This doesn't work:
pip install git+git://github.com/nih-
cfde/FAIR.git#egg=c2m2_frictionless&subdirectory=Demos/FrictionlessDataclass
But after some StackOverflowing, I found that this does (change git+git to git+https):
pip install git+https://github.com/nih-
cfde/FAIR.git#egg=c2m2_frictionless&subdirectory=Demos/FrictionlessDataclass
I'm happy to share/report this issue to the proper technical forum, whether that's creating a github
issue or interfacing directly with the tech team.
Another more encompassing issue I found with the cookbook is that it's actually a non-functional
skeleton of how a cookbook might look with pretty key parts missing. For example, the
lincs_fetchdata_iter() function--which in theory is responsible for fetching LINCS data assets the
tutorial is using to demonstrate C2M2 conversion--is just an empty placeholder. It's entirely possible this
was intentional and the LINCS crew understandably didn't want to explain to the public how to ping
their API a bunch of times. In either case, I just wanted to bring it to your attention in case you all were
thinking this was a true cookbook example that a na've user could easily run to get a more intuitive
understanding of C2M2 mechanics.
Response
We can certainly address some of these issues.. just to address them off the bat and we can decide how to proceed:
This doesn't work:
pip install git+git://github.com/nih-
cfde/FAIR.git#egg=c2m2_frictionless&subdirectory=Demos/FrictionlessDataclass
But after some StackOverflowing, I found that this does (change git+git to git+https):
pip install git+https://github.com/nih-
cfde/FAIR.git#egg=c2m2_frictionless&subdirectory=Demos/FrictionlessDataclass
This does work assuming you have git+ssh setup on your system as you might need to clone the repository.
[x] We can change it to https which requires slightly less setup
[x] STILL however, people who don't have access to this private repo will be unable to install this.
Another more encompassing issue I found with the cookbook is that it's actually a non-functional
skeleton of how a cookbook might look with pretty key parts missing. For example, the
lincs_fetchdata_iter() function--which in theory is responsible for fetching LINCS data assets the
tutorial is using to demonstrate C2M2 conversion--is just an empty placeholder
The cookbook walks through the actual working code available in the repository https://github.com/nih-cfde/FAIR/tree/master/LINCS/c2m2 without completely re-writing it. It describes how to write your own C2M2 conversion, details about LINCS API seem out of scope for anyone elses' API but if they want LINCS API, that code is in the repo..
[x] As it wasn't clear from the recipe we can clarify that the full code is available in the FAIR repository. We can update the recipe as we have done for the FAIR assessment recipe to explain that this repo is only accessible with access permissions to the repository.
[ ] We'd like to have clarification on what is expected out of this recipe.. There is no one-size-fits-all with ETL hence we described the LINCS experience -- if they have a table it's just
# install the DERIVA loader script
pip install git+git://github.com/fair-research/deriva-flow-client.git@client-dev
# output here is the directory with the output of the etl.py script
cfde run output
# check the status of the ingestion
cfde status
As described in section 5, but perhaps this belongs somewhere more pronounced and perhaps in a less specific cookbook than "experience from lincs" and more like "submitting your manifest to DERIVA". Please advise if there are additional changes we should make to this cookbook.
Context
Response
We can certainly address some of these issues.. just to address them off the bat and we can decide how to proceed:
This does work assuming you have git+ssh setup on your system as you might need to clone the repository.
The cookbook walks through the actual working code available in the repository https://github.com/nih-cfde/FAIR/tree/master/LINCS/c2m2 without completely re-writing it. It describes how to write your own C2M2 conversion, details about LINCS API seem out of scope for anyone elses' API but if they want LINCS API, that code is in the repo..
[x] As it wasn't clear from the recipe we can clarify that the full code is available in the FAIR repository. We can update the recipe as we have done for the FAIR assessment recipe to explain that this repo is only accessible with access permissions to the repository.
[ ] We'd like to have clarification on what is expected out of this recipe.. There is no one-size-fits-all with ETL hence we described the LINCS experience -- if they have a table it's just
As described in section 5, but perhaps this belongs somewhere more pronounced and perhaps in a less specific cookbook than "experience from lincs" and more like "submitting your manifest to DERIVA". Please advise if there are additional changes we should make to this cookbook.