general fixes 11-2025

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())))

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)
 

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)
 

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
 ----------------------------
 

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=<study-id>&data_type=16S``
 * Only Metagenomic BIOMs + mapping files: ``https://qiita.ucsd.edu/public_download/?data=biom&study_id=<study-id>&data_type=Metagenomic``
 * Only the sample information file: ``https://qiita.ucsd.edu/public_download/?data=sample_information&study_id=<study-id>``
-* Only the preparation information file: ``https://qiita.ucsd.edu/public_download/?data=data=prep_information&prep_id=<prep-id>``
+* Only the preparation information file: ``https://qiita.ucsd.edu/public_download/?data=prep_information&prep_id=<prep-id>``
 
 Where ``<study-id>/<prep-id>`` should be replaced with the appropriate study-id/prep-id.