Analysis page update

[tomneep]

Hi @tombch,

This is a first attempt at updating the analysis page for https://climb-tre.github.io/analyse/.

The changes are

• I removed parts where we showed "real" data. I still show a command that queries for control_type_details=zymo-mc_D6300, I just don't show what that command returns.
• I made the page use (linked) tabs for the CLI and Python APIs. For each tab group(?) I show the equivalent command for the two ways of interacting with Onyx. The linked part means that if you click on e.g. the Python tab it will change all the tabs on the page, which I think is useful rather than having to click on all of them to switch between the APIs.

Because I've removed the analysis that was showing real data, this page is now very similar to the onyx-client docs. I think there is still values have "just the basics", but I don't feel strongly about it.

Is this sort of what you had in mind for this page? I'm not really sure of the best way to have a live version to test other than locally so a couple of screenshots are below. Any feedback is welcome, and if this is completely the wrong direction to take that is fine too!

[tombch]

Hey Tom, this is looking good! Will give it a proper review soon

[tombch]

Hey Tom - sorry its taken a bit to get back but heres a review!

Its looking great overall - I've left some comments with suggestions, let me know if you have any questions about them !

[tombch]

Personally I would keep/rework this sentence, perhaps along the lines of "This tutorial is intended as a basic demonstration of whats possible..." rather than "This short example...". I think ending on this alongside the link to the Onyx documentation would be nice

[tomneep]

Yes that sounds nicer, this line now appears right at the start of the page in the Overview section. Is it ok there?

[tombch]

I think this multi command example could be used to continue on the zymo filtering as before. Something like:

import os
from onyx import OnyxConfig, OnyxEnv, OnyxClient
from onyx.exceptions import OnyxHTTPError


config = OnyxConfig(
    domain=os.environ[OnyxEnv.DOMAIN],
    token=os.environ[OnyxEnv.TOKEN],
)

with OnyxClient(config) as client:
    try:
        records = client.filter(
            project="mscape",
            fields={
                "control_type_details": "zymo-mc_D6300",
                "published_date__range": ["2025-01-01", "2025-05-01"],
            },
            include=["climb_id", "published_date", "taxon_reports"],
        )

        for record in records:
            climb_id = record["climb_id"]

            full_record = client.get(project="mscape", climb_id=climb_id)

            n_taxa_files = len(full_record["taxa_files"])
            print(f"CLIMB_ID: {climb_id} has {n_taxa_files} taxa files entries")

    except OnyxHTTPError as e:
        print(e.response.json())

I also think it would be worth mentioning somewhere in the tutorial that the client.filter(...) generator can be passed straight to a pandas Dataframe, e.g. pd.DataFrame(client.filter(...)), as pandas seems to be pretty popular with users

[tombch]

Im not quite sure where to put it, as you don't have any real data in the tutorial, but I think id re-incorporate a mention of how the taxon_reports can be accessed with either s3cmd or aws s3 commands.

Perhaps just a placeholder example such as s3cmd get <taxon-reports-path>

[tomneep]

I've put in a section on accessing data from s3 giving examples of doing it on the command line with s3cmd and with s3fs directly in python. Let me know if you think this is overkill.

[tombch]

I would also reintroduce a mention for the --format csv and --format tsv CLI arguments, as they provide an alternative to JSON. Theres also the Python client .to_csv method (documented here), so perhaps a CLI/python API example for this would be handy!

[tomneep]

I've started working on this and have replied to the points I've addressed so far. I've not finished yet so I'm not ignoring your other comments! I'll let you know once this is ready to look at again.

[tomneep]

I think that everything suggested should be implemented now, let me know if you have any further comments!