# Artifact API Import Error for Series of Sequences

**URL:** https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886
**Category:** User Support
**Tags:** artifact-api
**Created:** [July 28, 2020, 8:28pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886 "2020-07-28T20:28:22Z")
**Posts on this page:** 11
**Page:** 1

<div class="post-metadata">

### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [July 28, 2020, 8:28pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/1 "2020-07-28T20:28:22Z")

</div>

Hi all,

I recently upgraded to qiime2-2020.6. I have some old code from qiime2-2020.2 where I was importing some test data:

```python
import pandas as pd
from skbio import DNA
from qiime2 import Artifact

region1_db_seqs = Artifact.import_data('FeatureData[Sequence]', pd.Series({
    'seq1|seq2': DNA('GCGAAGCGGCTCAGG', metadata={'id': 'seq1|seq2'}),
    'seq3@0001': DNA('ATCCGCGTTGGAGTT', metadata={'id': 'seq3@0001'}),
    'seq3@0002': DNA('TTCCGCGTTGGAGTT', metadata={'id': 'seq3@0002'}),
    'seq5': DNA('CGTTTATGTATGCCC', metadata={'id': 'seq5'}),
    'seq6': DNA('CGTTTATGTATGCCT', metadata={'id': 'seq6'}), 
    }))

```

In the qiime2-2020.2 enviroment, it works fine.

I created a new enviroment, and I get a type error:

```auto
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-24-cb84a5d4a004> in <module>
      4 'seq3@0002': DNA('TTCCGCGTTGGAGTT', metadata={'id': 'seq3@0002'}),
      5 'seq5': DNA('CGTTTATGTATGCCC', metadata={'id': 'seq5'}),
----> 6 'seq6': DNA('CGTTTATGTATGCCT', metadata={'id': 'seq6'}),
      7 }))

~/miniconda3/envs/test/lib/python3.6/site-packages/qiime2/sdk/result.py in import_data(cls, type, view, view_type)
    239 provenance_capture = archive.ImportProvenanceCapture(format_, md5sums)
    240 return cls._from_view(type_, view, view_type, provenance_capture,
--> 241 validate_level='max')
    242 
    243 @classmethod

~/miniconda3/envs/test/lib/python3.6/site-packages/qiime2/sdk/result.py in _from_view(cls, type, view, view_type, provenance_capture, validate_level)
    252 % type)
    253 
--> 254 pm = qiime2.sdk.PluginManager()
    255 output_dir_fmt = pm.get_directory_format(type)
    256 

~/miniconda3/envs/test/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py in __new__ (cls, add_plugins)
     52 if cls.__instance is None:
     53 self = super(). __new__ (cls)
---> 54 self._init(add_plugins=add_plugins)
     55 cls.__instance = self
     56 else:

~/miniconda3/envs/test/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py in _init(self, add_plugins)
     81 plugin = entry_point.load()
     82 
---> 83 self.add_plugin(plugin, package, project_name)
     84 
     85 def add_plugin(self, plugin, package=None, project_name=None):

~/miniconda3/envs/test/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py in add_plugin(self, plugin, package, project_name)
    101 'for `project_name` or set `plugin.project_name`.')
    102 
--> 103 self._integrate_plugin(plugin)
    104 plugin.freeze()
    105 

~/miniconda3/envs/test/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py in _integrate_plugin(self, plugin)
    135 if output in self.transformers[input]:
    136 raise ValueError("Transformer from %r to %r already exists."
--> 137 % transformer_record)
    138 self.transformers[input][output] = transformer_record
    139 self._reverse_transformers[output][input] = transformer_record

TypeError: not all arguments converted during string formatting

```

I've also tried doing

```python
region1_db_seqs = Artifact.import_data('FeatureData[Sequence]', pd.Series({ 
     'seq1|seq2': 'GCGAAGCGGCTCAGG', 
     'seq3@0001': 'ATCCGCGTTGGAGTT', 
     'seq3@0002': 'TTCCGCGTTGGAGTT', 
     'seq5': 'CGTTTATGTATGCCC', 
     'seq6': 'CGTTTATGTATGCCT', 
      }))                                                                                                                                                             

```

Which throws the same error in the new version.

So, I'm not sure what's going on? I need this to work with the new version, so Im not sure where to go.

Thanks!  
Justine

---

<div class="post-metadata">

### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [July 28, 2020, 9:07pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/2 "2020-07-28T21:07:54Z")

</div>

Hi @jwdebelius,

I just tried this in my 2020.6 env and I got it to work by adding `skbio.` in front of `DNA`.

That is:

```auto
[1]: import pandas as pd 
   ...: import skbio 
   ...: from qiime2 import Artifact 
   ...:                                                                                                                

In [2]: region1_db_seqs = Artifact.import_data('FeatureData[Sequence]', pd.Series({ 
   ...: 'seq1|seq2': DNA('GCGAAGCGGCTCAGG', metadata={'id': 'seq1|seq2'}), 
   ...: 'seq3@0001': DNA('ATCCGCGTTGGAGTT', metadata={'id': 'seq3@0001'}), 
   ...: 'seq3@0002': DNA('TTCCGCGTTGGAGTT', metadata={'id': 'seq3@0002'}), 
   ...: 'seq5': DNA('CGTTTATGTATGCCC', metadata={'id': 'seq5'}), 
   ...: 'seq6': DNA('CGTTTATGTATGCCT', metadata={'id': 'seq6'}),  
   ...: }))                                                                                                        
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-2-cb84a5d4a004> in <module>
      1 region1_db_seqs = Artifact.import_data('FeatureData[Sequence]', pd.Series({
----> 2 'seq1|seq2': DNA('GCGAAGCGGCTCAGG', metadata={'id': 'seq1|seq2'}),
      3 'seq3@0001': DNA('ATCCGCGTTGGAGTT', metadata={'id': 'seq3@0001'}),
      4 'seq3@0002': DNA('TTCCGCGTTGGAGTT', metadata={'id': 'seq3@0002'}),
      5 'seq5': DNA('CGTTTATGTATGCCC', metadata={'id': 'seq5'}),

NameError: name 'DNA' is not defined

In [3]: region1_db_seqs = Artifact.import_data('FeatureData[Sequence]', pd.Series({ 
   ...: 'seq1|seq2': skbio.DNA('GCGAAGCGGCTCAGG', metadata={'id': 'seq1|seq2'}), 
   ...: 'seq3@0001': skbio.DNA('ATCCGCGTTGGAGTT', metadata={'id': 'seq3@0001'}), 
   ...: 'seq3@0002': skbio.DNA('TTCCGCGTTGGAGTT', metadata={'id': 'seq3@0002'}), 
   ...: 'seq5': skbio.DNA('CGTTTATGTATGCCC', metadata={'id': 'seq5'}), 
   ...: 'seq6': skbio.DNA('CGTTTATGTATGCCT', metadata={'id': 'seq6'}),  
   ...: }))                                                                                                        

In [4]: region1_db_seqs                                                                                                
Out[4]: <artifact: FeatureData[Sequence] uuid: 5975c241-ebdb-42b9-9e78-aa5c5efa4510>

In [5]: region1_db_seqs.view(pd.Series)                                                                               
Out[5]: 
seq1|seq2 (((G)), ((C)), ((G)), ((A)), ((A)), ((G)), ((C...
seq3@0001 (((A)), ((T)), ((C)), ((C)), ((G)), ((C)), ((G...
seq3@0002 (((T)), ((T)), ((C)), ((C)), ((G)), ((C)), ((G...
seq5 (((C)), ((G)), ((T)), ((T)), ((T)), ((A)), ((T...
seq6 (((C)), ((G)), ((T)), ((T)), ((T)), ((A)), ((T...
dtype: object

```

---

<div class="post-metadata">

### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [July 28, 2020, 9:17pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/3 "2020-07-28T21:17:01Z")

</div>

Hi @SoilRotifer,

Thanks! Its a different error from the one I'm getting. (Sorry, i mis-copied the imports, i'll fix those above!)

---

<div class="post-metadata">

### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [July 28, 2020, 9:25pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/4 "2020-07-28T21:25:15Z")

</div>

> [@jwdebelius](#):
>
> Thanks! Its a different error from the one I’m getting

Yeah, I forgot to comment on that bit. I am wondering if there is something else odd in your environment?

---

<div class="post-metadata">

### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [July 28, 2020, 9:29pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/5 "2020-07-28T21:29:16Z")

</div>

I have sparse, dask, and i moved numba back to 0.48. ...I can re-factor to do without sparse, but i need dask.

So, maybe the refactor is the answer. Again. 🙄 🙂 💻

---

<div class="post-metadata">

### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 28, 2020, 11:55pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/6 "2020-07-28T23:55:31Z")

</div>

Hey @jwdebelius!

This part of the first traceback jumped out at me:

> [@jwdebelius](#):
>
> ```auto
> 136 raise ValueError("Transformer from %r to %r already exists."
> --> 137 % transformer_record)
> 
> ```

That bit of the framework checks for duplicated transformers, and according to that it found one... What plugins do you have in this env?

---

<div class="post-metadata">

### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 29, 2020, 12:00am UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/7 "2020-07-29T00:00:01Z")

</div>

> [@jwdebelius](#):
>
> `TypeError: not all arguments converted during string formatting`

@Oddant1 can you look into this unrelated part of the error message - looks like the "transformer already exists" string interpolation might be broken (I suspect related to last fall's plugin manager project).

---

<div class="post-metadata">

### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [July 29, 2020, 12:19am UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/8 "2020-07-29T00:19:07Z")

</div>

It's a standard QIIME 2 install with the plugin Im developing installed. I've added several new transformers for new semantic types Im developing (mostly back and forth between pandas and metadata) and then a transformer to go from aligned sequences to a series.

The code isn't up on github because I threw the error trying to make sure my travis testing would work before I made the commit because I only have like 3 travis builds left.

Best,  
Justine

---

<div class="post-metadata">

### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [July 29, 2020, 12:39am UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/9 "2020-07-29T00:39:32Z")

</div>

Cool, yeah, I would double-check the transformers you've registered - transformers are global, maybe you accidentally re-registered one from q2-types.

---

<div class="post-metadata">

### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [July 29, 2020, 4:09pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/10 "2020-07-29T16:09:10Z")

</div>

You guys added a way to view aligned sequences as series without me updating! Cool

---

<div class="post-metadata">

### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [August 29, 2020, 10:09pm UTC](https://forum.qiime2.org/t/artifact-api-import-error-for-series-of-sequences/15886/11 "2020-08-29T22:09:10Z")

</div>

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.