# Juggle between semantic types and view types?
**URL:** https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332
**Category:** Developer Discussion
**Tags:** plugin-development
**Created:** [June 11, 2020, 2:24pm UTC](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332 "2020-06-11T14:24:11Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@lea\_si](https://forum.qiime2.org/u/lea_si)
#### Post date: [June 11, 2020, 2:24pm UTC](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332/1 "2020-06-11T14:24:11Z")
Dear all,
I am currently trying to develop my first QIIME2 plugin, and I admit having a hard time juggling between data types. I'd appreciate any guidance from someone more experienced with the API š
My aim is to automatically perform a series of analytical steps, the first one being to extract OTUs reference sequences from a specific taxa (I used _Escherichia_ as an example in the following code). For this, I'd like to use the `filter_seqs` function from `qiime2.plugins.taxa.methods`.
In `plugin_setup.py`, I am registering my method the following way:
```python
plugin.methods.register_function(
function=extract_escherichia,
inputs={
'rep_seqs': FeatureData[Sequence],
'taxonomy': FeatureData[Taxonomy]
},
outputs=[('escherichia_seqs', FeatureData[Sequence])],
...
...
)
```
Now [looking at the forum](https://forum.qiime2.org/t/plugin-error-issubclass-arg-1-must-be-a-class/2774), I realized that I need to use view types in my function, which I consequently defined as such:
```python
def extract_escherichia(rep_seqs: pd.Series, taxonomy: qiime2.Metadata) -> (pd.Series):
```
And here I am stuck to call `filter_seqs` in my method. Indeed, it seems that `filter_seqs` requires Semantic types as inputs, while I have Series & Metadata objects. Therefore the following call in my `extract_escherichia` method does not work:
```python
from qiime2.plugins.taxa.methods import filter_seqs
def extract_escherichia(rep_seqs: pd.Series, taxonomy: qiime2.Metadata) -> (pd.Series):
escherichia_seqs=filter_seqs(sequences=rep_seqs, taxonomy=taxonomy, include='Escherichia')
return escherichia_seqs
```
Should I, and if so how, convert my objects back to Artifacts to use `filter_seqs`, or is there an easier way to do things which I did not get? I'm sure that it's just a matter for me to better understand the API; I tried to look into the developers documentation, in existing plugins codes and directly in the forum but so far could not figure it out.
Thank you for your help!
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [June 11, 2020, 2:24pm UTC](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332/2 "2020-06-11T14:24:21Z")
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [June 11, 2020, 2:46pm UTC](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332/3 "2020-06-11T14:46:39Z")
Hi @lea_si, this is such a great question, thanks!
> [@lea\_si](#):
>
> I admit having a hard time juggling between data types
Wow, from my perspective it looks like you actually have it all figured out, I think with a little bit of nudging in a new direction you'll have it all squared away in no time.
> [@lea\_si](#):
>
> For this, Iād like to use the `filter_seqs` function from `qiime2.plugins.taxa.methods` .
This is where things are breaking down. In QIIME 2, if you want to use another [Action](https://dev.qiime2.org/latest/actions/) inside of your Action, then you need a [Pipeline](https://dev.qiime2.org/latest/actions/pipelines/).
> [@lea\_si](#):
>
> `from qiime2.plugins.taxa.methods import filter_seqs`
Importing a "vanilla" python function (that represents a QIIME 2 Action) has two disadvantages (over Pipelines):
1. It is up to you to negotiate the appropriate view type transformation (as you have seen first-hand!). That is super annoying, and is one of the QIIME 2 Framework's main jobs, so might as well let QIIME 2 handle it...
2. You lose all decentralized provenance of the imported function, since QIIME 2 doesn't "know" that you're using `filter_seqs`
Okay, so, converting your Method into a Pipeline, its pretty straightforward:
First, register `extract_escherichia` as a pipeline, rather than a method.
```python
plugin.pipelines.register_function(
...
)
```
Second, update your function's signature. Pipeline's have a mandatory first argument called `ctx` - this is the QIIME 2 context, and gives you access to things like other QIIME 2 actions, etc. Note, pipeline's don't use the view annotation syntax in the function signature
```python
import pandas as pd
import qiime2
# note I am no longer importing `filter_seqs` using a Python import statement
def extract_escherichia(ctx, rep_seqs, taxonomy):
# first, let's get a reference to filter_seqs:
filter_seqs = ctx.get_action('taxa', 'filter_seqs')
# since the rep_seqs and taxonomy are already Artifacts, we can just pass them right along:
e_seqs_results = filter_seqs(sequences=rep_seqs, taxonomy=taxonomy, include='Escherichia')
# the return value is a QIIME 2 Results object:
# https://dev.qiime2.org/latest/api-reference/sdk/#qiime2.sdk.Results
# it's just a namedtuple with your outputs in it
# you can look up the name of the action's output directly:
filtered_e_seqs = e_seqs_results.filtered_sequences
# In your original function signature, you were requesting views of pd.Series and qiime2.Metadata,
# so I'll assume you need those in that format for later code. Here is how you can do that:
rep_seqs_series = rep_seqs.view(pd.Series)
taxonomy_md = taxonomy.view(qiime2.Metadata)
# now you can do things with the series and metadata in subsequent lines of code!
# returning the filtered seqs, just to match what you had in your original example function
return filtered_e_seqs
```
* * *
Hope that helps - keep us posted, really excited to see more of this plugin in the future!
:qiime2:
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [June 11, 2020, 2:46pm UTC](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332/4 "2020-06-11T14:46:44Z")
---
### Author:  [@lea\_si](https://forum.qiime2.org/u/lea_si)
#### Post date: [June 12, 2020, 1:45pm UTC](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332/5 "2020-06-12T13:45:29Z")
Dear @thermokarst,
Thank you so much for your detailed answer, I've totally overlooked the concept of pipelines which makes my life way easier! Your code example was perfect to follow, things work like a charm now (at least the first step of the plugin š )
I won't hesitate to reach out if I have more issues as I go along, and anyway to share when the plugin will be ready!