Merge branch 'main' into update-type-slot-migrator

microbiomedata · Sep 12, 2024 · 7acd724 · 7acd724
2 parents 6836fa5 + 3a56db9
commit 7acd724
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Showing 5 changed files with 33 additions and 8 deletions.
diff --git a/...grators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_12.py b/...grators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_12.py
@@ -35,7 +35,7 @@ def standardize_failure_where_enum_ns(self, read_qc_analysis: dict):
             "Extraction": "Extraction",
             "LibraryPreparation": "LibraryPreparation",
             "MetagenomeAssembly": "MetagenomeAssembly",
-            "MetatranscriptomeActivity": "MetatranscriptomeAnalysis",
+            "MetatranscriptomeActivity": "MetatranscriptomeExpressionAnalysis",
             "MagsAnalysisActivity": "MagsAnalysis",
             "ReadQcAnalysisActivity": "ReadQcAnalysis",
             "ReadBasedTaxonomyAnalysisActivity": "ReadBasedTaxonomyAnalysis",

diff --git a/src/data/invalid/MetatranscriptomeExpressionAnalysis-invalid-type.yaml b/src/data/invalid/MetatranscriptomeExpressionAnalysis-invalid-type.yaml
@@ -0,0 +1,14 @@
+- id: nmdc:wfmt-99-4d83z.1
+  type: nmdc:MetatranscriptomeAnalysis
+  name: human gut metatranscriptome expression
+  has_input:
+    - nmdc:dobj-99-9t74d
+  has_output:
+   - nmdc:dobj-99-6y6j
+  ended_at_time: '2023-08-03T16:00:00Z'
+  execution_resource: JGI
+  git_url: https://github.com/microbiomedata/metatranscriptome_annotation/releases/tag/v2.5.0
+  was_informed_by: nmdc:dgns-12-dfa84a
+  started_at_time: '2023-08-03T10:00:00Z'
+  img_identifiers:
+    - img.taxon:2763570002
diff --git a/src/data/valid/Database-interleaved.yaml b/src/data/valid/Database-interleaved.yaml
@@ -3849,8 +3849,8 @@ workflow_execution_set:
     scaf_bp: 567890123.0
     ctg_n50: 10000.0
   - id: nmdc:wfmt-99-4d83z.1
-    type: nmdc:MetatranscriptomeAnalysis
-    name: human gut metatranscriptome annotation
+    type: nmdc:MetatranscriptomeExpressionAnalysis
+    name: human gut metatranscriptome expression
     has_input:
       - nmdc:dobj-99-9t74d
     has_output:
@@ -3863,8 +3863,8 @@ workflow_execution_set:
     img_identifiers:
       - img.taxon:2763570002
   - id: nmdc:wfmt-99-74dk4.1
-    type: nmdc:MetatranscriptomeAnalysis
-    name: soil metatranscriptome analysis
+    type: nmdc:MetatranscriptomeExpressionAnalysis
+    name: soil metatranscriptome expression
     has_input:
       - nmdc:dobj-99-74d83z
     has_output:

diff --git a/src/schema/basic_classes.yaml b/src/schema/basic_classes.yaml
@@ -810,6 +810,8 @@ enums:
     permissible_values:
       NucleotideSequencing:
         description: A failure has occurred during nucleotide sequencing, a data generation process.
+      MassSpectrometry:
+        description: A failure has occurred during mass spectrometry, a data generation process.
       Pooling:
         description: A failure has occurred in pooling, a lab process.
       Extraction:
@@ -818,8 +820,8 @@ enums:
         description: A failure has occurred in library preparation, a lab process.
       MetagenomeAssembly:
         description: A failure has occurred in metagenome assembly, a workflow process.
-      MetatranscriptomeAnalysis:
-        description: A failure has occurred in metatranscriptome analysis, a workflow process.
+      MetatranscriptomeExpressionAnalysis:
+        description: A failure has occurred in metatranscriptome expression analysis, a workflow process.
       MagsAnalysis:
         description: A failure has occurred in binning, a workflow process to generate metagenome-assembled genomes (MAGS).
       ReadQcAnalysis:
@@ -828,3 +830,13 @@ enums:
         description: A failure has occurred in reads based taxonomy, a workflow process.
       MetagenomeAnnotation:
         description: A failure has occurred in annotation, a workflow process.
+      MetatranscriptomeAssembly:
+        description: A failure has occurred in assembly, a workflow process.
+      MetatranscriptomeAnnotation:
+        description: A failure has occurred in annotation, a workflow process.
+      MetabolomicsAnalysis:
+        description: A failure has occurred in analyzing metabolomics data.
+      MetaproteomicsAnalysis:
+        description: A failure has occurred in analyzing metaproteomics data.
+      NomAnalysis:
+        description: A failure has occurred in analyzing NOM data.
diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml
@@ -141,7 +141,6 @@ classes:
           syntax: "^gold:Ga[0-9]+$"
           interpolated: true
 
-
   MetatranscriptomeExpressionAnalysis:
     is_a: WorkflowExecution
     description: >-