Feature rm expwarn (#93)

* remove warnings caused by blastn asset file

* lower case all names

* rename job assets

synphage/assets/__init__.py

@@ -2,11 +2,11 @@
 
 from . import ncbi_connect, user_data, status, blaster, viewer
 
-NCBI_CONNECT = "NCBI_connect"
-USERS_INPUT = "Users_input"
-STATUS = "Status"
-BLASTER = "Blaster"
-VIEWER = "Viewer"
+NCBI_CONNECT = "ncbi_connect"
+USERS_INPUT = "users_input"
+STATUS = "status"
+BLASTER = "blaster"
+VIEWER = "viewer"
 
 ncbi_connect_assets = load_assets_from_package_module(
     package_module=ncbi_connect,

synphage/assets/blaster/n_blaster.py

@@ -1,13 +1,16 @@
-from dagster import asset
+from dagster import asset, ExperimentalWarning
 
 import os
 import pickle
+import warnings
 import polars as pl
 
 from pathlib import Path
 from typing import List
 from collections import namedtuple
 
+warnings.filterwarnings("ignore", category=ExperimentalWarning)
+
 
 FastaNRecord = namedtuple("FastaNRecord", "new,history")
 BlastNRecord = namedtuple("BlastNRecord", "new,history")

synphage/assets/viewer/static_graph.py

@@ -1,11 +1,10 @@
-from dagster import asset, Config, MetadataValue, AssetObservation, AssetSpec, ExperimentalWarning
+from dagster import asset, Config, MetadataValue, AssetObservation, AssetSpec
 
 import enum
 import os
 import base64
 import math
 import tempfile
-import warnings
 
 import polars as pl
 
@@ -25,7 +24,6 @@
 from string import Template
 from PIL import ImageColor
 
-warnings.filterwarnings("ignore", category=ExperimentalWarning)
 
 TEMP_DIR = tempfile.gettempdir()
 

synphage/jobs.py

@@ -15,61 +15,61 @@
 
 # Job 1 : get data from the user
 get_user_data = define_asset_job(
-    name="get_user_data",
+    name="step_1a_get_user_data",
     selection=(
-        AssetSelection.groups("Users_input")
-        | AssetSelection.groups("Status")
+        AssetSelection.groups("users_input")
+        | AssetSelection.groups("status")
         & AssetSelection.assets("genbank_history").downstream(depth=2)
     ),
 )
 
 # Job 2 : download gb files from the ncbi database
 download = define_asset_job(
-    name="download",
+    name="step_1b_download",
     selection=(
-        AssetSelection.groups("NCBI_connect")
-        | AssetSelection.groups("Status")
+        AssetSelection.groups("ncbi_connect")
+        | AssetSelection.groups("status")
         & AssetSelection.assets("genbank_history").downstream(depth=2)
     ),
 )
 
 # Job 3 : validations with to reload + refresh UI
 validations = define_asset_job(
-    name="make_validation",
-    selection=AssetSelection.groups("Status")
+    name="step_2_make_validation",
+    selection=AssetSelection.groups("status")
     & AssetSelection.assets("reload_ui_asset").downstream(depth=3),
 )
 
 # Job 4 : blastn
 blastn = define_asset_job(
-    name="make_blastn",
+    name="step_3a_make_blastn",
     selection=(
         AssetSelection.assets("append_processed_df")
-        | AssetSelection.groups("Blaster")
+        | AssetSelection.groups("blaster")
         & AssetSelection.assets("create_fasta_n").downstream()
     ),
 )
 
 # Job 5 : blastp
 blastp = define_asset_job(
-    name="make_blastp",
+    name="step_3b_make_blastp",
     selection=(
         AssetSelection.assets("append_processed_df")
-        | AssetSelection.groups("Blaster")
+        | AssetSelection.groups("blaster")
         & AssetSelection.assets("create_fasta_p").downstream()
     ),
 )
 
 # Job 6 : blastn and blastp combined
 all_blast = define_asset_job(
-    name="make_all_blast",
+    name="step_3c_make_all_blast",
     selection=(
-        AssetSelection.assets("append_processed_df") | AssetSelection.groups("Blaster")
+        AssetSelection.assets("append_processed_df") | AssetSelection.groups("blaster")
     ),
 )
 
 # Job 7 : create the synteny diagram
 plot = define_asset_job(
-    name="make_plot",
-    selection=AssetSelection.groups("Viewer"),
+    name="step_4_make_plot",
+    selection=AssetSelection.groups("viewer"),
 )