diff --git a/qiita_db/software.py b/qiita_db/software.py index 076a19fac..3119b118a 100644 --- a/qiita_db/software.py +++ b/qiita_db/software.py @@ -1617,8 +1617,10 @@ def load(cls, command, json_str=None, values_dict=None): "but not both") elif json_str is not None: parameters = loads(json_str) + error_msg = ("The provided JSON string doesn't encode a " - "parameter set for command %s" % command.id) + "parameter set for command '%s (ID: %s)'" % ( + command.name, command.id)) else: if not isinstance(values_dict, dict): raise qdb.exceptions.QiitaDBError( @@ -1658,6 +1660,7 @@ def load(cls, command, json_str=None, values_dict=None): % (error_msg, key)) if parameters: + error_msg += f'--- {cmd_reqd_params} --- {cmd_opt_params}' raise qdb.exceptions.QiitaDBError( "%s. Extra parameters: %s" % (error_msg, ', '.join(parameters.keys()))) diff --git a/qiita_pet/handlers/download.py b/qiita_pet/handlers/download.py index 60e029f29..30db5ad24 100644 --- a/qiita_pet/handlers/download.py +++ b/qiita_pet/handlers/download.py @@ -387,7 +387,7 @@ def get(self, prep_template_id): info, bioms and coverage """ user = self.current_user - if user.level not in ('admin', 'web-lab admin'): + if user.level not in ('admin', 'wet-lab admin'): raise HTTPError(403, reason="%s doesn't have access to download " "the data release files" % user.email) diff --git a/qiita_pet/handlers/study_handlers/tests/test_processing.py b/qiita_pet/handlers/study_handlers/tests/test_processing.py index 53e607dcf..d064f0848 100644 --- a/qiita_pet/handlers/study_handlers/tests/test_processing.py +++ b/qiita_pet/handlers/study_handlers/tests/test_processing.py @@ -152,7 +152,8 @@ def test_post(self): self.assertEqual(response.code, 200) exp = {'status': 'error', 'workflow_id': None, 'job': None, 'message': "The provided JSON string doesn't encode a parameter" - " set for command 3. Missing required parameter: " + " set for command 'Pick closed-reference OTUs " + "(ID: 3)'. Missing required parameter: " "input_data"} self.assertDictEqual(loads(response.body), exp) diff --git a/qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst b/qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst index 0abc62e51..4b496be63 100755 --- a/qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst +++ b/qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst @@ -72,7 +72,7 @@ Shotgun sequencing ------------------ Qiita currently has one active shotgun metagenomics data analysis pipeline: a per sample, paired-end -bowtie2 alignment step with Woltka classification using either the WoLr2 (default) or RS210 databases. +bowtie2 alignment step with Woltka classification using either the WoLr2 (default) or RS225 databases. Below you will find more information about each of these options. .. note:: @@ -197,6 +197,23 @@ Note that some of these are legacy option but not available for new processing. - Genera: 6,811 - Species: 12,258 +#. RS225: Collection of reference microbial genomes sampled from the NCBI + RefSeq genome database, as of 2024-08-01. This time point corresponds to + RefSeq release 225. RS225 contains 40,987 genomes from NCBI RefSeq and + 11,771 genomes from external sources. The total number of genomes, 52,758, + represents an 78% increase from the previous version of the database. + + - Total number of genomes: 52,758 + - Total length of genomes (after adding linkers): 170,326,480,530 bp + - Number of genomes by category: + - Archaea: 870 + - Bacteria: 32,894 + - Fungi: 610 + - Protozoa: 93 + - Viral: 18,279 + - SynDNA Constructs: 12 + + #. RS210: Collection of reference microbial genomes sampled from the NCBI RefSeq genome database, as of 2022-01-01. This time point corresponds to RefSeq release 210. @@ -212,6 +229,7 @@ Note that some of these are legacy option but not available for new processing. - Protozoa: 93 - Viral: 7,493 + #. WoLr1 ("Web of Life" release 1): An even representation of microbial diversity, selected using an prototype selection algorithm based on the MinHash distance matrix among all non-redundant bacterial and archaeal genomes from NCBI (RefSeq and GenBank, complete and draft), plus several genome quality control criteria. A @@ -236,6 +254,7 @@ Note that some of these are legacy option but not available for new processing. - Strains: 89 - Note: Nucleotide sequences per genome were concatenated with a linker of 20 "N"s. + #. Rep200: NCBI representative and reference microbial genomes, corresponding to RefSeq release 200 (2020-05-14) - Genomes: 11,955 @@ -249,6 +268,7 @@ Note that some of these are legacy option but not available for new processing. - Protozoa: 88 - Viral: 48 + #. Rep94: NCBI representative and reference microbial genomes, corresponding to RefSeq release 94. - Domains: Bacteria, Archaea @@ -266,6 +286,7 @@ Note that some of these are legacy option but not available for new processing. - Species: 5,636 - Strains: 84 + #. Rep82: NCBI representative and reference microbial genomes, corresponding to RefSeq release 82. - Not available anymore for new processing @@ -284,6 +305,7 @@ Note that some of these are legacy option but not available for new processing. - Species: 11,852 - Strains: 4,263 + Metatranscriptome processing ---------------------------- diff --git a/qiita_pet/support_files/doc/source/reanalysis/reanalysis.rst b/qiita_pet/support_files/doc/source/reanalysis/reanalysis.rst index 76b853563..3bfdf09d5 100644 --- a/qiita_pet/support_files/doc/source/reanalysis/reanalysis.rst +++ b/qiita_pet/support_files/doc/source/reanalysis/reanalysis.rst @@ -109,7 +109,7 @@ Other tutorials (e.g. the :ref:`Statistical Analysis`) explain how to process th * Only 16S raw data: ``https://qiita.ucsd.edu/public_download/?data=raw&study_id=&data_type=16S`` * Only Metagenomic BIOMs + mapping files: ``https://qiita.ucsd.edu/public_download/?data=biom&study_id=&data_type=Metagenomic`` * Only the sample information file: ``https://qiita.ucsd.edu/public_download/?data=sample_information&study_id=`` -* Only the preparation information file: ``https://qiita.ucsd.edu/public_download/?data=data=prep_information&prep_id=`` +* Only the preparation information file: ``https://qiita.ucsd.edu/public_download/?data=prep_information&prep_id=`` Where ``/`` should be replaced with the appropriate study-id/prep-id.