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rm create qiime mapping file #3043
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rm create qiime mapping file #3043
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* 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]>
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Looks good. One question, should this include changes to the documentation? Reflecting these changes?
qiita_db/handlers/prep_template.py
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'status': pt.status, | ||
'qiime-map': pt.qiime_map_fp, | ||
# get_filepaths returns an ordered list of [filepath_id, | ||
# filepath] and we want the latests |
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# 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() |
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Unrelated to this line, but would it be a good time to rename this method to _build_sample_metadata
?
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Well, in practice it is still merging sample/prep info files so building mapping files ...
qiita_pet/handlers/download.py
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sqmf = qmf | ||
if qmf.startswith(basedir): | ||
sqmf = qmf[basedir_len:] | ||
# the latests prep template file is always the first [1] tuple and |
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# 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 %} |
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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.
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That's 100% correct!
I'm planning to add to the change log; AFAIK there is no information about the qiime-map in any of the documentation. |
Thanks @antgonza! |
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