optimizer configs
model.compile(loss='categorical_crossentropy',
              optimizer='adam',
              metrics=['accuracy'])

model.fit(padValInt, train_label, nb_epoch=1)
score, acc = model.evaluate(padValInt, train_label)
print('Accuracy calculated by Keras:', acc*100)

#########################
##### Manual Accuracy ###
#########################
correct=0.0
incorrect=0.0
inversed_label_map = {v: k for k, v in labMap.items()}
for k in range(0, len(padValInt)):
    s = padValInt[k]
    out = model.predict(s)
    predLabels = []
    for e in out:
        for c in e:
            x = np.argmax(c)
            pl = inversed_label_map.get(x)
            predLabels.append(pl)

    #throw away the padded, leading zeros
    fromIdx = (len(predLabels)-len(labels[k]))
    predLabels = predLabels[fromIdx:]

    for i in range(0, len(labels[k])):

        if labels[k][i] == predLabels[i]:
            correct+=1
        else:
            incorrect+=1

acc = correct / (correct+incorrect) * 100
print("Manually calculated accuracy: ", acc)

Without running your code, a possibility is that the model is running a different type of accuracy metric than you expect. Given your predLabels and calculated accuracy, what do you get when you run the following?
keras.metrics.binary_accuracy(labels, predLabels)
keras.metrics.categorical_accuracy(labels, predLabels)
keras.metrics.sparse_categorical_accuracy(labels, predLabels)

Hi,
I get different accuracy values for the metrics you mention but non is the one that I calculate by hand.
The difference is sometimes only small but I have cases in which Keras says the accuracy is zero but when printing gold/prediction values I get at least one or two predictions right.

I think Keras does some rounding internally, could that be it? How different are your values?

I modified my example from the first post with the new initialisation of the variables. I still have differences which cannot be explained by rounding. Here the results I get after running 4x times above code:
Accuracy calculated by Keras: 5.05050505051
Manually calculated accuracy:  7.246376811594203

Accuracy calculated by Keras: 14.1414141414
Manually calculated accuracy:  14.492753623188406

Accuracy calculated by Keras: 18.1818181818
Manually calculated accuracy:  21.73913043478261

Accuracy calculated by Keras: 7.07070707071
Manually calculated accuracy:  5.797101449275362

Either I am doing something fundamentally wrong with retrieving/converting the output of Keras or the the accuracy Keras computes is wrong

@Horsmann Yes, Even I had this problem. I don't know what 'accuracy' metric is calculating but it is far beyond the actual accuracy. Try to give 'categorical_accuracy' as your metric. That will give you correct values.

I had the same problem with wrong scores and i "solved" it by using the sklearn's metrics in a custom callback.

@Horsmann When I try to run the code example you provided, I get the following error:

Exception: A target array with shape (3, 33, 17) was passed for an output of shape (None, None, 17) while using as loss categorical_crossentropy. This loss expects targets to have the same shape as the output.

@lebavarois I use the Theano backend. I just tried the code again it (still) works for me
My problem was the zero padding. I kind of expected that Keras would exclude the zero-padded values from its evaluation but it doesn't.


Fix/one spawn per project

This PR has the following goals:

[x] Massive refactor of the code.
[x] Analyze the whole project, not only the currently open file, so allowing for any engine and including previously missing issues like duplicated code.
[x] Debounce the linting process, so multiple files from the same project can merge into one unique analysis.
[x] Remove some code that doesn't make sense or it's outdated.
[x] Fix all currently reported issues on CodeClimate. I've managed to comply with the cognitive complexity. Hope @Arcanemagus likes the final refactor :wink:
[x] Proper docblocks for each function.

And still waiting for the following bugs to be fixed in their respective repos:

phpmd/phpmd: duplicated issues
steelbrain/exec: bug when exitCode is null

There are some issues left that are very annoying, but I don't have any clue on how to fix them, and can be the subject of future PRs:

On the first Atom run (right after opening Atom for the first time or reloading it with control + shift + F5), the CLI is ran multiple times (typically two). The debounced linting cannot address this issue because the time between the executions exceeds 2s, and setting the debounce timeout to that feels overkilling, and make the whole point of this PR useless.
When starting Atom with multiple files open, changing from one to another still triggers a new analysis. This could be addressed to improve performance.
When starting Atom with multiple files open, the CodeClimate issues are generated correctly for AtomLinter, but they never get added. User need to manually re-trigger analysis by saving a file to get the issues included in AtomLinter pane.

Also, this PR...
Fixes #75
Fixes #76
Closes #77 with a temporary workaround
Fixes #81
Closes #69, since it should be supported by CodeClimate CLI in first place, and it should miss some issues (like duplicated code), which this PR aims to solve.
Closes #74
Closes #77
Closes #78
Edited by @Arcanemagus to automatically close issues/PRs.

The tests seem to hang, cannot make them even print any error.
Anyone that could lend me a hand on this? This PR can be installed and tested locally with:
git clone -b 'fix/one-spawn-per-project' https://github.com/cgalvarez/linter-codeclimate.git linter-codeclimate-pr
cd ./linter-codeclimate-pr
apm link --dev
apm install
atom -d .

Wow, I was about to give up, but the tests take ~273s on CI to finish!! Locally ~20s. What an amazing difference... but finally get it working and passing!! :tada: :tada: :tada:

Looks like the Code Climate people aren't maintaining this 😆😢.
Taking a look over this now, that diff summary looks daunting 😮.

@Arcanemagus Thank you very much for detailed review. I'll take a look at all your reported issues ASAP and make a new commit to fix them all.

I've just fixed all your reported issues. Let me know If I've missed something or you want me to make a rebase or something :wink:
I think it would be desirable to disable some Code Climate engines run in CI to make tests run faster.

Since CI is passing, and I can't run this locally (Windows), I'll go ahead and merge this. 😆

@cgalvarez Assuming @AtomLinter/linter-codeclimate has no issues with it, if you want to be brought on as a maintainer for this project I would be fine with that 😉.

Published in v0.3.0 🎉.

@Arcanemagus Great! I will be glad to help anytime I can.


Handle empty schema as AnyProperty instead of NoneProperty

Closes #389.

@dbanty I know you're probably busy, but any updates on when you might be able to take a look at this PR (and the other 2 I've submitted)?

@forest-benchling I'm planning on knocking out a few more PRs this weekend, and probably will try to release 0.10.0 (which will include most of the work in progress) next weekend.
Can you resolve any conflicts to make that process a bit speedier?

Codecov Report

Merging #417 (7ae9ad1) into main (605c246) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##              main      #417   +/-   ##
=========================================
  Coverage   100.00%   100.00%
=========================================
  Files           47        47
  Lines         1563      1563
=========================================
  Hits          1563      1563

Impacted Files
Coverage Δ

openapi_python_client/parser/openapi.py
100.00% <100.00%> (ø)

...penapi_python_client/parser/properties/__init__.py
100.00% <100.00%> (ø)

openapi_python_client/parser/responses.py
100.00% <100.00%> (ø)

Continue to review full report at Codecov.

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Looks great @forest-benchling , thanks! I am going to fix the template to not need that extra if, so I'll include your changes in #445 instead of merging this one.

Thanks @dbanty. @GitOnUp @packyg this is the last piece we will need to fix the MyPy issues, by making Field have type Any.


BUG_Tasks schedulers does not move task on other workers in the pool after submission.

Describe the bug
The tasks distribution only occurs at submission. That means that submitting all tasks at once can lead to have them all running on the same worker in the pool, and any tasks running forever (like an HTTP server) are never reassigned to other workers in the pool given the tasks scheduling algorithm in use.
To fix it, a tasks list with their status need to be added and tasks schedulers using tasks runtime need to be run to redistribute idle tasks to workers in the pool.

Task moving between workers is a prerequisite. And probably neither easy to implement nor a light operation.

The tasks queuing feature can mitigate a bit that bug in case of tasks submission done once at a time.

I think tasks that are not one-shot need to be identified at worker creation. The worker code is using runInAsyncScope to avoid any tasks to block the worker event loop.
Tasks classification: end/terminate/stop with the response returned or not, stateless or not.
Once we know the type of tasks, preemptive tasks scheduling on pool workers can be eventually considered at first for tasks not ending with the response and with states.
Use cases:

Stateless services (HTTP, SMTP, ...): RR tasks scheduling at startup with number of workers = number of servers. So one server per worker. No rescheduling is needed, but poolifier needs to be properly setup for that use case.
Issues:

Task timeouting is pointless
Some task statistics are not relevant
Worker restart on error does not work (no further tasks submission)

Clients (HTTP, SMTP, ...):

One shot task ending with the response, already handled by poolifier


Additional information on low-cost open access publishing

During the eLife Innovation Sprint 2020, we plan to extend the Low-cost Open Access table to incorporate information on all life sciences. Currently, the table contains information on journals whose scope is mostly computational biology.
We will use this Google document to capture the additional information before we add it to the Affordabee site which will host the content of this repo.

This paper has the most comprehensive list of publishers and details of their waiver practices.


Generating java 8 bytecode

Now that our compiler is rebased on top of java 8's javac we can generate java 8 bytecode/.class files (major version 52). In other words our compiler can start using java 8 features such as default interface methods (#1616) and lambdas (#1617). However, we don't want to stop generating Java 7 bytecode (major version 51) (android support being the main reason). So this issue is about how we can do both.

Previously we've said that we'd have some mechanism whereby we could generate an extra artifact in the output repository (the Java 8 car file, essentially). That raises two questions:

How do we know that we should generate this extra thing. Generating it will slow compilation times, so we probably don't want it generated by default.

How do we know when to use this other car:

At compile time and
At runtime

Note that when things go wrong, we will sometimes need to know that we which car we were using.

Note that Android N comes with some Java 8 support now: http://developer.android.com/preview/j8-jack.html
This means Android now supports all we need.
This issue is then mostly about older versions of Android. Note that the previous Android link talks about how you can still use Java 8 features on older versions of Android:

Note: The Android N bases its implementation of lambda expressions on anonymous classes. This approach allows them to be backwards compatible and executable on earlier versions of Android. To test lambda expressions on earlier versions, remember to go to your build.gradle file, and set compileSdkVersion and targetSdkVersion to 23 or lower.

Now, we could do something similar, but it doesn't really talk about default interface methods, or how this works with existing class files (compiled by Javac 8 and not Jack).

For 2a. we could always use the 8car when running on a jvm >=8. But that means CMR needs to know that resolving an 8car is acceptable. In particular, when fetching from a remote repo should it would need to fetch both cars. So that once cached the local repo knows that an 8car is available should it need to link it in a jvm >=8.

For 1. The obvious thing is to use a compiler & config file option. That makes eight-ness a per-project setting rather than per-module one. I don't think that's a problem, but it was when we were developing --target and wanting to compile the SDK.

For 1. you could decide to generate 8cars for modules that are native("jvm") and that import java.base "8"?

For 1. The obvious thing is to use a compiler & config file option.

This seems like the right thing to me.

How do we know when to use this other car:
a. At compile time and
b. At runtime

This should be automatic, and not require user-intervention.

For 1. you could decide to generate 8cars for modules that are native("jvm") and that import java.base "8"?

I have three objections to this:

Many (most?) modules aren't native.
Java 8 should be the default.
Often, we'll want to generate both flavors.

Let the the 200-comment begin.

If we use an annotation like javaTarget(7) and consider that Java 8 is now the default, you could make the typechecker warn you that you are trying to import a Java 8 compatible module from a Java 7 compatible module.
Also, instead of changing extensions we could perhaps introduce qualifiers, like maven does?

Of course an alternative to generating a whole new artifact would be to just put those .class files which make use of new features somewhere else within the existing .car file, and adjust classesloaders etc to find those alternatives when on a jvm that supports them. So for example a "normal" ceylon class would just have a version 51 class file generated, but we'd generate two classes for an interface with default methods, one version 51 using the existing transformation, and another version 52 using default interface methods. Tools (such as ceylon jigsaw) could repackage discarding version 52 classfiles.

Doesn't work: even users of default methods have to be version 52.
http://openjdk.java.net/jeps/238 is what you're describing though.

Doesn't work: even users of default methods have to be version 52.

Well, that just means places where we use the default method get two class files generated. Obviously keeping track of which classes require multiple versions is an issue.

Let's please try to go for the JEPS/238 Stef links to. The other mentioned solution seem to me exercises in complexity that are bound to be causing problems all over the place. Not that the linked solution will be easy I guess, but at least it limits the effect of supporting this to a very specific place in the system: the class loader. Otherwise we'll have to deal with this in the CMR and all the tools dealing with module artifacts, etc. (Very hard to make backward compatible for example)

By the time Ceylon is relevant for Android development, Android N will be widespread. It supports a useful subset of Java 8, so if you generate code within that subset, no problems.
I suspect the Jack toolchain will be backported to at least M.
https://developer.android.com/preview/j8-jack.html

@quintesse well it's not just the classloader.

Classloader changes (which might not be amenable given its in JBoss Modules)
Compiler changes (CeylonFileManager)
Changes in our compiler to track which classes get generated multiple times
Changes in our other tools e.g. ceylon jigsaw, maybe ceylon war
Changes in ceylon test (so you can test with both).

It's not clear to me that it's less work, merely that it's different work. And then JEP 238 gets implemented in Java 9 and there's more work to ensure we're compatible with it. Presumably ultimately we end up with less code to maintain. Perhaps we can glean enough from https://bugs.openjdk.java.net/browse/JDK-8047305 and their repos to ensure we're compatible at the car file level.
But I agree that having a new artifact is a lot of work too:

Changes in CMR
Changes in the compiler (simpler ones though)
Changes in Herd
Changes in lots of our existing tools ceylon copy, ceylon info, ceylon compile, ceylon run, ceylon test, ceylon classpath

But we end up with something quite different to what Java 9 might get with 238, and maybe end up having to support 238 anyway.

well, I do not understand.
In our module.ceylon file, I can declare module dependency on java.base and you have to specify Java version java.base "8" or java.base "7" -- that should be enough to choose which java byte code to generate.
If there is no explicit dependency on java.* library, but you depend on a non-ceylon java library (i.e. maven dependency), those libraries and their transitive dependencies have possibly a range of class versions. let's say they fall into the range of Java 6 to Java 8. That is class version range [50,52].
In order to be able to use libraries in the dependencies, we need to generate byte code with the highest possible class version of all of our dependencies. Including the the byte code version of ceylon.language and all the ceylon-sdk libraries.
Also, as a last override, we need a configuration and command line option (and the API support for tools like Gradle and Maven plugins) to explicitly set the target byte code version.
We might end up supporting JEP 238, and we might not, but in order to be able to support that, we must have ability to choose (smartly) what is the bytecode we produce.
And in any case -- the lowest possible byte code version we support is dictated by the version of the byte code of the ceylon-language -- whatever we compile it with, is the lower bound of our language support.

From what I've gleaned from the JEP 238 patches, it will only supports META-INF/versions/n for n  >= 9, so even if we did the same thing as them, our cars would not be considered multi-release by java 9.


[BUG] Unable to execute query on postgres Mock DB table.

Description
DB throws error for querying database with camelCase naming. From error, it could be inferred that the query converted the table name camelCase internally to camelcase which is an invalid table.

Important Details

Version: Cloud
OS: MacOs 10.14.6
Browser: Firefox 80.0.1 (64-bit).

Similar issue occurred with update query on columnName.

Similar issue occurred with update query on columnName.

Explanation here: https://github.com/appsmithorg/appsmith/issues/640#issuecomment-696078648

This worked with single quote around columnName and tableName.


[FLINK-20848][connector/kafka] Fix Kafka consumer client ID with subtask ID suffix

What is the purpose of the change
This pull request fixes a bug of assigning subtask ID after creating Kafka consumer client ID, which will lead to all consumer client ID used uninitialized subtask ID 0 as suffix.
Brief change log

Move subtask ID assignment above creating Kafka consumer client ID

Verifying this change
This change is a trivial rework / code cleanup without any test coverage.
Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): (no)
The public API, i.e., is any changed class annotated with @Public(Evolving): (no)
The serializers: (no)
The runtime per-record code paths (performance sensitive): (no)
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Kubernetes/Yarn/Mesos, ZooKeeper: (no)
The S3 file system connector: (no)

Documentation

Does this pull request introduce a new feature? (no)
If yes, how is the feature documented? (not applicable)

An NPE is thrown from SourceOperator in the UnalignedCheckpointITCase. I'm investigating the reason of it.

An NPE is thrown from SourceOperator in the UnalignedCheckpointITCase. I'm investigating the reason of it.

There's already a ticket for this issue. See FLINK-20781

There's already a ticket for this issue. See FLINK-20781

Thanks for the patch. LGTM.

Thanks for the patch. LGTM.

Merged.
Master: 9313b01a73d5d05fab2fc8be8fac21a3ede039d6
release-1.12: e203e24cf775e4d5cdd0469b9db3cf2894b2f9c5

Merged.
Master: 9313b01a73d5d05fab2fc8be8fac21a3ede039d6
release-1.12: e203e24cf775e4d5cdd0469b9db3cf2894b2f9c5


Fold this repo into XBlock

This repository is useful to XBlock developers, and it is tightly coupled to XBlock. So, let's merge it into the XBlock repository.
Considerations:

It should be isolated to a sub-directory and have its own requirements file. The requirements file should be available via extras-require. This way, edx-platform can run pip install xblock[django] (so that it doesn't pull in sdk dev tool packages) and developers can run pip install xblock[sdk].

We don't have a paved path for this setup, so this will take some creativity. repo-tools does a more complicated version of this: it has EXTRAS_REQUIRE defined for every subdirectory with requirements. We don't need to go that far, but the example might be helpful.

FYI @feanil


Add licence text to the introduction

It would be useful to add a copy of the licence text from the repo README to the introduction of the book, as it's not that obvious if you're just reading the book online.

Closed by #226