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Break out system

fossasia/meilix

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  • Issue type: Bug report <!– delete the one that does not apply –>

Short description

<!– Explain in a few sentences what the issue/request is –> The system seems to breaks out after merging of commits and the desktop seems as: ned

Updated 20/08/2017 04:43

Introduction message

ProjectCopilot/mailroom

When a user submits a case request through concierge, volunteers can send texts to the user through an unknown phone number without any sort of context. When a user fills out a case, we need to send an introductory SMS message immediately with something like “This is an automated message from Copilot, we’ll be in touch soon” and likewise with referrals something like “Your friend referred you for Copilot, we’ll be in touch soon”.

Of course, we would need to craft these messages in accordance to mental health standards.

Updated 18/08/2017 23:54

Types within Types_ B missing from export

haffonist/igamt

Per Mead: One thing I am looking for is to be able to define data type flavors for components within a data type. These do not seem to come through on the export.

I am attaching my most recent. Look for HD_BR_AA, and SAD_BR. Both are declared within the tool, used within data types – you can see the references in the export, but not actually exported. I had thought this was a feature to be included. Am I mistaken there? HL7-Version-2.6-Implementation-Guide–Vital-Records-Birth–Fetal-Death-Reporting-Release-1—US-Realm-5898caa884ae9be46ff21abc_20170817_155419.docx

Updated 18/08/2017 20:29

Gillespie on a grid does not seem to work

sys-bio/roadrunner

When running the following model I expected 10 points on a grid between 0 and 50, instead I get ten point up to time 0.928226 not 50 as expected.

import tellurium as te

r = te.loada ('''
    $Xo -> S1; k1 * Xo;
    S1 -> S2; k2*S1;
    S2 -> $X1; k3*S2;

    Xo = 50; S1 = 0; S2 = 0;
    k1 = 0.2; k2 = 0.4; k3 = 2;
''')

m = r.gillespie (0, 50, 10, ["time", "S1", "S2"])
r.plot()

The docs says that will be generate data on a grid, I would have expected time points of 0, 5.555, etc up to 50?

The delta between each time point is even on a grid:

   time, S1, S2

[[ 0, 0, 0], [ 0.309877, 1, 0], [ 0.394769, 2, 0], [ 0.418176, 3, 0], [ 0.470306, 2, 1], [ 0.592212, 3, 1], [ 0.75872, 4, 1], [ 0.760471, 5, 1], [ 0.815037, 6, 1], [ 0.928226, 7, 1]]

PS This code appears to work:

import tellurium as te
import numpy

r = te.loada ('''
    $Xo -> S1; k1 * Xo;
    S1 -> S2; k2*S1;
    S2 -> $X1; k3*S2;

    Xo = 50; S1 = 0; S2 = 0;
    k1 = 0.2; k2 = 0.4; k3 = 2;
''')

m = r.gillespie(0, 30)  #<-- no selection list
Updated 19/08/2017 04:20 16 Comments

Update meta data for value set

haffonist/igamt

Remove description remove comment add internal author note Add NA for extensibility, stability and content definition Move extensibility, stability and content definition, code systems to the definition tab. If NA for extensibility then definition is not editable.
Move PHINVADs description to pre-text field

Updated 15/08/2017 21:51

Next button doesn't do anything

haffonist/igamt

We creating a new IG, the pop-up box includes a “Next” button, but clicking it doesn’t do anything. You have to directly click on “Message Events” to switch screens (I assume that is what “Next” should do). I suggest you either enable the button or remove it completely (I don’t have a strong preference which one you do although the “Message Events” is pretty easy to miss)

image

Updated 15/08/2017 14:49 2 Comments

Multi word tags support

c0deLab/tech.soa.cmu.edu

@naher94 Need to change the structure for Tag front matter across the site to handle multi word tags. Use the following syntax:

tag: [Fabrication, CNC Routing]

I’ve already updated for the workshops entries.

Updated 08/08/2017 04:38 3 Comments

in route planner, route goes off to [0,0] and back for no apparent reason

bcgov/api-specs

https://routerdlv.api.gov.bc.ca/directions.json?apikey=11dd756f680c47b5aef5093d95543738&criteria=fastest&roundTrip=false&points=-133.7017906%2C59.5663764%2C-116.5130556%2C49.0975

response: {“routeDescription”:“”,“searchTimestamp”:“2017-08-05 17:52:49.509”,“executionTime”:3836,“version”:“1.4.0”,“disclaimer”:“http://www2.gov.bc.ca/gov/content/home/disclaimer”,“privacyStatement”:“http://www2.gov.bc.ca/gov/content/home/privacy”,“copyrightNotice”:“Copyright 2015 Province of British Columbia - Open Government License”,“copyrightLicense”:“http://www.data.gov.bc.ca/local/dbc/docs/license/OGL-vbc2.0.pdf”,“srsCode”:4326,“criteria”:“fastest”,“distanceUnit”:“km”,“points”:[[-133.70179,59.56638],[-116.51306,49.0975]],“routeFound”:true,“distance”:50.639,“time”:3142,“timeText”:“52 minutes 22 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5217,49.10667],[-116.52113,49.10629],[-116.52028,49.10566],[-116.51991,49.10529],[-116.5196,49.10486],[-116.51929,49.10423],[-116.51908,49.10283],[-116.51885,49.10171],[-116.51822,49.10057],[-116.51751,49.09912],[-116.51704,49.09824],[-116.51662,49.09779],[-116.51408,49.09778],[-116.51343,49.09777],[-116.51343,49.0975]],“directions”:[{“text”:“Continue onto Taku Dr for 350 m (29 seconds)”,“point”:[-133.7022,59.56631]},{“text”:“Turn slight right onto Mill St for 150 m (18 seconds)”,“point”:[-133.70308,59.56869]},{“text”:“Continue onto 1st St for 100 m (13 seconds)”,“point”:[-133.70225,59.56994]},{“text”:“Turn right onto Watson Ave for 80 m (7 seconds)”,“point”:[-133.70293,59.57087]},{“text”:“Turn slight left onto 2nd St for 450 m (39 seconds)”,“point”:[-133.7016,59.57113]},{“text”:“Turn right onto Discovery Ave for 750 m (54 seconds)”,“point”:[-133.70411,59.57484]},{“text”:“Continue onto Surprise Lake Rd for 1.2 km (55 seconds)”,“point”:[-133.69138,59.57711]},{“text”:“Turn right for 9.3 km (13 minutes 53 seconds)”,“point”:[-133.67076,59.58072]},{“text”:“Continue onto Sanca Creek FSR for 150 m (12 seconds)”,“point”:[-116.72495,49.37864]},{“text”:“Turn left onto Hwy 3A for 300 m (17 seconds)”,“point”:[-116.72638,49.37921]},{“text”:“Continue onto Sanca Creek Bridge for 45 m (2 seconds)”,“point”:[-116.72644,49.37657]},{“text”:“Continue onto Hwy 3A for 13 km (12 minutes 48 seconds)”,“point”:[-116.72664,49.37617]},{“text”:“Continue onto Boulder Creek Bridge for 35 m (2 seconds)”,“point”:[-116.65372,49.28291]},{“text”:“Continue onto Hwy 3A for 9.1 km (8 minutes 6 seconds)”,“point”:[-116.65361,49.28262]},{“text”:“Turn slight right onto Boulder Creek Bridge for 70 m (3 seconds)”,“point”:[-116.59646,49.21448]},{“text”:“Continue onto Hwy 3A for 13 km (10 minutes 9 seconds)”,“point”:[-116.59625,49.21386]},{“text”:“Continue onto Northwest Blvd for 2.4 km (2 minutes 43 seconds)”,“point”:[-116.52353,49.1186]},{“text”:“Turn left onto Vancouver St for 250 m (20 seconds)”,“point”:[-116.51662,49.09779]},{“text”:“Turn right onto 10th Ave for 30 m (2 seconds)”,“point”:[-116.51343,49.09777]},{“text”:“Finish!”,“point”:[-116.51343,49.0975]}]}

Updated 08/08/2017 19:15 2 Comments

Update text on landing page for unregistered users that have gone through Auth0 process

ClinGen/clincoded

When a potential user hits login but is not registered with us, they are prompted to create an Auth0 account. If they do so and try to log in, they reach a page that indicates the interfaces are only open to ClinGen users. Remove current text and change it to the following:


Note: If you do not wish to register for the interfaces, but want to explore a demo version of them, select the “Demo Login” menu option in the header, above. Your name will display as “ClinGen Test Curator” in the interfaces, along with others who use the “Demo Login.”

If you wish to continue registering your own account and display name, please follow the instructions below:

Step 1: Register your user name and password with Auth0, a third-party system that will manage your password √ Completed

Step 2: Request an account for the ClinGen interfaces by emailing clingen-helpdesk@lists.stanford.edu the following information:

  1. The email address associated with your newly created Auth0 account
  2. Preferred name for display in the ClinGen interfaces (first and last name)
  3. Any affiliation you have with ClinGen (note: a ClinGen affiliation is not required for use of the Variant Curation Interface)
  4. Intended use of ClinGen interface(s) – select all that apply:
  5. ClinGen curation activity
  6. Non-ClinGen variant curation (please note the Variant Curation Interface is open for public use but the Gene Curation Interface is currently restricted to use by ClinGen curators – contact ClinGen if you wish to collaborate on gene curation)
  7. Demo only exploration of the interfaces using test data and your own account and display name

Please contact us with any questions regarding registration at clingen-helpdesk@lists.stanford.edu.


Notes – we had √ Completed in green, if that’s possible (or some other icon)

If there is a way to patch this in it would be great as its possible there are people registering with Auth0 and being discouraged by the current message

Updated 19/08/2017 01:52 18 Comments

Create training machines

ISISComputingGroup/IBEX

In the week commencing 4th September, we will be running the IBEX and genie_python training courses alongside Mantid.

The CDF at RAL in the Atlas building has been selected as the venue. They have 14 training workstations and a central server that can be used to distribute software.

For practical purposes, it would be advantageous for each trainee to have a working copy of IBEX. Each workstation will need the following:

  • IBEX
    • Server
    • Client
    • genie_python
    • prerequisites (e.g. MySQL)
  • Utilities
    • Notepad++
  • Mantid

We suggest creating a standard machine image using hyper-v terminal and then deploy it to the target machines. Final configuration will be achieved using a script.

I suggest the following steps:

  1. Contact CDF
    1. Check this plan is feasible
    2. Establish the best way to transfer and deploy the machine image
  2. Create a clean Windows 7 image. Someone in the office with Windows 10 (suggest John) should be able to do this.
  3. Access the new machine and install the required software
    1. Check that IBEX runs as expected, especially scripting
    2. Pair with someone from Mantid to install and verify it
      • Mantid installation instructions: http://www.mantidproject.org/MBC_Getting_set_up
      • please install Latest Release 3.10.1 (the link is on that page)
  4. Add a configuration that contains everything needed for the genie_python course. This can be found in the user_manual repository.
  5. Write a script that will update the machine to work with a given instrument name. I expect it will need to do the following:
    1. Change the directory name in C:\Instrument\settings\configurations\....
    2. Change the name of the file originally C:\Instrument\settings\configurations\[Machine name]\Python\init_inst_name.py
  6. Export the machine image (again, you might need someone with hyper-v terminal to do this).
  7. Send the image to CDF as agreed
  8. Once the image has been deployed to the training machines, run the configuration script to update them to work with the new machine names
  9. Verify that the deployment has been successful. For example (but not limited to):
    1. Launch IBEX
    2. Check the DAE, configuration and blocks are accessed successfully
    3. Run a simple script
Updated 18/08/2017 11:09 3 Comments

--maxCores being respected?

BD2KGenomics/toil

Hello Toil team,

While testing Toil with bcbio_test_cwl we found out that passing, i.e --maxCores 1 to the commandline in run_toil.sh does not seem to enforce that limit.

I guess that, i.e, on torque/PBS systems I could just pass --maxCores N to #PBS -l ncpus=N and be done with it, but I wonder if you had any refactoring plans on that regard?

It is definitely a critical feature we need in order to limit bcbio’s use of cores and threads. We do it via ipyparallel and bcbio at the moment, but we would love to have this possibility in CWLToil too.

/cc @chapmanb @ohofmann

Updated 17/08/2017 20:08 2 Comments

msgpack exception when unpacking middle size network sent from traph through twisted

medialab/hyphe

When the corpus grows, the network computed by the traph can’t be sent back to the core anymore. Although it’s working like a charm for small corpora.

Problem occurred twice : 3337 web entities, 3561 pages crawled, 31972 pages discovered, 93010 links discovered 3364 web entities, 4388 pages crawled, 57417 pages discovered, 274329 links discovered

The client generates an extraData exception.

After checking around on the web, the extraData often pops out when corrupt data are passed on.

I’ve tried to serialized the network data in a file before sending it rhought msgpack/twisted. The file was correct (json format). I also tried a simple test to pack and unpack the serialized data with messagepack in a python console : works.

The data returned by the Traph is not a pure dict but a dict of counter objects. I tried to convert into pure dict but doesn’t change a thing (hopefully).

If we pass a pre-serialized version of the data (using json.dumps), the message does pass (although this breaks the rest of the client job of course).

So the problem seems to rely on a twisted / msgpack friction ?

ps: encoding exceptions are caused only by the error message logging data which I commented to generate the more precise stacktrace below

2017-08-02 17:29:35 [INFO - nantes-num-rique] Collecting WebEntities and WebEntityLinks...
2017-08-02 17:29:35 [INFO - nantes-num-rique] Traph client query: get_webentities_inlinks () {'include_auto': False}
2017-08-02 17:29:39 [INFO - nantes-num-rique] Unpack failed: error = 0
2017-08-02 17:29:39 [-] Unhandled error in Deferred:
2017-08-02 17:29:39 [-] (debug:  C: Deferred was created:
     C:  File "/home/pgi/.virtualenvs/hyphe/bin/twistd", line 11, in <module>
     C:    sys.exit(run())
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/scripts/twistd.py", line 29, in run
     C:    app.run(runApp, ServerOptions)
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 662, in run
     C:    runApp(config)
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/scripts/twistd.py", line 25, in runApp
     C:    _SomeApplicationRunner(config).run()
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 384, in run
     C:    self.postApplication()
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/scripts/_twistd_unix.py", line 262, in postApplication
     C:    self.startReactor(None, self.oldstdout, self.oldstderr)
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 396, in startReactor
     C:    self.config, oldstdout, oldstderr, self.profiler, reactor)
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 311, in runReactorWithLogging
     C:    reactor.run()
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/base.py", line 1243, in run
     C:    self.mainLoop()
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/base.py", line 1252, in mainLoop
     C:    self.runUntilCurrent()
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/base.py", line 878, in runUntilCurrent
     C:    call.func(*call.args, **call.kw)
     C:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/task.py", line 189, in start
     C:    deferred = self._deferred = defer.Deferred()
     I: First Invoker was:
     I:  File "/home/pgi/.virtualenvs/hyphe/bin/twistd", line 11, in <module>
     I:    sys.exit(run())
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/scripts/twistd.py", line 29, in run
     I:    app.run(runApp, ServerOptions)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 662, in run
     I:    runApp(config)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/scripts/twistd.py", line 25, in runApp
     I:    _SomeApplicationRunner(config).run()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 384, in run
     I:    self.postApplication()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/scripts/_twistd_unix.py", line 262, in postApplication
     I:    self.startReactor(None, self.oldstdout, self.oldstderr)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 396, in startReactor
     I:    self.config, oldstdout, oldstderr, self.profiler, reactor)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/application/app.py", line 311, in runReactorWithLogging
     I:    reactor.run()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/base.py", line 1243, in run
     I:    self.mainLoop()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/base.py", line 1255, in mainLoop
     I:    self.doIteration(t)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/epollreactor.py", line 235, in doPoll
     I:    log.callWithLogger(selectable, _drdw, selectable, fd, event)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/log.py", line 103, in callWithLogger
     I:    return callWithContext({"system": lp}, func, *args, **kw)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/log.py", line 86, in callWithContext
     I:    return context.call({ILogContext: newCtx}, func, *args, **kw)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/context.py", line 122, in callWithContext
     I:    return self.currentContext().callWithContext(ctx, func, *args, **kw)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/context.py", line 85, in callWithContext
     I:    return func(*args,**kw)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/posixbase.py", line 597, in _doReadOrWrite
     I:    why = selectable.doRead()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/unix.py", line 191, in doRead
     I:    return self._dataReceived(data)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/tcp.py", line 214, in _dataReceived
     I:    rval = self.protocol.dataReceived(data)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/endpoints.py", line 125, in dataReceived
     I:    return self._wrappedProtocol.dataReceived(data)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/protocols/basic.py", line 454, in dataReceived
     I:    self.lineReceived(line)
     I:  File "/home/pgi/dev/hyphe/hyphe_backend/traph/client.py", line 321, in lineReceived
     I:    self.deferred.errback(e)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 500, in errback
     I:    self._startRunCallbacks(fail)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 567, in _startRunCallbacks
     I:    self._runCallbacks()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 653, in _runCallbacks
     I:    current.result = callback(current.result, *args, **kw)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 1442, in gotResult
     I:    _inlineCallbacks(r, g, deferred)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 1432, in _inlineCallbacks
     I:    deferred.errback()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 500, in errback
     I:    self._startRunCallbacks(fail)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 567, in _startRunCallbacks
     I:    self._runCallbacks()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 653, in _runCallbacks
     I:    current.result = callback(current.result, *args, **kw)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 1442, in gotResult
     I:    _inlineCallbacks(r, g, deferred)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 1432, in _inlineCallbacks
     I:    deferred.errback()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 500, in errback
     I:    self._startRunCallbacks(fail)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 567, in _startRunCallbacks
     I:    self._runCallbacks()
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/defer.py", line 653, in _runCallbacks
     I:    current.result = callback(current.result, *args, **kw)
     I:  File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/task.py", line 236, in eb
     I:    d.errback(failure)
    )
    Traceback (most recent call last):
    Failure: msgpack.exceptions.UnpackValueError: Unpack failed: error = 0

2017-08-02 17:29:39 [INFO - nantes-num-rique] 'NoneType' object has no attribute 'callback'
2017-08-02 17:29:39 [TraphClientProtocol,client] Unhandled Error
    Traceback (most recent call last):
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/log.py", line 103, in callWithLogger
        return callWithContext({"system": lp}, func, *args, **kw)
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/log.py", line 86, in callWithContext
        return context.call({ILogContext: newCtx}, func, *args, **kw)
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/context.py", line 122, in callWithContext
        return self.currentContext().callWithContext(ctx, func, *args, **kw)
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/python/context.py", line 85, in callWithContext
        return func(*args,**kw)
    --- <exception caught here> ---
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/posixbase.py", line 597, in _doReadOrWrite
        why = selectable.doRead()
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/unix.py", line 191, in doRead
        return self._dataReceived(data)
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/tcp.py", line 214, in _dataReceived
        rval = self.protocol.dataReceived(data)
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/internet/endpoints.py", line 125, in dataReceived
        return self._wrappedProtocol.dataReceived(data)
      File "/home/pgi/.virtualenvs/hyphe/local/lib/python2.7/site-packages/twisted/protocols/basic.py", line 454, in dataReceived
        self.lineReceived(line)
      File "/home/pgi/dev/hyphe/hyphe_backend/traph/client.py", line 321, in lineReceived
        self.deferred.errback(e)
    exceptions.AttributeError: 'NoneType' object has no attribute 'errback'

2017-08-02 17:29:39 [-] Stopping factory <hyphe_backend.traph.client.TraphClientFactory instance at 0x7f6c353dc3f8>
Updated 02/08/2017 15:49

Users are unable to change their password in fat-client mode

RechercheTech/mss

Students are unable to change their passwords on their own when booting into fat-client mode.

After hitting OK if the password is unacceptable due to rules then it reverts but if the password is a qualifying one there is no revert and it continues waiting or even if it returns with an affirmative, the password remains unchanged. Have also tried logging off, rebooting and relogin after a password change attempt.

Password change does not work through terminal also, it appears to do so but it doesn’t.

Users being able to easily change their own password is critical to the workflow and ease of use of the MSS.

How can we make that happen even if we have to make it happen via the terminal? One method is by user doing a ssh to the server. Need something simpler.

Updated 31/07/2017 10:06 2 Comments

File paths have C:\ 2 times

KeitIG/museeks

When i try to play a song, it gives me that error (with lastest update): Uncaught Error: ENOENT: no such file or directory, open ‘C:\C:\Users\Cocon\Music\Uptown Funk.mp3’ events.js:160

Updated 13/08/2017 12:21 7 Comments

Formulate and implement grid "coarsening", probably as re-meshing

geo-fluid-dynamics/phaseflow-fenics

FEniCS does not have any native support for grid coarsening, which I label as the major drawback when compared to deal.II.

Without coarsening, we will be wasting the majority of computations as the PCI evolves away from its previous positions.

While we cannot directly “coarsen” the mesh, it seems reasonable to me to simply re-mesh, adaptively sampling the existing solution from the previous fine mesh onto the new mesh. I actually did something like this with deal.II when I was moving the mesh in https://github.com/geo-fluid-dynamics/peclet, when the heat source’s position was updated by https://github.com/geo-fluid-dynamics/heat-source-trajectory-pcm

We probably want to begin with re-meshing at some specified time interval, since obviously doing this frequently will kill performance.

Updated 17/08/2017 09:54 2 Comments

In route tab, a previous route is sometimes left on the map when a new route is displayed

bcgov/ols-devkit

Pick a random start point around the greater victoria area. Repeatedly pick a random end point. Eventually, you will get a previous route left on the map. I have had multiple previous routes left on the map after about thirty random end points. It appears to have something to do with random points that are near the boundary of the map view.

Updated 11/08/2017 05:42 2 Comments

ETA to completion

davidedelvento/runnerup

It would be nice to have a audio cue which will tell how long it’ll be to completion, assuming everything goes as scheduled: if all the intervals will take the allotted time, or if that distance will be completed at the expected pace. Bonus point if the info is optionally adjusted for “how well we did so far”, i.e. if one has been 30% slower/faster than what scheduled so far, than the time to completion is adjusted accordingly.

Updated 10/08/2017 03:28 2 Comments

Add FROGS to gvl

gvlproject/gvl.ansible.playbook

I’ve a lot of interest from GVL users to get the French metagenomics pipeline frogs into Galaxy. Unfortunately, it is not in the tool shed and would be very difficult to get in there due mainly to the way the software is structured (it is quite poor). Therefore an ansible script would be required to install it. It will need to be installed on GVL’s with the command-line install option.. It is not for the faint hearted!

Updated 26/07/2017 02:19 1 Comments

Adjust pace by elevation gain/loss

davidedelvento/runnerup

In the graph, and/or in the audio cues.

Add either or both

  • Daniels rule Work by Jack Daniels, of Daniels Running Formula fame, produced a “rule of thumb” described by Daniels several years ago online. His rule states that every percent gradient of incline (going uphill) will slow you by 12-15 seconds per mile, and every percent gradient of decline (going downhill) will aid you by 8 seconds per mile.

  • Kellogg rule John Kellogg, of LetsRun fame had a simpler rule. Every 10 feet of elevation change alters your time by 1.74 seconds, regardless of the horizontal distance covered, and if going up or down (of course this is an approximation)

See https://runnersconnect.net/hill-running-training/

Updated 10/08/2017 03:29

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