refactor(db): Reflect metadata view columns.

Ecogenomics · Apr 29, 2024 · e880a39 · e880a39
1 parent d2c0eb5
commit e880a39
Showing 1 changed file with 18 additions and 28 deletions.
diff --git a/api/db/models.py b/api/db/models.py
@@ -273,17 +273,6 @@ class MetadataView(GtdbBase):
     organism_name = Column(Text)
     description = Column(Text)
     username = Column(Text)
-    study_description = Column(Text)
-    sequencing_platform = Column(Text)
-    read_files = Column(Text)
-    qc_program = Column(Text)
-    assembly_program = Column(Text)
-    gap_filling_program = Column(Text)
-    mapping_program = Column(Text)
-    binning_program = Column(Text)
-    scaffolding_program = Column(Text)
-    genome_assessment_program = Column(Text)
-    refinement_description = Column(Text)
     scaffold_count = Column(Integer)
     gc_count = Column(Integer)
     longest_scaffold = Column(Integer)
@@ -313,12 +302,12 @@ class MetadataView(GtdbBase):
     checkm_genome_count = Column(Integer)
     checkm_marker_set_count = Column(Integer)
     checkm_strain_heterogeneity = Column(DOUBLE_PRECISION)
-    checkm2_completeness = Column(DOUBLE_PRECISION)
-    checkm2_contamination = Column(DOUBLE_PRECISION)
-    checkm2_model = Column(Text)
     lsu_23s_count = Column(Integer)
     lsu_5s_count = Column(Integer)
     checkm_strain_heterogeneity_100 = Column(DOUBLE_PRECISION)
+    checkm2_completeness = Column(DOUBLE_PRECISION)
+    checkm2_contamination = Column(DOUBLE_PRECISION)
+    checkm2_model = Column(Text)
     ncbi_taxonomy = Column(Text)
     gtdb_class = Column(Text)
     gtdb_species = Column(Text)
@@ -381,6 +370,7 @@ class MetadataView(GtdbBase):
     ncbi_genome_category = Column(Text)
     ncbi_wgs_formatted = Column(Text)
     ncbi_cds_count = Column(Integer)
+    ncbi_untrustworthy_as_type = Column(Boolean)
     ssu_gg_taxonomy = Column(Text)
     ssu_gg_blast_bitscore = Column(DOUBLE_PRECISION)
     ssu_gg_blast_subject_id = Column(Text)
@@ -410,20 +400,6 @@ class MetadataView(GtdbBase):
     lsu_5s_query_id = Column(Text)
     lsu_5s_length = Column(Integer)
     lsu_5s_contig_len = Column(Integer)
-    gtdb_taxonomy = Column(Text)
-    mimag_high_quality = Column(Boolean)
-    mimag_medium_quality = Column(Boolean)
-    mimag_low_quality = Column(Boolean)
-    gtdb_genus_type_species = Column(Boolean)
-    gtdb_species_type_strain = Column(Boolean)
-    gtdb_cluster_size = Column(BIGINT)
-    gtdb_clustered_genomes = Column(Text)
-    gtdb_type_designation_ncbi_taxa = Column(Text)
-    gtdb_type_designation_ncbi_taxa_sources = Column(Text)
-    lpsn_type_designation = Column(Text)
-    dsmz_type_designation = Column(Text)
-    lpsn_priority_year = Column(Integer)
-    gtdb_type_species_of_genus = Column(Boolean)
     seqcode_id = Column(Integer)
     seqcode_name = Column(Text)
     seqcode_rank = Column(Text)
@@ -444,6 +420,20 @@ class MetadataView(GtdbBase):
     seqcode_updated_at = Column(Text)
     seqcode_url = Column(Text)
     seqcode_priority_date = Column(Text)
+    gtdb_taxonomy = Column(Text)
+    mimag_high_quality = Column(Boolean)
+    mimag_medium_quality = Column(Boolean)
+    mimag_low_quality = Column(Boolean)
+    gtdb_genus_type_species = Column(Boolean)
+    gtdb_species_type_strain = Column(Boolean)
+    gtdb_cluster_size = Column(BIGINT)
+    gtdb_clustered_genomes = Column(Text)
+    gtdb_type_designation_ncbi_taxa = Column(Text)
+    gtdb_type_designation_ncbi_taxa_sources = Column(Text)
+    lpsn_type_designation = Column(Text)
+    dsmz_type_designation = Column(Text)
+    lpsn_priority_year = Column(Integer)
+    gtdb_type_species_of_genus = Column(Boolean)
 
 
 class GenomeLists(GtdbBase):  # OK