From 25237a552df3be54b3ad42acc2ef7c3b932caa9e Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Thu, 10 Oct 2024 13:17:32 -0600 Subject: [PATCH] Doc improvements (#3437) * doc improvemnts * doc improvements * METAGENOMICS -> Metagenomics * 2024.10 * scp -O --- .github/workflows/qiita-ci.yml | 2 +- CHANGELOG.md | 8 +++++--- qiita_core/__init__.py | 2 +- qiita_db/__init__.py | 2 +- qiita_pet/__init__.py | 2 +- qiita_pet/handlers/api_proxy/__init__.py | 2 +- qiita_pet/support_files/doc/source/faq.rst | 7 ++++++- qiita_ware/__init__.py | 2 +- qiita_ware/ebi.py | 3 ++- qiita_ware/test/test_ebi.py | 10 +++++----- setup.py | 2 +- 11 files changed, 25 insertions(+), 17 deletions(-) diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml index 51bae2a9b..dd596af87 100644 --- a/.github/workflows/qiita-ci.yml +++ b/.github/workflows/qiita-ci.yml @@ -179,7 +179,7 @@ jobs: echo "Connecting as $USER@localhost" # this line (and the -o StrictHostKeyChecking=no) is so the server # is added to the list of known servers - scp -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1 + scp -O -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1 - name: Main tests shell: bash -l {0} diff --git a/CHANGELOG.md b/CHANGELOG.md index 03ad1593d..41c4c821b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,9 +1,9 @@ # Qiita changelog -Version 2024.09 +Version 2024.10 --------------- -Deployed on September 23rd, 2024 +Deployed on October 14th, 2024 * Added update_resource_allocation_redis and companion code, so resource allocations summaries are available for review. Thank you @Gossty! * Now is possible to have default workflows with only one step. @@ -11,7 +11,9 @@ Deployed on September 23rd, 2024 * Initial changes in `qiita_client` to have more accurate variable names: `QIITA_SERVER_CERT` -> `QIITA_ROOTCA_CERT`. Thank you @charles-cowart! * Added `get_artifact_html_summary` to `qiita_client` to retrieve the summary file of an artifact. * Re-added github actions to `https://github.com/qiita-spots/qiita_client`. -* `Woltka v0.1.6, paired-end` superseded `Woltka v0.1.6` in `qp-woltka`; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/woltka_pairedend.html). Thank you to @qiyunzhu for the benchmarks! +* `SortMeRNA v4.3.7` superseded `Sortmerna v2.1b`, which relies on Silva 138 and now produced even mates. Thank you @ekopylova and @biocodz for the support. +* `Remove SynDNA reads` superseded `SynDNA Woltka`, which now generates even mates. +* `Woltka v0.1.7, paired-end` superseded `Woltka v0.1.6` in `qp-woltka`; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/woltka_pairedend.html). Thank you to @qiyunzhu for the benchmarks! * Other general fixes, like [#3424](https://github.com/qiita-spots/qiita/pull/3424), [#3425](https://github.com/qiita-spots/qiita/pull/3425). diff --git a/qiita_core/__init__.py b/qiita_core/__init__.py index e7cd25423..95d73a276 100644 --- a/qiita_core/__init__.py +++ b/qiita_core/__init__.py @@ -6,4 +6,4 @@ # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- -__version__ = "2024.09" +__version__ = "2024.10" diff --git a/qiita_db/__init__.py b/qiita_db/__init__.py index 165823462..814bbffaf 100644 --- a/qiita_db/__init__.py +++ b/qiita_db/__init__.py @@ -27,7 +27,7 @@ from . import user from . import processing_job -__version__ = "2024.09" +__version__ = "2024.10" __all__ = ["analysis", "artifact", "archive", "base", "commands", "environment_manager", "exceptions", "investigation", "logger", diff --git a/qiita_pet/__init__.py b/qiita_pet/__init__.py index e7cd25423..95d73a276 100644 --- a/qiita_pet/__init__.py +++ b/qiita_pet/__init__.py @@ -6,4 +6,4 @@ # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- -__version__ = "2024.09" +__version__ = "2024.10" diff --git a/qiita_pet/handlers/api_proxy/__init__.py b/qiita_pet/handlers/api_proxy/__init__.py index 0077522c0..b27c938f7 100644 --- a/qiita_pet/handlers/api_proxy/__init__.py +++ b/qiita_pet/handlers/api_proxy/__init__.py @@ -38,7 +38,7 @@ from .user import (user_jobs_get_req) from .util import check_access, check_fp -__version__ = "2024.09" +__version__ = "2024.10" __all__ = ['prep_template_summary_get_req', 'data_types_get_req', 'study_get_req', 'sample_template_filepaths_get_req', diff --git a/qiita_pet/support_files/doc/source/faq.rst b/qiita_pet/support_files/doc/source/faq.rst index 17fdf73f8..be56ae7b2 100755 --- a/qiita_pet/support_files/doc/source/faq.rst +++ b/qiita_pet/support_files/doc/source/faq.rst @@ -414,13 +414,18 @@ Are you planning a workshop or class? ------------------------------------------------------------------- We encourage users to use Qiita for their classes and/or workshops and to facilitate processing -we urge users to request a special reservation in the system. A reservation should help your +we urge them to request a special reservation in the system. A reservation should help your and your participant jobs to move quicker in the system. If you are interested, please send us an email to qiita.help@gmail.com and add the name of your workshop/course, the number of participants, the expected days this will happen. Note that reservations are only available for analysis and not for sequencing processing, and that the reservation can be added/edited during the creation of the analysis or at any point within each individual analysis page. +You can add the reservation string to the analysis at the time of creation (bottom of the creation +page), or the analysis page via the reservation button (top right). Note that once the reservation +time finishes, your jobs will fail as the reservation will no longer exist so you will need to +remove it - we suggest doing this before submitting new jobs. + How to cite Qiita? ------------------ diff --git a/qiita_ware/__init__.py b/qiita_ware/__init__.py index e7cd25423..95d73a276 100644 --- a/qiita_ware/__init__.py +++ b/qiita_ware/__init__.py @@ -6,4 +6,4 @@ # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- -__version__ = "2024.09" +__version__ = "2024.10" diff --git a/qiita_ware/ebi.py b/qiita_ware/ebi.py index ec6b084c9..7c7861ec4 100644 --- a/qiita_ware/ebi.py +++ b/qiita_ware/ebi.py @@ -110,6 +110,7 @@ class EBISubmission(object): 'ILLUMINA MISEQ', 'ILLUMINA MINISEQ', 'ILLUMINA NOVASEQ 6000', + 'ILLUMINA NOVASEQ X', 'NEXTSEQ 500', 'NEXTSEQ 550', 'UNSPECIFIED'], @@ -539,7 +540,7 @@ def generate_experiment_xml(self, samples=None): library_name.text = self._get_library_name(sample_name) lg = ET.SubElement(library_descriptor, 'LIBRARY_STRATEGY') - lg.text = escape(clean_whitespace(library_strategy.upper())) + lg.text = escape(clean_whitespace(library_strategy)) # hardcoding some values, # see https://github.com/biocore/qiita/issues/1485 diff --git a/qiita_ware/test/test_ebi.py b/qiita_ware/test/test_ebi.py index 7ef1b0b08..e28fd39d3 100644 --- a/qiita_ware/test/test_ebi.py +++ b/qiita_ware/test/test_ebi.py @@ -1358,7 +1358,7 @@ def test_parse_EBI_reply(self): %(study_id)s.Sample1" /> %(study_id)s.Sample1 - METAGENOMICS + Metagenomics METAGENOMIC PCR @@ -1393,7 +1393,7 @@ def test_parse_EBI_reply(self): %(study_id)s.Sample2" /> %(study_id)s.Sample2 - METAGENOMICS + Metagenomics METAGENOMIC PCR @@ -1428,7 +1428,7 @@ def test_parse_EBI_reply(self): %(study_id)s.Sample3" /> %(study_id)s.Sample3 - METAGENOMICS + Metagenomics METAGENOMIC PCR @@ -1469,7 +1469,7 @@ def test_parse_EBI_reply(self): 1.SKB2.640194 - METAGENOMICS + Metagenomics METAGENOMIC PCR @@ -1558,7 +1558,7 @@ def test_parse_EBI_reply(self): 1.SKB3.640195 - METAGENOMICS + Metagenomics METAGENOMIC PCR diff --git a/setup.py b/setup.py index 1b7d111d6..230cec3a2 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ from setuptools import setup from glob import glob -__version__ = "2024.09" +__version__ = "2024.10" classes = """