Add example workflow or use case

olgabot commented 5 years ago

In reading the JOSS paper and looking over the repo, it seems extremely useful, and I'm having trouble forming in my mind an explicit example workflow using SODAR core. Would it be possible to add an example workflow in either a diagram or prose format? e.g. "SODAR core can be used to upload CSVs from plate readers, manage Illumina samplesheets from these samples, and link them to their sequencing data and results." (I just made this one up). Or something like a "user story" format would be great, too.

RE: https://github.com/openjournals/joss-reviews/issues/1584

Thank you! Warmest, Olga

holtgrewe commented 5 years ago

Excellent, we'll add this once @mikkonie is back in office.

rbatorsky commented 5 years ago

Hello,

Please excuse that I am commenting again, as I hope that my issue is related enough to this one. An example workflow would be very helpful. Specifically, once I get sodar_django_site up and running and log in, I am not sure what to do!

I have read through the documentation, and am pretty sure that I I create a category, then a project, then invite a user. However, I'm struggling to find step by step instructions for a new site. The examples under Usage show a site already populated with projects.

Thank you, Rebecca

holtgrewe commented 5 years ago

Hi @rbatorsky no, that's an excellent question (as this indicates that the documentation needs improvement, so far we've locally had @mikkonie walk us through things and have not had an external user). However, I'm not 100% positive that I understand what you mean. Maybe the nomenclauture in the documentation could be confusing if you're new to the system.

The word "site" is used in the following contents in the documentation page that you linked to:

Django site -- Your django "web app" that uses SODAR-core (what you created in your derived/modifeid copy of sodar_django_site).
their LDAP/AD credentials from a supported site -- An LDAP/ActiveDirectory server/domain.
admin site -- The django administration UI.
site-wide apps -- A kind of "SODAR Core" app that, in contrast to "project apps" is not bound to a specific project but has "installation-wide scope" of "site" (the "django web app" from above)
site info -- Information about your installation, a site-wide app.
When setting up a new site -- Your installation.
Remote Site Access/source site/target site -- As explained in the documentation, you can have the installation of a SODAR-based web application marked as "target" that can then sync over projects, roles, and user information from a "source" instance of a SODAR-based web application. One of the very nice features is that this does not have to be the same source code but you can actually have a "central data repository app" that is the source and then "specialized satellite apps" that are connected upstream and sync the projects that they are allowed to. We are using this feature for setting up a central "SODAR" instance with Omics data and meta data (to be published once it's complete but that might take some months) and then, e.g., have a dashboard hosting web app and a variant filtration web app syndicating information.

[If I'm misrepresenting anything here, I'm certain @mikkonie will correct me when he's back.]

I hope this comment helps. I'm agreeing that the documentation can be improved here, maybe with a more step-by-step workflow. We'll go back to our text editors and think how we could improve this. In the meantime, are you lacking any information to proceed in your review right now?

rbatorsky commented 5 years ago

Thank you again for your reply. My usage of the word site is the first of the ones you listed: Django site. I look forward to reading the updated documentation so that I can complete the final steps of the review.

mikkonie commented 5 years ago

Hi @rbatorsky. As @holtgrewe said, you raise very good points here. Next week I'll be working on improving the documentation from this perspective.

So far I've identified the following improvements which should help with this issue:

Add a user story to help describe in how to use SODAR Core in research projects
Add a general glossary to clarify terms in one place (e.g. the site issue)
Make sure the site terminology is clearly used within the documentation
Write out a more high level and user friendly description of the project into the "getting started" section
Look into adding some helpful graphs to visualize the "big picture", architecture etc.

Please let me know if you would also like to see something else to help in clarifying these issues.

mikkonie commented 5 years ago

@olgabot and @rbatorsky: I've updated the documentation in an attempt to clarify the issues raised here.

There is a new Overview section providing a bit more context and an example use case.
Also added is the Glossary to clarify some commonly used terms.
Furthermore, I made multiple general improvements aimed at documenting the package more clearly, most of these can be found in this commit.

I hope this is helpful with the issue at hand, please let me know if I should improve the docs regarding these questions.

rbatorsky commented 5 years ago

Hello, I've gone through the documentation and found it helpful. Thanks.

olgabot commented 5 years ago

Thank you for this! Unfortunately this is not enough for a Django newbie like me. I was able to install the package just fine using the pip install command on the Getting Started page and from there I see I need to configure the projectroles app but I don't understand what command to run. E.g. I see django-sodar-core referenced several times but can't tell if this is a command to run, and it seems like it is not:

(sodar_core)
 ♥ 30%  Fri  1 Nov - 18:48  ~ 
  django-sodar-core
zsh: command not found: django-sodar-core

Would it be possible to add a full use case with all the commands and their outputs, e.g. for the servers you have already set up?

Gory installation details

``` (base) ✘  ♥ 39%  Fri 1 Nov - 18:33  ~   conda create -n sodar_core python=3.7 Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /anaconda3/envs/sodar_core added / updated specs: - python=3.7 The following packages will be downloaded: package | build ---------------------------|----------------- libcxx-9.0.0 | h89e68fa_1 1.0 MB conda-forge pip-19.3.1 | py37_0 1.9 MB conda-forge setuptools-41.6.0 | py37_1 650 KB conda-forge ------------------------------------------------------------ Total: 3.5 MB The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h01d97ff_1 ca-certificates conda-forge/osx-64::ca-certificates-2019.9.11-hecc5488_0 certifi conda-forge/osx-64::certifi-2019.9.11-py37_0 libcxx conda-forge/osx-64::libcxx-9.0.0-h89e68fa_1 libffi bioconda/osx-64::libffi-3.2.1-1 ncurses conda-forge/osx-64::ncurses-6.1-h0a44026_1002 openssl conda-forge/osx-64::openssl-1.1.1c-h01d97ff_0 pip conda-forge/osx-64::pip-19.3.1-py37_0 python conda-forge/osx-64::python-3.7.3-h93065d6_1 readline conda-forge/osx-64::readline-8.0-hcfe32e1_0 setuptools conda-forge/osx-64::setuptools-41.6.0-py37_1 sqlite conda-forge/osx-64::sqlite-3.30.1-h93121df_0 tk conda-forge/osx-64::tk-8.6.9-h2573ce8_1003 wheel conda-forge/osx-64::wheel-0.33.6-py37_0 xz conda-forge/osx-64::xz-5.2.4-h1de35cc_1001 zlib conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006 Downloading and Extracting Packages setuptools-41.6.0 | 650 KB | ##################################################################################################################################################################### | 100% pip-19.3.1 | 1.9 MB | ##################################################################################################################################################################### | 100% libcxx-9.0.0 | 1.0 MB | ##################################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate sodar_core # # To deactivate an active environment, use # # $ conda deactivate (base) ♥ 36%  Fri 1 Nov - 18:35  ~   conda activate sodar_core (sodar_core) ♥ 36%  Fri 1 Nov - 18:40  ~   pip install -e git+https://github.com/bihealth/sodar_core.git@v0.7.0#egg=django-sodar-core Obtaining django-sodar-core from git+https://github.com/bihealth/sodar_core.git@v0.7.0#egg=django-sodar-core Cloning https://github.com/bihealth/sodar_core.git (to revision v0.7.0) to ./src/django-sodar-core Running command git clone -q https://github.com/bihealth/sodar_core.git /Users/olgabot/src/django-sodar-core Collecting django-autocomplete-light==3.2.10 Downloading 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Unidecode-0.4.21 alabaster-0.7.12 amqp-2.5.1 argon2-cffi-19.1.0 awesome-slugify-1.6.5 babel-2.7.0 billiard-3.5.0.5 celery-4.1.1 cffi-1.13.1 chardet-3.0.4 cryptography-2.8 django-1.11.25 django-autocomplete-light-3.2.10 django-crispy-forms-1.7.2 django-db-file-storage-0.5.3 django-docs-0.3.1 django-environ-0.4.5 django-markupfield-1.5.1 django-model-utils-3.2.0 django-pagedown-1.0.6 django-rest-knox-4.1.0 django-sodar-core djangorestframework-3.10.3 docutils-0.15.2 idna-2.8 imagesize-1.1.0 importlib-metadata-0.23 kombu-4.6.5 markdown-3.1.1 mistune-0.8.4 more-itertools-7.2.0 packaging-19.2 psycopg2-binary-2.8.4 pycparser-2.19 pyparsing-2.4.2 pytz-2019.3 regex-2019.11.1 requests-2.22.0 rules-2.1 six-1.12.0 snowballstemmer-2.0.0 sphinx-rtd-theme-0.4.3 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 urllib3-1.25.6 versioneer-0.18 vine-1.3.0 zipp-0.6.0 ```

mikkonie commented 4 years ago

@olgabot: I'm sorry the context of the package remains unclear. It is indeed a complex issue for someone not used to working with the Django framework.

In the Django ecosystem, it is commonplace to have packages which provide additions to the base web framework, either in form of applications, middleware or both. django-sodar-core refers to the SODAR Core package, which is installed on top of a Django web site project in the aforementioned manner. It is a set of enhancements over the base Django web framework aimed at developing web based systems for scientific research projects.

Hence the package is not usable by itself, but is expected to be installed to an existing Django web site project. An example of a minimal Django project with the web framework and the django-sodar-core package installed can be seen in the sodar_django_site project. On top of this, the actual research project applications are developed.

As I mentioned here, we have several systems using the package for actual scientific apps. Those would provide a view to the entire use case for using this package, but sadly publications on them are still pending.

One possibility would be to develop a demo application, which represents e.g. an analysis process and how it would be implemented on SODAR Core. In case this would sound like a good approach, anything more specific you would be looking for in such an application?

holtgrewe commented 4 years ago

Dear @olgabot and @rbatorsky, thanks for raising these points. As pointed out in #6, we now provide a section that gives the precise commands to setup a sodar-core site based on the template that we provide:

https://sodar-core.readthedocs.io/en/latest/for_the_impatient.html#for-the-impatient

Please have a look at this whether it addresses all of your questions and points. Please re-open this issue if you feel that we left a point unanswered and this could use some more work.

bihealth / sodar-core-legacy

Add example workflow or use case #4

Gory installation details