minor changes after deployment (#3426)

* minor changes after deployment

* update qiime 2

* update conda qiime2 to 3.10

* install tiny Q2

* rm conda update

* qtp-biom

* tiny -> amplicon

* fix workflow GUI

* nltk<=3.8.1

Author: antgonza

.github/workflows/qiita-ci.yml

@@ -104,9 +104,7 @@ jobs:
       - name: Install plugins
         shell: bash -l {0}
         run: |
-          wget https://data.qiime2.org/distro/core/qiime2-2022.11-py38-linux-conda.yml
-          conda env create --quiet -n qtp-biom --file qiime2-2022.11-py38-linux-conda.yml
-          rm qiime2-2022.11-py38-linux-conda.yml
+          conda env create -n qtp-biom --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
           export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg
           export REDBIOM_HOST="http://localhost:7379"

qiita_db/artifact.py

@@ -1342,23 +1342,6 @@ def _helper(sql_edges, edges, nodes):
                         # If the job is in success we don't need to do anything
                         # else since it would've been added by the code above
                         if jstatus != 'success':
-                            # Connect the job with his input artifacts, the
-                            # input artifacts may or may not exist yet, so we
-                            # need to check both the input_artifacts and the
-                            # pending properties
-                            for in_art in n_obj.input_artifacts:
-                                iid = in_art.id
-                                if iid not in nodes and iid in extra_nodes:
-                                    nodes[iid] = extra_nodes[iid]
-                                _add_edge(edges, nodes[iid], nodes[n_obj.id])
-
-                            pending = n_obj.pending
-                            for pred_id in pending:
-                                for pname in pending[pred_id]:
-                                    in_node_id = '%s:%s' % (
-                                        pred_id, pending[pred_id][pname])
-                                    _add_edge(edges, nodes[in_node_id],
-                                              nodes[n_obj.id])
 
                             if jstatus != 'error':
                                 # If the job is not errored, we can add the
@@ -1380,6 +1363,34 @@ def _helper(sql_edges, edges, nodes):
                                     queue.append(cjob.id)
                                     if cjob.id not in nodes:
                                         nodes[cjob.id] = ('job', cjob)
+
+                                    # including the outputs
+                                    for o_name, o_type in cjob.command.outputs:
+                                        node_id = '%s:%s' % (cjob.id, o_name)
+                                        node = TypeNode(
+                                            id=node_id, job_id=cjob.id,
+                                            name=o_name, type=o_type)
+                                        if node_id not in nodes:
+                                            nodes[node_id] = ('type', node)
+
+                            # Connect the job with his input artifacts, the
+                            # input artifacts may or may not exist yet, so we
+                            # need to check both the input_artifacts and the
+                            # pending properties
+                            for in_art in n_obj.input_artifacts:
+                                iid = in_art.id
+                                if iid not in nodes and iid in extra_nodes:
+                                    nodes[iid] = extra_nodes[iid]
+                                _add_edge(edges, nodes[iid], nodes[n_obj.id])
+
+                            pending = n_obj.pending
+                            for pred_id in pending:
+                                for pname in pending[pred_id]:
+                                    in_node_id = '%s:%s' % (
+                                        pred_id, pending[pred_id][pname])
+                                    _add_edge(edges, nodes[in_node_id],
+                                              nodes[n_obj.id])
+
                     elif n_type == 'type':
                         # Connect this 'future artifact' with the job that will
                         # generate it

qiita_db/support_files/patches/test_db_sql/91.sql renamed to qiita_db/support_files/patches/91.sql

@@ -2775,7 +2775,7 @@ def update_resource_allocation_table(weeks=1, test=None):
     sacct = [
         'sacct', '-p',
         '--format=JobID,ElapsedRaw,MaxRSS,Submit,Start,End,CPUTimeRAW,'
-        'ReqMem,AllocCPUs,AveVMSize', '--starttime',
+        'ReqMem,AllocCPUs,AveVMSize,MaxVMSizeNode', '--starttime',
         dates[0].strftime('%Y-%m-%d'), '--endtime',
         dates[1].strftime('%Y-%m-%d'), '--user', 'qiita', '--state', 'CD']
 
@@ -2894,6 +2894,7 @@ def merge_rows(rows):
     df['MaxRSSRaw'] = df.MaxRSS.apply(lambda x: MaxRSS_helper(str(x)))
     df['ElapsedRawTime'] = df.ElapsedRaw.apply(
         lambda x: timedelta(seconds=float(x)))
+    df.replace({np.nan: None}, inplace=True)
 
     for index, row in df.iterrows():
         with qdb.sql_connection.TRN:

qiita_db/util.py

@@ -105,7 +105,7 @@
       install_requires=['psycopg2', 'click', 'bcrypt', 'pandas<2.0',
                         'biom-format', 'tornado<6.0', 'toredis', 'redis',
                         'scp', 'pyparsing', 'h5py',  'natsort', 'nose', 'pep8',
-                        'networkx', 'humanize', 'wtforms<3.0.0', 'nltk',
+                        'networkx', 'humanize', 'wtforms<3.0.0', 'nltk<=3.8.1',
                         'openpyxl', 'sphinx-bootstrap-theme', 'Sphinx<3.0',
                         'gitpython', 'redbiom', 'pyzmq', 'sphinx_rtd_theme',
                         'paramiko', 'seaborn',  'matplotlib', 'scipy<=1.10.1',