updates

cli/specdb

@@ -146,14 +146,15 @@ if   sdb.command == 'create':
 		print('Aborting')
 		sys.exit()
 
-	if not sdb.backup.endswith('.db'):
-		print(f'{sdb.backup} does not end in .db')
-		print('change database name with .db at the end')
-		print('Aborting')
-		sys.exit()
+	if sdb.backup:
+		if not sdb.backup.endswith('.db'):
+			print(f'{sdb.backup} does not end in .db')
+			print('change database name with .db at the end')
+			print('Aborting')
+			sys.exit()
 
 	specdb_path = os.path.abspath(sdb.db)
-	backup_path = os.path.abspath(sdb.backup)
+	if sdb.backup: backup_path = os.path.abspath(sdb.backup)
 
 	if os.path.isfile(specdb_path):
 		print(f'db file {sdb.db} already exists')
@@ -169,7 +170,7 @@ if   sdb.command == 'create':
 
 	# initial SQLite database at SPECDB_DB location
 	Create.init(location=specdb_path)
-	Create.init(location=backup_path)
+	if sdb.backup: Create.init(location=backup_path)
 	print('db configured and initialized')
 	print('Done')
 

sql/specdb.sql

@@ -136,7 +136,7 @@ CREATE TABLE buffer_components ( -- describe the component(s) of a buffer, REQUI
 	buffer_id              TEXT NOT NULL,                                                              -- `buffer_id` this component goes to, must already be in buffer table, Ex: hn4071
 	buffer_component       TEXT CHECK( length(buffer_component)                 <= 64 ) NOT NULL,      -- name of the component, len <= 64, Ex: NaCl
 	buffer_component_value FLOAT NOT NULL,                                                             -- the numeric concentration value of the component, Ex: 100.0
-	buffer_component_unit  TEXT CHECK( buffer_component_unit in ('mM', '% (v/v)', 'mg/mL') ) NOT NULL, -- unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM
+	buffer_component_unit  TEXT CHECK( buffer_component_unit in ('mM', 'uM', 'x', '% (v/v)', 'mg/mL') ) NOT NULL, -- unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM
 	isotopic_labeling      TEXT DEFAULT "natural abundance",
 	UNIQUE(buffer_id, buffer_component),
 	FOREIGN KEY ([buffer_id]) REFERENCES "buffer" ([buffer_id]) ON DELETE NO ACTION ON UPDATE CASCADE
@@ -211,6 +211,10 @@ CREATE TABLE batch_components ( -- describe the purification batches in a pst, R
 	FOREIGN KEY ([batch_id]) REFERENCES "purification_batch"  ([batch_id]) ON DELETE NO ACTION ON UPDATE CASCADE
 );
 
+INSERT INTO batch_components (pst_id, batch_id, conc, conc_unit)
+VALUES
+	("NONE", "NONE", "0.0", "mM");
+
 CREATE TABLE spectrometer ( -- spectrometer information, REQUIRED: `spectrometer_id`, `manufacturer``, `field_strength`
 	id                   INTEGER PRIMARY KEY NOT NULL,
 	spectrometer_id      TEXT CHECK( spectrometer_id NOT LIKE '% %' and length(spectrometer_id) <= 32 ) NOT NULL,         -- text identifier for spectrometer, must be unique, no spaces, len <= 32, EX: HU800