Move SUPeR Viewer UMAP + pseudobulk endpoints to feature/steven-changes

Removes Steven's umap_expression and super_viewer_gene_expression
endpoints, their tests, namespace registration, the 7 pseudobulk
databases' schema-catalog/config/combined_master.json entries, and the
14 UMAP+pseudobulk MySQL binds/init.sh imports from this branch -- all
preserved on feature/steven-changes instead. Database count in
test_efp_schemas.py drops from 198 back to 191.

Author: rmobmina

api/__init__.py

@@ -93,8 +93,6 @@ def create_app():
     from api.resources.llama3 import llama3
     from api.resources.gene_expression import gene_expression
     from api.resources.gene_density import gene_density
-    from api.resources.umap_expression import umap_expression
-    from api.resources.super_viewer_gene_expression import super_viewer_gene_expression
 
     bar_api.add_namespace(gene_information)
     bar_api.add_namespace(gaia)
@@ -112,8 +110,6 @@ def create_app():
     bar_api.add_namespace(llama3)
     bar_api.add_namespace(gene_expression)
     bar_api.add_namespace(gene_density)
-    bar_api.add_namespace(umap_expression)
-    bar_api.add_namespace(super_viewer_gene_expression)
     bar_api.init_app(bar_app)
     return bar_app
 

api/models/efp_schemas.py

@@ -57,12 +57,6 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec:
     "affydb",
     "apple",
     "arabidopsis_ecotypes",
-    "arabidopsis_NIE_pseudobulk",
-    "arabidopsis_flower_lee_pseudobulk",
-    "arabidopsis_root_rs_pseudobulk",
-    "arabidopsis_seed_martin_pseudobulk",
-    "arabidopsis_silique_lee_pseudobulk",
-    "arabidopsis_stem_lee_pseudobulk",
     "arachis",
     "atgenexp",
     "atgenexp_hormone",
@@ -184,7 +178,6 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec:
     "rice_maize_comparison",
     "rice_mas",
     "rice_metabolite",
-    "rice_OW_pseudobulk",
     "rice_rma",
     "rice_root",
     "rohan",

api/resources/super_viewer_gene_expression.py

@@ -44,18 +44,4 @@ SQLALCHEMY_BINDS = {
     'tomato_sequence' :  'mysql://root:root@localhost/tomato_sequence',
     'triphysaria' :  'mysql://root:root@localhost/triphysaria',
     'gaia' : 'mysql://root:root@localhost/gaia',
-    'arabidopsis_NIE_pseudobulk': 'mysql://root:root@localhost/arabidopsis_NIE_pseudobulk',
-    'arabidopsis_flower_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_flower_lee_pseudobulk',
-    'arabidopsis_root_rs_pseudobulk': 'mysql://root:root@localhost/arabidopsis_root_rs_pseudobulk',
-    'arabidopsis_seed_martin_pseudobulk': 'mysql://root:root@localhost/arabidopsis_seed_martin_pseudobulk',
-    'arabidopsis_silique_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_silique_lee_pseudobulk',
-    'arabidopsis_stem_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_stem_lee_pseudobulk',
-    'rice_OW_pseudobulk': 'mysql://root:root@localhost/rice_OW_pseudobulk',
-    'arabidopsis_NIE_umap': 'mysql://root:root@localhost/arabidopsis_NIE_umap',
-    'arabidopsis_flower_lee_umap': 'mysql://root:root@localhost/arabidopsis_flower_lee_umap',
-    'arabidopsis_root_shahan_umap': 'mysql://root:root@localhost/arabidopsis_root_shahan_umap',
-    'arabidopsis_seed_martin_umap': 'mysql://root:root@localhost/arabidopsis_seed_martin_umap',
-    'arabidopsis_silique_lee_umap': 'mysql://root:root@localhost/arabidopsis_silique_lee_umap',
-    'arabidopsis_stem_lee_umap': 'mysql://root:root@localhost/arabidopsis_stem_lee_umap',
-    'rice_OW_umap': 'mysql://root:root@localhost/rice_OW_umap'
 }

api/resources/umap_expression.py

@@ -54,24 +54,6 @@ mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/tomato_nssnp.sql
 mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/tomato_sequence.sql
 mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/triphysaria.sql
 
-# SUPeR Viewer pseudobulk + UMAP databases (real per-gene dumps with an extra
-# data_signal_std column on the pseudobulk side, and a separate umap_coords /
-# umap_expression pair on the UMAP side).
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_NIE_pseudobulk_dump.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_flower_lee_pseudobulk_dump.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_root_rs_pseudobulk_dump.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seed_martin_pseudobulk_dump.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_silique_lee_pseudobulk_dump.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_stem_lee_pseudobulk_dump.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/rice_OW_pseudobulk_dump.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_NIE_umap.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_flower_lee_umap.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_root_shahan_umap.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seed_martin_umap.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_silique_lee_umap.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_stem_lee_umap.sql
-mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < ./config/databases/rice_OW_umap.sql
-
 echo "Data are now loaded. Preparing API config"
 echo "Please manually edit config file!"