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PhenoMeNal Cloud Research Environment

Home Page: http://portal.phenomenal-h2020.eu

TypeScript 70.19% JavaScript 0.42% HTML 23.18% CSS 6.21%

ng2-phenomenal-portal's Introduction

Angular PhenoMeNal Portal

This project was generated with angular-cli.

Development server

To setup a development environment:

update the URLs of the portal back-ends within the proxy.config.json configuration file;
run ng serve --proxy-config proxy.config.json [--port <PORT>] [--host <HOST>] for a dev server (default HOST is localhost; default PORT is 3000).

Navigate to http://<HOST>:<PORT>/.

The app will automatically reload if you change any of the source files.

Code scaffolding

Run ng generate component component-name to generate a new component. You can also use ng generate directive/pipe/service/class/module.

Build

Run ng build to build the project. The build artifacts will be stored in the dist/ directory. Use the -prod flag for a production build.

Running unit tests

Run ng test to execute the unit tests via Karma.

Running end-to-end tests

Run ng e2e to execute the end-to-end tests via Protractor. Before running the tests make sure you are serving the app via ng serve.

Deploying to GitHub Pages

Run ng github-pages:deploy to deploy to GitHub Pages.

Further help

To get more help on the angular-cli use ng help or go check out the Angular-CLI README.

ng2-phenomenal-portal's People

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lucalianas kikkomep

ng2-phenomenal-portal's Issues

Link highlight colour used in page footer makes font invisible

The links in the footer are highlighted when the cursor hovers over them. The highlight colour is almost the same as the font colour, making the text almost invisible.

Deployment blocked "Removing existing application"

Deployment gets stuck "Removing existing application" if a user has performed previously deployed Cerebellin. User needs to remove the application manually to get the deployment to proceed.

Deployment to OpenStack stuck at `"Validating credentials..."`

Hi, I am trying to deploy to Giessen using
https://portaldev.phenomenal-h2020.eu/cloud-research-environment-setup

but I am stuck at "Validating credentials..." until the timeout.
This is different from #21, where I didn't get flavours. Yours, Steffen

Hardcoded "phenomenal.cloud" domain

Hi,
there are two places where the phenomenal.cloud domain is hardcoded:

ng2-phenomenal-portal/src/app/shared/service/deployer/deployment.ts

Line 383 in 0a09537

    
           deployment['galaxyUrl'] = protocol + 'galaxy' + separator + deployment['assignedInputs'][i]['assignedValue'] + '.phenomenal.cloud';

ng2-phenomenal-portal/documentation/components/CreDashboardComponent.html

Line 2052 in 760c794

    
           deployment[&#x27;galaxyUrlName&#x27;] &#x3D; &#x27;http://galaxy.&#x27; + deployment[&#x27;assignedInputs&#x27;][i][&#x27;assignedValue&#x27;] + &#x27;.phenomenal.cloud&#x27;;

As long as that is the case, one has to manually navigate to the PhenoMeNal services
like Galaxy or Jupyter if the Cloudflare zone is not phenomenal.cloud

Yours,
Steffen

Empty flavours in Giessen (again)

Hi, it seems the issue #21 has resurfaced. The portaldev can successfully authenticate,
but flavours / networks are empty. Tested on firefox and chrome.
Console shows
Failed to load resource: the server responded with a status of 401 (https://api.portal.tsi.ebi.ac.uk/application/)

I tried both my existing and working RC file, and a fresh openstackrc,
but manually comparing the file and also the OS_* variable shows no differences between the two.
The OpenStack in Giessen has recently been upgraded to the queens release.
A deployment to Bielefeld worked directly afterwards.

Yours, Steffen

More precise time requirement indication

While the CRE is being deployed, the user gets to see a message that says

"This may take a while, please be patient"

It would be better to give an idea of how much time to expect. We could say something like

"It's normal for this to take 15 minutes or more.  Please be patient"

RC file parsing does not take comments properly into account

Hi, for debugging purposes I had this RC file, which included a commented-out OS_AUTH_URL

#!/usr/bin/env bash

# To use an OpenStack cloud you need to authenticate against the Identity
[...]
# Image API v1.1, Block Storage API v2, and Compute API v2.0. OS_AUTH_URL is
# only for the Identity API served through keystone.

#export OS_AUTH_URL=https://cloud.computational.bio.uni-giessen.de:35357/v3
export OS_AUTH_URL=https://cloud.computational.bio.uni-giessen.de:5000/v3
[...]

It seems that https://github.com/phnmnl/ng2-phenomenal-portal/blob/develop/src/app/shared/service/cloud-provider-metadata/cloud-provider-metadata.service.ts#L99 is happily extracting the value from the commented-out line, which goes to a non-reachable port, causing a timeout. I can verify by swapping
the ports, putting the invalid URL into the normal line (sic!), and the real one is commented out.

Apparently the "remove all comments" in https://github.com/phnmnl/ng2-phenomenal-portal/blob/develop/src/app/shared/service/cloud-provider-metadata/cloud-provider-metadata.service.ts#L89 does not do its job ?!
Yours, Steffen

Provide links to tool collections based on search or tags

Hi portal team, if I go to the https://portal.phenomenal-h2020.eu/app-library I can search some term, e.g. "isa" and see the matching tools. Can I also have a link to a query ? like https://portal.phenomenal-h2020.eu/app-library/search/isa ? Or similarily, link to tags, as in https://portal.phenomenal-h2020.eu/app-library/tag/preprocessing+raman+glycomics ? Yours, Steffen

Bottom shadow missing on partner provider "button"

On the "Create new CRE" page, the partner provider button at the bottom of the page has not bottom shadow (unlike the "regular" cloud provider buttons)

On Enter press "Next" when entering openstack password in portal

Currently if I enter Password in text field (OpenStack deployment) and press "Enter" my browser presses "Previous" and not "Next". Google Chrome on Ubuntu 16.04

Advanced deployment parameter configuration on OpenStack seems broken

Trying a to configure advanced parameters for a deployment on EBI's OpenStack cloud. The "Deploy" button never gets activated.

Warn user when closing tab before deployment request is fully transmitted

When creating a new deployment there's a time window between when the user clicks the "Deploy" button and when the deployment action has been successfully transmitted to the TSI portal, during which closing the tab will cause the user to lose the deployment attempt.

A workable solution would be to have the browser popup a confirmation prompt if the user tries to close the tab before it's safe to do so.

Galaxy link on new deployment box doesn't take to login page

Currently, the Galaxy link for a new deployment points to the base galaxy URL, which means that the user isn't prompted to authenticate. The link should be modified to point to ..../login

Enhancement: Follow logfiles / scroll to end

Hi, it is not very convenient to follow a deployment logfile.
It would be great to have an "scroll-to-end" button/arrow,
and/or have a "scroll/follow end of log" button, like on travis:
https://travis-ci.org/sneumann/mzR/
Yours, Steffen

Portal portability

We'd be keen on the ability to have independent portal deployments.

The blocker issue here is the portal's dependence on the TSI portal for its CRE deployment functionality.

Other portal components are already nicely containerized and configurable and can be easily deployed on any cluster.

AWS credential verification slow

When creating a deployment on AWS, I click "Next" after inserting my credentials in the "Please insert your Cloud Provider credentials" page. There is a noticeable lag before the portal advances to the next page. Moreover, if one clicks "next" again before the next page is presented, the portal will practically skip over the "Setup your Cloud instances" page using default values and go to the third page of the procedure.

Dalcotidine deployment configures version "Cerebellin" on TSI portal

When verifying the configuration of a deployment through the TSI portal web site (by clicking on the "i") I get this configuration:

Phenomenal Virtual Research Environment/Cloud

Source
https://github.com/phnmnl/cloud-deploy-kubenow-dalcotidine.git

Version
2.0-Cerebellin-20180628```

portal sometimes fails to record deployment creation time

Not quite sure exactly under what conditions, but I see that the portal sometimes records that a deployment attempt was made (creates a new row in the deployment table) but leaves the created field NULL

Configuring Network while instead already deploying containers

Hi, the bold status line says Configuring network while in fact
we are already deploying containers wait for galaxyphnlkd1oq to be responding.
Yours, Steffen

Integrate SSO

Only the last occurance of a value in RC file should be considered

Hi, if a user had

OS_AUTH="first"
OS_AUTH="second"

she'd expect "second" to be the authoritative value.
Yours, Steffen

Move feedback link from Help section to footer

The feedback/suggestions link is currently hidden in the "Help" section. We should move it down to the Footer.

Progress bar is totally off

The "weights" that represent the portion of the progress bar to advance with each respective step of the deployment procedure don't reflect reality. I'm currently looking at a deployment that is risking timing out on one of the last steps (waiting for Galaxy) and the progress bar has advanced maybe 5% of the way to full.

Destroy process marked as failed on Portal when in fact it was succesfull at EBI Portal

Currently happening for this AWS deployment:

https://portal.tsi.ebi.ac.uk/deployments/TSI1519745447731

Destroy logs say:

data.template_file.instance_bootstrap: Refreshing state...

data.aws_ami.kubenow: Refreshing state...

aws_ebs_volume.extra_disk: Refreshing state... (ID: vol-0404b0df2b51d12c7)

aws_vpc.created: Refreshing state... (ID: vpc-446cc222)

aws_key_pair.main: Refreshing state... (ID: phguxqo3-keypair)

aws_internet_gateway.main: Refreshing state... (ID: igw-75af2412)

aws_subnet.created: Refreshing state... (ID: subnet-e1925687)

aws_security_group.main: Refreshing state... (ID: sg-3056c94a)

aws_route_table.main: Refreshing state... (ID: rtb-7c877e05)

aws_main_route_table_association.main: Refreshing state... (ID: rtbassoc-cbfc7eb3)

aws_route_table_association.main: Refreshing state... (ID: rtbassoc-48fa7830)

aws_instance.instance: Refreshing state... (ID: i-0cd590bb6c2e7535d)

data.template_file.instance_bootstrap: Refreshing state...

data.template_file.instance_bootstrap: Refreshing state...

data.template_file.instance_bootstrap: Refreshing state...

aws_instance.instance: Refreshing state... (ID: i-0b489725fbbc41e2e)

aws_instance.instance.1: Refreshing state... (ID: i-09772657d3904b957)

aws_instance.instance.0: Refreshing state... (ID: i-0d0c336dce6ad4228)

cloudflare_record.rec.3: Refreshing state... (ID: e43515732e635493037c23c249be54e9)

cloudflare_record.rec.1: Refreshing state... (ID: 9dcea0b1aef9d727a83939546d8cdce3)

cloudflare_record.rec.2: Refreshing state... (ID: c0aecc672b615556d06959a5ffb11d78)

cloudflare_record.rec: Refreshing state... (ID: b38829c6c492894ee1a99692f32f4f49)

aws_volume_attachment.attach_extra_disk: Refreshing state... (ID: vai-2653721439)

null_resource.generate-inventory: Refreshing state... (ID: 143053489815075686)

module.edge.data.template_file.instance_bootstrap: Destroying... (ID: 4c4eae9a9bd338232d61c881f6a444dcbfc8f9db3b52f802fdb3b359141cd73e)

module.edge.data.template_file.instance_bootstrap: Destruction complete

module.cloudflare.cloudflare_record.rec.1: Destroying... (ID: 9dcea0b1aef9d727a83939546d8cdce3)

module.cloudflare.cloudflare_record.rec.2: Destroying... (ID: c0aecc672b615556d06959a5ffb11d78)

module.cloudflare.cloudflare_record.rec: Destroying... (ID: b38829c6c492894ee1a99692f32f4f49)

module.generate-inventory.null_resource.generate-inventory: Destroying... (ID: 143053489815075686)

module.cloudflare.cloudflare_record.rec.3: Destroying... (ID: e43515732e635493037c23c249be54e9)

module.generate-inventory.null_resource.generate-inventory: Destruction complete

module.cloudflare.cloudflare_record.rec.1: Destruction complete

module.cloudflare.cloudflare_record.rec: Destruction complete

module.cloudflare.cloudflare_record.rec.3: Destruction complete

module.cloudflare.cloudflare_record.rec.2: Destruction complete

module.node.aws_instance.instance.1: Destroying... (ID: i-09772657d3904b957)

module.node.aws_instance.instance.0: Destroying... (ID: i-0d0c336dce6ad4228)

module.glusternode.aws_volume_attachment.attach_extra_disk: Destroying... (ID: vai-2653721439)

module.subnet.aws_route_table_association.main: Destroying... (ID: rtbassoc-48fa7830)

module.subnet.aws_main_route_table_association.main: Destroying... (ID: rtbassoc-cbfc7eb3)

module.subnet.aws_main_route_table_association.main: Destruction complete

module.subnet.aws_route_table_association.main: Destruction complete

module.subnet.aws_route_table.main: Destroying... (ID: rtb-7c877e05)

module.subnet.aws_route_table.main: Destruction complete

module.subnet.aws_internet_gateway.main: Destroying... (ID: igw-75af2412)

module.node.aws_instance.instance.0: Still destroying... (ID: i-0d0c336dce6ad4228, 10s elapsed)

module.node.aws_instance.instance.1: Still destroying... (ID: i-09772657d3904b957, 10s elapsed)

module.glusternode.aws_volume_attachment.attach_extra_disk: Still destroying... (ID: vai-2653721439, 10s elapsed)

module.glusternode.aws_volume_attachment.attach_extra_disk: Destruction complete

module.glusternode.aws_instance.instance: Destroying... (ID: i-0b489725fbbc41e2e)

module.glusternode.aws_ebs_volume.extra_disk: Destroying... (ID: vol-0404b0df2b51d12c7)

module.glusternode.aws_ebs_volume.extra_disk: Destruction complete

module.subnet.aws_internet_gateway.main: Still destroying... (ID: igw-75af2412, 10s elapsed)

module.node.aws_instance.instance.1: Still destroying... (ID: i-09772657d3904b957, 20s elapsed)

module.node.aws_instance.instance.0: Still destroying... (ID: i-0d0c336dce6ad4228, 20s elapsed)

module.glusternode.aws_instance.instance: Still destroying... (ID: i-0b489725fbbc41e2e, 10s elapsed)

module.subnet.aws_internet_gateway.main: Still destroying... (ID: igw-75af2412, 20s elapsed)

module.node.aws_instance.instance.1: Still destroying... (ID: i-09772657d3904b957, 30s elapsed)

module.node.aws_instance.instance.0: Still destroying... (ID: i-0d0c336dce6ad4228, 30s elapsed)

module.glusternode.aws_instance.instance: Still destroying... (ID: i-0b489725fbbc41e2e, 20s elapsed)

module.subnet.aws_internet_gateway.main: Still destroying... (ID: igw-75af2412, 30s elapsed)

module.node.aws_instance.instance.1: Still destroying... (ID: i-09772657d3904b957, 40s elapsed)

module.node.aws_instance.instance.0: Still destroying... (ID: i-0d0c336dce6ad4228, 40s elapsed)

module.node.aws_instance.instance.1: Destruction complete

module.node.aws_instance.instance.0: Destruction complete

module.node.data.template_file.instance_bootstrap: Destroying... (ID: e133ec1a3624947166afb32a9c0edf528b24c095b7f5cc17e2cc83a8caafb508)

module.node.data.template_file.instance_bootstrap: Destruction complete

module.glusternode.aws_instance.instance: Still destroying... (ID: i-0b489725fbbc41e2e, 30s elapsed)

module.glusternode.aws_instance.instance: Destruction complete

module.glusternode.data.template_file.instance_bootstrap: Destroying... (ID: b53f4eae9b4134112772f0885c889ceeadeeacd7106f10aa67a864fe237e3cc4)

module.glusternode.data.template_file.instance_bootstrap: Destruction complete

module.master.aws_instance.instance: Destroying... (ID: i-0cd590bb6c2e7535d)

module.subnet.aws_internet_gateway.main: Still destroying... (ID: igw-75af2412, 40s elapsed)

module.master.aws_instance.instance: Still destroying... (ID: i-0cd590bb6c2e7535d, 10s elapsed)

module.subnet.aws_internet_gateway.main: Still destroying... (ID: igw-75af2412, 50s elapsed)

module.master.aws_instance.instance: Still destroying... (ID: i-0cd590bb6c2e7535d, 20s elapsed)

module.subnet.aws_internet_gateway.main: Still destroying... (ID: igw-75af2412, 1m0s elapsed)

module.subnet.aws_internet_gateway.main: Destruction complete

module.master.aws_instance.instance: Still destroying... (ID: i-0cd590bb6c2e7535d, 30s elapsed)

module.master.aws_instance.instance: Destruction complete

data.aws_ami.kubenow: Destroying... (ID: ami-f5f4ec93)

data.aws_ami.kubenow: Destruction complete

module.subnet.aws_subnet.created: Destroying... (ID: subnet-e1925687)

module.security_group.aws_security_group.main: Destroying... (ID: sg-3056c94a)

module.master.data.template_file.instance_bootstrap: Destroying... (ID: 3a4ef9de9ba7646dec1f405a62654cb500ea386a82d2e395b2f4015036b743a0)

module.keypair.aws_key_pair.main: Destroying... (ID: phguxqo3-keypair)

module.master.data.template_file.instance_bootstrap: Destruction complete

module.keypair.aws_key_pair.main: Destruction complete

module.subnet.aws_subnet.created: Destruction complete

module.security_group.aws_security_group.main: Destruction complete

module.vpc.aws_vpc.created: Destroying... (ID: vpc-446cc222)

module.vpc.aws_vpc.created: Destruction complete
Destroy complete! Resources: 24 destroyed.

This is from a deployment that failed (see slack channel at around 3:46 PM UK time on 27/02/18)

Cache invalidation issue

The portal has a problem with caching on the user side. When code updates are deployed, the update isn't downloaded by the client (they need to clear their cache to trigger a download). This might also be related to the problems we've see with images not being loaded -- it looks like the server is returning HTTP 304 in those cases (NOT MODIFIED).

Deployment of different PhenoMeNal releases partly broken

If one tries to deploy release A while having previous deployment of release B, the portal will silently deploy release B.

FAQ shouldn't be hardcoded in ng2 project

The content available at https://portal.phenomenal-h2020.eu/help/faq is currently hard coded here apparently. The FAQ should be populated very much in the same way that the wiki and app library pages are, which depend on content populated and independently updated from the phenomenal git repos.

Deployment fails on deNBI/Bielefeld

I just tried https://portaldev.phenomenal-h2020.eu/cloud-research-environment-setup in Bielefeld, and was unfortunately not very successful: I didn't get past the Verify.
OS credentials have been checked, local cloud-deploy-kubenow works nicely. Yours, Steffen

Deployment: initially logfile button/link undefined

Hi,
for a fresh deployment, log file button points to
https://portaldev.phenomenal-h2020.eu/logs?id=undefined
and only after the instances are up changes to
https://portaldev.phenomenal-h2020.eu/logs?id=TSI15.......87

-> Button should be disabled / Waiting for logfiles or the
id=undefinedpage should have static content "will be available in a few minutes".

Yours, Steffen

Make CRE list more informative when it's empty

The CRE list isn't very informative when it's empty. People who don't understand what the "+" means right away might feel lost.

I suggest:

change the page title/header to "Your Cloud Research Environments";
consider, when the list is empty, placing a note that tells the user to "click on the '+' to create a new CRE"

Galaxy admin credentials not set

Hi, I just created an instance from portaldev on Amazon (TSI1519243606387).
After the deployment, my https://portaldev.phenomenal-h2020.eu/cloud-research-environment-dashboard
showed the admin eMail and Password-Key-Button. I could not log into Galaxy
with these credentials. I could add (register) a new user in Galaxy
with sneumann(at)ipb-halle.de which otherwise I would expect to collide
with the automated one. Yours, Steffen

Check password strength

Consider informing the user about the strength of the password they're setting for their new instance. A simple warning for weak passwords might suffice.

This issue was brought up by @sneumann in KubeNow.

Deployment fails on deNBI/Giessen

I tried to deploy in Giessen, and got past the Verify, but still stuck with no flavours, which is the old issue we've had already last year. Need to dig up the diagnostics we had back then. CLI cloud-deploy-kubenow works nicely. Yours, Steffen

Spelling error: ‘OPPS no app found”

Deployment status needs to give users more info

The deployment progress bar should probably be accompanied by a list of steps that are completed sequentially, with some rough time estimate for each, including an overall time estimate. This data could be drawn from the logs file that the tsi portal can inspect (which I presume must be available through some API call).

We should also display a deployment ID that is not very notorious, but that would make it into any screenshot that the user uses for reporting a problem. This will allow us to map error reports with the files made available on the slack channel for deployment errors.

App Library tick boxes should implement AND query

The current logic in the app library ORs the tick boxes together, rather than ANDing them.