inveniosoftware/invenio

Invenio digital library framework

Dan Granville

@dfdan

hcvlg

Daniel Kopecký

@Semtexcz

Hi all, I am writing new extension for Invenio (https://github.com/oarepo/invenio-taxonomies). In setup.py, I have dependency on our wrapper for installing Invenio (https://github.com/oarepo/oarepo).

I tried to init invenio database in my venv:

invenio db init

And I got this responce (traceback):

Traceback (most recent call last):
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/bin/invenio", line 8, in <module>
    sys.exit(cli())
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/flask/cli.py", line 586, in main
    return super(FlaskGroup, self).main(*args, **kwargs)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/decorators.py", line 21, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/flask/cli.py", line 426, in decorator
    return __ctx.invoke(f, *args, **kwargs)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/flask_migrate/cli.py", line 31, in init
    _init(directory, multidb)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/flask_migrate/__init__.py", line 96, in wrapped
    f(*args, **kwargs)
  File "/home/semtex/GoogleDrive/Projekty/Pracovní/oarepo/invenio-taxonomies/venv/lib/python3.8/site-packages/flask_migrate/__init__.py", line 126, in init
    directory = current_app.extensions['migrate'].directory
KeyError: 'migrate'

For complete imformation, here is pip list:

https://pastebin.com/54KPXD5v

Does anybody know, why I got error that Flask-Migrate is missing in extensions, altough it is in pip list? Invenio shell is working and current_app.extensions are following: https://pastebin.com/XwYfvTex

1 reply

Lars Holm Nielsen

@lnielsen

Invenio-DB uses Flask-Alembic instead of Flask-Migrate for configuring Alembic, so that’s likely why……..

alternatively, it might be you can register Flask-Migrate on the Invenio application……not sure if it’s going to working, but it might

Mirek Simek

@mesemus

Hi folks, I've added a pull request for invenio-jsonschemas - handling nested allOf + fixing isort build problems. Please consider merging. Thanks.

Lars Holm Nielsen

@lnielsen

:+1:

ugswork

@ugswork

@ntarocco In my application using Invenio v3.3, I am trying to add/change styles. In which file should i add the changes in virtualenv and run any command (like invenio webpack buildall)? I tried adding them to styles.scss in virtualenv. They don't get picked up. Thank you.

Lars Holm Nielsen

@lnielsen

Heads up

We are planning a move from Gitter to Discord as the primary chat application for Invenio projects. We have been testing out Discord for the past months on the InvenioRDM project. Gitter development has been staled for quite some time, and the applications (desktop/mobile) is at often buggy. In addition to a more stable application, Discord have integrated video calls. We are planning an official move during the coming week. Instructions will be posted here and on inveniosoftware.org on how to gain access to Discord.

Eugenio Corso

@EugenioCorso

@ntarocco In my application using Invenio v3.3, I am trying to add/change styles. In which file should i add the changes in virtualenv and run any command (like invenio webpack buildall)? I tried adding them to styles.scss in virtualenv. They don't get picked up. Thank you.

i have the same issue when i deploy the app with the docker-compose.full.yml, i have modified the css in my_site/theme/assets/scss/my_site/theme.scss, added some js files in my_site/theme/assets/js/my_site/ and finally added images in my_site/theme/static/images but none of this are found

Volodymyr Kushnarenko

@vkush

@osoo_gitlab Invenio comes with an object store API, so filenames are in fact “keys” that can contain slashes etc, that you could use to build a file hierarchy
:point_up: 7. Juli 2020 17:35

Dear community, do we have already some module to represent a file hierarchy in GUI (e.g. like in Dataverse - http://guides.dataverse.org/en/latest/user/dataset-management.html#file-path)? Is such implementation planned in InvenioRDM? Currently I can not find some real Invenio Instance, which has a file hierarchy in GUI (folders, subfolders). Many thanks in advance. It is an important feature for preservation of digital legacy materials in archives.

Lars Holm Nielsen

@lnielsen

@vkush Each object in the object store (Invenio-Files-REST) defines a key. Most of the time, this is simply a filename, however it can include a path components (e.g. afolder/bfolder/myfile.txt) so that you can represent a directory structure

In the rendering of the landing page (UI side of things), there’s no special rendering implemented. It would be up to you to implement.

That said, many times a Zip file does as good a job - we’re displaying the file hierarchy in the previewer and it’s easy to download + zip is good for preservation

also, in terms of preservation, actually single files without structure is much easier to preserve because you remove complexity of direcotry structure above it.

Mirek Simek

@mesemus

Hi folks, one enhancement question: would it be possible to add extra signals during invenio loading? We already have app_loaded (at https://github.com/inveniosoftware/invenio-base/blob/master/invenio_base/app.py#L123) and for my use-case (modifying RECORDS_REST_ENDPOINTS dynamically after extensions are loaded but before loading blueprints) it would be great to have extensions_loadedand maybe even config_loaded. If it makes sense I'd create an issue and pull request. thanks.

Lars Holm Nielsen

@lnielsen

Have you tried to see if blueprint.record() or blueprint.record_once() could be used? But yes, in principle we could add the signals: app_config_loaded, app_converters_loaded, app_extensions_loaded

Mirek Simek

@mesemus

Unfortunately these I can not use - I cat get the blueprint too late when it is already registered within the application and thus unmodifiable. I've added an issue inveniosoftware/invenio-base#156 and will prepare a pull request if it helps. Thanks.

Sébastien Délèze

@sebastiendeleze

Hi, when a SVG file is uploaded with invenio-files-rest, the mime type is well guessed:

{
    "links": {
        "self": "https://localhost:5000/api/files/2615f001-65a8-4ece-85da-87d120bcc7f7/logo.svg",
        "version": "https://localhost:5000/api/files/2615f001-65a8-4ece-85da-87d120bcc7f7/logo.svg?versionId=8e455c6c-cb34-444a-9fed-21abd3cca4af",
        "uploads": "https://localhost:5000/api/files/2615f001-65a8-4ece-85da-87d120bcc7f7/logo.svg?uploads"
    },
    "is_head": true,
    "delete_marker": false,
    "version_id": "8e455c6c-cb34-444a-9fed-21abd3cca4af",
    "created": "2020-09-01T09:29:22.312312+00:00",
    "tags": {},
    "mimetype": "image/svg+xml",
    "checksum": "md5:8fef00abde7378bed4e9de313fe7cfe3",
    "updated": "2020-09-01T09:29:22.327441+00:00",
    "key": "logo.svg",
    "size": 1294
}

But when trying to get the file, the mime type is text/plain. I think it's because image/svg+xml is not present in the MIMETYPE_WHITELIST list. I would be great if this whitelist could be configured per project.

Nicola

@ntarocco

@sebastiendeleze what do you mean with I would be great if this whitelist could be configured per project.?

You can se tthe MIMETYPE_WHITELIST variable if you need

Sébastien Délèze

@sebastiendeleze

@ntarocco Thanks for you answer, but MIMETYPE_WHITELIST is defined in file helpers.py and is not configurable. I think it should be in config.py, and MIMETYPE_TEXTFILES, MIMETYPE_PLAINTEXT, too.

Johnny Mariéthoz

@jma

Hello if I have invenio-userprofile installed can my users can log to the system with the username instead of the email address?

Johnny Mariéthoz

@jma

Hello I try to use invenio-accounts 1.3 REST API. I post a JSON request to the https://localhost:5000/api/login but I go an error that suggest that I have a problem with Flask-Login which defined /api/login/ and invenio-accounts that defines /api/login. Here is the error: flask.debughelpers.FormDataRoutingRedirect: b'A request was sent to this URL (https://localhost:5000/api/login) but a redirect was issued automatically by the routing system to "https://localhost:5000/api/login/". Any idea?

Zacharias Zacharodimos

@zzacharo

Hey @jma which version of invenio-accounts are you using?

Zacharias Zacharodimos

@zzacharo

Have you set the ACCOUNTS_REGISTER_BLUEPRINT variable? It should be left to None if so...

Johnny Mariéthoz

@jma

@zzacharo version 1.3.0 with ACCOUNTS_REGISTER_BLUEPRINT = True

Zacharias Zacharodimos

@zzacharo

@jma can you set it to None? Or actually don't set it at all? invenio-accounts is doing the correct job out of the box....I think that config variable it confuses a bit....

Johnny Mariéthoz

@jma

@zzacharo ok probably I miss the meaning of this configuration can you explain me what is the purpose of this? Thanks in advance.

Zacharias Zacharodimos

@zzacharo

@jma the variable is used to register or not the flask-security blueprints. In the latest version of invenio-accounts we integrated the rest views from invenio-accounts-rest and we register all the endpoints that flask-security was registering in the InvenioAccountsREST extension. That said, when setting the ACCOUNTS_REGISTER_BLUEPRINT variable, initially controlling the registration of the flask-security blueprints, it works fine for the UI application e.g /login, /logout etc. but it conflicts with the REST application i.e /api/login, /api/logout. The problem is that it tries to register twice the same endpoints and thus giving you the error you saw...

In your application do you need to access the authentication views i.e login, logout etc through jinja or you have an SPA making requests to the API application? The scope of the REST application is to give back a REST response instead of rendering the corresponding templates e.g for the login page...

Johnny Mariéthoz

@jma

@zzacharo both, we use jinja2 view for public view and REST API for professional view.

Lanxin Ma

@malanxin_gitlab

Hello, When I run "./docker/build-images.sh" I get many errors, i.e. Installing dependencies from Pipfile.lock (c5dba8)â¦
An error occurred while installing alembic==1.4.3 --hash=sha256:4e02ed2aa796bd179965041afa092c55b51fb077de19d61835673cc80672c01c --hash=sha256:5334f32314fb2a56d86b4c4dd1ae34b08c03cae4cb888bc699942104d66bc245! Will try again.
An error occurred while installing amqp==2.6.1 --hash=sha256:70cdb10628468ff14e57ec2f751c7aa9e48e7e3651cfd62d431213c0c4e58f21 --hash=sha256:aa7f313fb887c91f15474c1229907a04dac0b8135822d6603437803424c0aa59! Will try again.

What does cause these errors ? I am an newer on Invenio. Could any body help ? Thx.

Lanxin Ma

@malanxin_gitlab

Hello, I am settin up my own INvenio3.3 instance. When I run './scripts/bootstrap', I get the error .

[2020-10-15 19:00:30,556] ERROR in app: Failed to initialize entry point: invenio_previewer = invenio_previewer:InvenioPreviewer
Traceback (most recent call last):
File "/root/.local/share/virtualenvs/invenio3-gVyQboDv/lib/python3.6/site-packages/pkg_resources/init.py", line 2736, in requires
deps.extend(dm[safe_extra(ext)])
KeyError: 'execute'
....

"/root/.local/share/virtualenvs/invenio3-gVyQboDv/lib/python3.6/site-packages/pkg_resources/init.py", line 2740, in requires
) from e
pkg_resources.UnknownExtra: nbconvert 6.0.7 has no such extra feature 'execute'

I do not understand the error. Could anybody help ? Thx.

Johnny Mariéthoz

@jma

@malanxin_gitlab Try to add this requirement contraint: nbconvert = {version = ">=5.6.1,<6.0.0", extras = ["execute"]} this has been done in the master branch of invenio-previewer but not yet in the release: https://github.com/inveniosoftware/invenio-previewer/blob/340121b967f3bc8e942ee947bbce7fd332ba93d9/setup.py#L58

Arjun K

@arjunKay

Hi. I am trying to connect to use Amazon Elasticsearch Service with Invenio. As per the currrent implementation, I configure the Elasticsearch params -as shown in this tutorial - in SEARCH_ELASTIC_HOSTS . But the problem with this is that the session_token passed in the AWS4Auth object expires after a while which would cause the subsequent requests to fail.

Since the Elasticsearch parameters are configured during app initialization, there seems to be no way to refresh the token and/or re-initialize the ES object with a new token. Is there any way to handle this issue?

Michael Groh

@wuschLOR

Hi. I'm trying to set up my first invenio instance for evaluation at my university. But every method I tried ends with unresolved dependencies with pipenv. This happens both under debian10/python7 Ubuntu20.04/python7 and Ubuntu18.04/python6 (tutorial ova) . Unfortunately I have no previous experience with pipenv and therefore I am not sure how to solve the problem.
If someone could help me over this barrier it would help me a lot.

Osagie Sammy

@osagiesammy

Good afternoon great to be here

This is my first time.

I have a question do not really know the etiquette here, has anyone deploy Invenio in AWS?

Kanász-Nagy Zoltán

@kanasznagyzoltan

Hello Guys,

We have stucked in the middle of a fresh Invenio RDM Installation process.
Could anyone in this room could help us?

My colleague sent me how he is trying the installation:

Hi all! I don't know if its's the right place (I hope). I currently trying to install an invenio-rdm instance on one of our linux servers. I could install the invenio-cli, init the rdm project, and even install it (with --pre and --development), but after whether I try run, servicesor containers I get an error, saying AttributeError: 'NoneType' object has no attribute 'group'. Im running on python 3.6.9 with pip 20.3.1, and invenio-cli 0.19.4 . Can someone help me, what have I missed? Thank you!

We are really thank you for your help.

Lars Holm Nielsen

@lnielsen

We are no longer using Gitter for chats but Discord......you'll find the link to Discord on https://inveniosoftware.org/products/rdm/

Kanász-Nagy Zoltán

@kanasznagyzoltan

Thank you Lars, we are switching to the platform.

Mohamed Nizharudeen

@nizardeen

Hello everyone, i am facing an issue in invenio API. In app.config['RECORDS_REST_ENDPOINTS'] = error_handlers{} are not handling multiple exceptions in it.

Osagie Sammy

@osagiesammy

cd ..

Mamadou Diaw

@mams84_gitlab

Hi
I'm new to invenio application and I want your assistance to repair an existing installation that crashes, when I try to repair the database.
I get EMERGENCY: Errors found. You should check consistency of the idxWORD09F - idxWORD09R tables.
Running 'bibindex --repair' is recommended.
can you assist me to finding a solution to this problem

aw-bib

@aw-bib:matrix.org

[m]

@mams84_gitlab: I fear you'll not get too much help on invenio 1.x anymore.
Anyway, it tries ot tell you that one of your indices is broken. You should log in to the console of your server and initiate as it tells you bibindex --repair. (Usually, bibindex lives in /opt/invenio/bin) This will add a job to your bibsched. In case this one is on halt (manual mode) you may run it from there using R short cut. (Open the scheduler by just calling it via bibsched. Mind that you usually need to be the same user as the invenio user to do all this stuff, so sudo or su will be required, depending on your setup.)
the interesting question will be why your index broke. usually it's quite stable and I didn't see this for ages. However, nothing helps against a full hard drive e.g.

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