Skip to content

rm create qiime mapping file #3043

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 11 commits into from
Nov 10, 2020

Conversation

antgonza
Copy link
Member

@antgonza antgonza commented Nov 6, 2020

No description provided.

antgonza and others added 10 commits September 16, 2020 16:57
* inject study_type in EBI and improvements to current automatic processing pipeline (qiita-spots#3023)

* inject study_type in ebi and improvements to current automatic proecssing pipeline

* addressing @ElDeveloper comments

* some general fixes/additions for next release (qiita-spots#3026)

* some general fixes/additions for next release

* adding test for not None job.release_validator_job

* fix qiita-spots#2839

* fix qiita-spots#2868 (qiita-spots#3028)

* fix qiita-spots#2868

* 2nd round

* fix errors

* more changes

* fix errors

* fix ProcessingJobTest

* fix PY_PATCH

* add missing TRN.add

* encapsulated_query -> perform_as_transaction

* fix qiita-spots#3022 (qiita-spots#3030)

* fix qiita-spots#3022

* adding tests

* fix qiita-spots#2320 (qiita-spots#3031)

* fix qiita-spots#2320

* adding prints to debug

* children -> 1

* APIArtifactHandlerTest -> APIArtifactHandlerTests

* configure_biom

* qdb.util.activate_or_update_plugins

* improving code

* almost there

* add values.template

* fix filepaths

* filepaths -> files

* fixing errors

* add prep.artifact insertion

* addressing @ElDeveloper comments

* fix artifact_definition active command

* != -> ==

* Added three tutorial sections to the Qiita documentation (qiita-spots#3032)

* Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab.

* Update redbiom.rst

* Update redbiom.rst

* Update redbiom.rst

* Further updates to redbiom.rst and the Stats tutorial.

* update redbiom.rst

* Finished proof-reading

* Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data

* added a new introduction, with links to the three sections

* Added figures to stats tutorial and contexts explanation

* Added figures to stats tutorial and contexts explanation

* Apply suggestions from code review [skip ci]

Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>

Co-authored-by: Antonio Gonzalez <[email protected]>
Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>

* 092020 (qiita-spots#3033)

* 092020

* connect artifact with job

* rm INSERT qiita.artifact_processing_job

* Apply suggestions from code review [skip ci]

Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>

Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>

Co-authored-by: Daniel McDonald <[email protected]>
Co-authored-by: Mirte Kuijpers <[email protected]>
Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
@antgonza antgonza changed the title [WIP] rm create qiime mapping file rm create qiime mapping file Nov 10, 2020
Copy link
Contributor

@ElDeveloper ElDeveloper left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good. One question, should this include changes to the documentation? Reflecting these changes?

'status': pt.status,
'qiime-map': pt.qiime_map_fp,
# get_filepaths returns an ordered list of [filepath_id,
# filepath] and we want the latests
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
# filepath] and we want the latests
# filepath] and we want the last pair

@@ -1040,13 +1040,16 @@ def _build_mapping_file(self, samples, rename_dup_samples=False):
with qdb.sql_connection.TRN:
all_ids = set()
to_concat = []
sample_infos = dict()
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Unrelated to this line, but would it be a good time to rename this method to _build_sample_metadata?

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Well, in practice it is still merging sample/prep info files so building mapping files ...

sqmf = qmf
if qmf.startswith(basedir):
sqmf = qmf[basedir_len:]
# the latests prep template file is always the first [1] tuple and
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
# the latests prep template file is always the first [1] tuple and
# the latest prep template file is always the first [0] tuple and

@@ -429,7 +429,9 @@ <h4>
<span id="prep-name-span">{{name}}</span> - ID {{prep_id}} ({{data_type}})
<a class="btn btn-default" data-toggle="modal" data-target="#update-prep-name"><span class="glyphicon glyphicon-pencil"></span> Edit name</a>
<a class="btn btn-default" href="{% raw qiita_config.portal_dir %}/download/{{download_prep_id}}"><span class="glyphicon glyphicon-download-alt"></span> Prep info</a>
<a class="btn btn-default" href="{% raw qiita_config.portal_dir %}/download/{{download_qiime_id}}"><span class="glyphicon glyphicon-download-alt"></span> QIIME map</a>
{% if download_qiime_id is not None %}
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is for backwards compatibility, right? This means that unless a QIIME mapping file has already been created then we won't show this button.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

That's 100% correct!

@antgonza
Copy link
Member Author

I'm planning to add to the change log; AFAIK there is no information about the qiime-map in any of the documentation.

@ElDeveloper ElDeveloper merged commit 8cef17e into qiita-spots:dev Nov 10, 2020
@ElDeveloper
Copy link
Contributor

Thanks @antgonza!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants