Remove enum of _entity_experimental_src.host_org_scientific_name

CHANGELOG

@@ -3,7 +3,7 @@
   Updated dictionary NMR-STAR v3.2.1.15 to v3.2.1.18.
   Updated xsd2pgschema to 4.2.1.
   Added remediation for '_chem_comp_identifier.type' for bmr archive.
-  Updated dictionary and translation profiles for processing entries released on 2019-03-13, 2019-05-15, 2019-05-29, 2019-08-28, 2019-12-04, 2020-01-15, 2020-02-05, 2020-07-15, 2020-07-22, 2020-09-02, 2020-09-23, 2020-09-30.
+  Updated dictionary and translation profiles for processing entries released on 2019-03-13, 2019-05-15, 2019-05-29, 2019-08-28, 2019-12-04, 2020-01-15, 2020-02-05, 2020-07-15, 2020-07-22, 2020-09-02, 2020-09-23, 2020-09-30, 2021-08-25.
   Fixed definition of backbone atoms of GLY.
   Added remediation for database accesion code and EC number.
   Added remediation for '_heteronucl_t1rho_list.temp_control_method'.

bmr_src/BMRxTool_DOM.java

@@ -8568,7 +8568,7 @@ private static void write_util_entityexperimentalsrc(String src_dir_name, String
 
 			buffw.write("\t\t}\n\n");
 
-			buffw.write("\t\tif ((" + empty_check("ncbi_taxonomy_id") + ") && (" + empty_check("scientific_name") + " || scientific_name.equalsIgnoreCase(\"not applicable\") || scientific_name.equalsIgnoreCase(\"chemical synthesis\")))\n");
+			buffw.write("\t\tif ((" + empty_check("ncbi_taxonomy_id") + ") && (" + empty_check("scientific_name") + " || scientific_name.equalsIgnoreCase(\"not applicable\") || scientific_name.equalsIgnoreCase(\"chemical synthesis\") || scientific_name.equalsIgnoreCase(\"in vitro\") || scientific_name.equalsIgnoreCase(\"in-vitro\") || scientific_name.equalsIgnoreCase(\"in vitro transcription\")))\n");
 			buffw.write("\t\t\treturn \"na\";\n\n");
 
 			buffw.write("\t\treturn ncbi_taxonomy_id;\n");

bmr_src/BMRxTool_Java.java

@@ -1190,6 +1190,28 @@ else if (class_name.equalsIgnoreCase("PeakGeneralChar")) {
 
 				write_invoke_string_method(buffw);
 
+				// item='host_org_scientific_name'
+				buffw.write("\n\tprivate static boolean set_string_host_org_scientific_name(" + abs_class_name + " list, String method_name, String nil_method_name, boolean required, String val_name, Connection conn_tax, String ncbi_taxonomy_id, FileWriter logw) {\n\n");
+
+				buffw.write("\t\tboolean nil = false;\n\n");
+
+				buffw.write("\t\tString _val_name = val_name;\n\n");
+
+				buffw.write("\t\tif (" + file_prefix + "_" + BMRxTool_DOM.util_main + ".remediate_xml)\n");
+				buffw.write("\t\t\tval_name = " + file_prefix + "_" + BMRxTool_DOM.util_tax + ".getOrganismScientificName(val_name, conn_tax, ncbi_taxonomy_id);\n\n");
+
+				buffw.write("\t\tif (" + file_prefix + "_" + BMRxTool_DOM.util_main + ".remediate_xml && (" + empty_check("val_name") + "))\n");
+				buffw.write("\t\t\tval_name = \"unidentified\";\n\n");
+
+				write_remed_log_code(buffw);
+
+				buffw.write("\t\tif (" + empty_check("val_name") + ")\n");
+				buffw.write("\t\t\tnil = true;\n\n");
+
+				write_missing_log_code(buffw);
+
+				write_invoke_string_method(buffw);
+
 			}
 
 			// category='BMRBx:entity_natural_src'
@@ -3053,8 +3075,8 @@ else if (attr_name_lower.equals("species") && class_name.equalsIgnoreCase("Entit
 						else if (attr_name_lower.equals("organism_name_common") && class_name.equalsIgnoreCase("EntityNaturalSrc"))
 							buffw.write("\t\t\t\t\tif (!set_string_organism_name_common(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, ncbi_taxonomy_id, logw))\n\t\t\t\t\t\tcontinue;\n");
 						// item='organism_name_scientific', category='BMRBx:entity_natural_src'
-						else if ((attr_name_lower.equals("organism_name_scientific")) && class_name.equalsIgnoreCase("EntityNaturalSrc"))
-							buffw.write("\t\t\t\t\tif (!set_string_" + attr_name_lower +"(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, entry_id, ncbi_taxonomy_id, logw, errw))\n\t\t\t\t\t\tcontinue;\n");
+						else if (attr_name_lower.equals("organism_name_scientific") && class_name.equalsIgnoreCase("EntityNaturalSrc"))
+							buffw.write("\t\t\t\t\tif (!set_string_organism_name_scientific(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, entry_id, ncbi_taxonomy_id, logw, errw))\n\t\t\t\t\t\tcontinue;\n");
 
 						// item='host_org_genus', category='BMRBx:entity_experimental_src'
 						else if (attr_name_lower.equals("host_org_genus") && class_name.equalsIgnoreCase("EntityExperimentalSrc"))
@@ -3065,6 +3087,9 @@ else if (attr_name_lower.equals("host_org_species") && class_name.equalsIgnoreCa
 						// item='host_org_name_common', category='BMRBx:entity_experimental_src'
 						else if (attr_name_lower.equals("host_org_name_common") && class_name.equalsIgnoreCase("EntityExperimentalSrc"))
 							buffw.write("\t\t\t\t\tif (!set_string_host_org_name_common(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, ncbi_taxonomy_id, logw))\n\t\t\t\t\t\tcontinue;\n");
+						// item='host_org_scientific_name', category='BMRBx:entity_experimental_src'
+						else if (attr_name_lower.equals("host_org_scientific_name") && class_name.equalsIgnoreCase("EntityExperimentalSrc"))
+							buffw.write("\t\t\t\t\tif (!set_string_host_org_scientific_name(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, ncbi_taxonomy_id, logw))\n\t\t\t\t\t\tcontinue;\n");
 
 						// item='database_code', category='BMRBx:natural_source_db'
 						else if (attr_name_lower.equals("database_code") && class_name.equalsIgnoreCase("NaturalSourceDb"))
@@ -3613,7 +3638,7 @@ else if ((attr_name_lower.equals("experimental_method") || attr_name_lower.equal
 							buffw.write("\t\tif (val_name != null)\n");
 							buffw.write("\t\t\tval_name = " + file_prefix + "_" + BMRxTool_DOM.util_chemcompbond + ".getAromaticFlag(val_name);\n\n");
 
-						}						
+						}
 
 						// item='type'
 						if (attr_name_lower.equals("type")) {
@@ -4261,7 +4286,7 @@ else if ((attr_name_lower.equals("experimental_method") || attr_name_lower.equal
 						if (attr_name_lower.equals("type")) {
 
 							buffw.write("\t\tif (val_name != null)\n");
-							buffw.write("\t\t\tval_name = ent.getType(val_name);\n\n");							
+							buffw.write("\t\t\tval_name = ent.getType(val_name);\n\n");
 
 							buffw.write("\t\tif (" + empty_check("val_name") + ")\n");
 							buffw.write("\t\t\tval_name = \"macromolecule\";\n\n");

bms_src/BMSxTool_DOM.java

@@ -8676,7 +8676,7 @@ private static void write_util_entityexperimentalsrc(String src_dir_name, String
 
 			buffw.write("\t\t}\n\n");
 
-			buffw.write("\t\tif ((" + empty_check("ncbi_taxonomy_id") + ") && (" + empty_check("scientific_name") + " || scientific_name.equalsIgnoreCase(\"not applicable\") || scientific_name.equalsIgnoreCase(\"chemical synthesis\")))\n");
+			buffw.write("\t\tif ((" + empty_check("ncbi_taxonomy_id") + ") && (" + empty_check("scientific_name") + " || scientific_name.equalsIgnoreCase(\"not applicable\") || scientific_name.equalsIgnoreCase(\"chemical synthesis\") || scientific_name.equalsIgnoreCase(\"in vitro\") || scientific_name.equalsIgnoreCase(\"in-vitro\") || scientific_name.equalsIgnoreCase(\"in vitro transcription\")))\n");
 			buffw.write("\t\t\treturn \"na\";\n\n");
 
 			buffw.write("\t\treturn ncbi_taxonomy_id;\n");

bms_src/BMSxTool_Java.java

@@ -1171,6 +1171,28 @@ else if (class_name.equalsIgnoreCase("PeakGeneralChar")) {
 
 				write_invoke_string_method(buffw);
 
+				// item='host_org_scientific_name'
+				buffw.write("\n\tprivate static boolean set_string_host_org_scientific_name(" + abs_class_name + " list, String method_name, String nil_method_name, boolean required, String val_name, Connection conn_tax, String ncbi_taxonomy_id, FileWriter logw) {\n\n");
+
+				buffw.write("\t\tboolean nil = false;\n\n");
+
+				buffw.write("\t\tString _val_name = val_name;\n\n");
+
+				buffw.write("\t\tif (" + file_prefix + "_" + BMSxTool_DOM.util_main + ".remediate_xml)\n");
+				buffw.write("\t\t\tval_name = " + file_prefix + "_" + BMSxTool_DOM.util_tax + ".getOrganismScientificName(val_name, conn_tax, ncbi_taxonomy_id);\n\n");
+
+				buffw.write("\t\tif (" + file_prefix + "_" + BMSxTool_DOM.util_main + ".remediate_xml && (" + empty_check("val_name") + "))\n");
+				buffw.write("\t\t\tval_name = \"unidentified\";\n\n");
+
+				write_remed_log_code(buffw);
+
+				buffw.write("\t\tif (" + empty_check("val_name") + ")\n");
+				buffw.write("\t\t\tnil = true;\n\n");
+
+				write_missing_log_code(buffw);
+
+				write_invoke_string_method(buffw);
+
 			}
 
 			// category='BMRBx:entity_natural_src'
@@ -3109,6 +3131,10 @@ else if (attr_name_lower.equals("species") && class_name.equalsIgnoreCase("Entit
 						// item='organism_name_common', category='BMRBx:entity_natural_src'
 						else if (attr_name_lower.equals("organism_name_common") && class_name.equalsIgnoreCase("EntityNaturalSrc"))
 							buffw.write("\t\t\t\t\tif (!set_string_organism_name_common(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, ncbi_taxonomy_id, logw))\n\t\t\t\t\t\tcontinue;\n");
+						// item='organism_name_scientific', category='BMRBx:entity_natural_src'
+						else if ((attr_name_lower.equals("organism_name_scientific")) && class_name.equalsIgnoreCase("EntityNaturalSrc"))
+							buffw.write("\t\t\t\t\tif (!set_string_organism_name_scientific(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, entry_id, ncbi_taxonomy_id, logw, errw))\n\t\t\t\t\t\tcontinue;\n");
+
 						// item='host_org_genus', category='BMRBx:entity_experimental_src'
 						else if (attr_name_lower.equals("host_org_genus") && class_name.equalsIgnoreCase("EntityExperimentalSrc"))
 							buffw.write("\t\t\t\t\tif (!set_string_host_org_genus(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, ncbi_taxonomy_id, logw))\n\t\t\t\t\t\tcontinue;\n");
@@ -3118,9 +3144,9 @@ else if (attr_name_lower.equals("host_org_species") && class_name.equalsIgnoreCa
 						// item='host_org_name_common', category='BMRBx:entity_experimental_src'
 						else if (attr_name_lower.equals("host_org_name_common") && class_name.equalsIgnoreCase("EntityExperimentalSrc"))
 							buffw.write("\t\t\t\t\tif (!set_string_host_org_name_common(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, ncbi_taxonomy_id, logw))\n\t\t\t\t\t\tcontinue;\n");
-						// item='organism_name_scientific', category='BMRBx:entity_natural_src'
-						else if ((attr_name_lower.equals("organism_name_scientific")) && class_name.equalsIgnoreCase("EntityNaturalSrc"))
-							buffw.write("\t\t\t\t\tif (!set_string_" + attr_name_lower +"(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, entry_id, ncbi_taxonomy_id, logw, errw))\n\t\t\t\t\t\tcontinue;\n");
+						// item='host_org_scientific_name', category='BMRBx:entity_experimental_src'
+						else if (attr_name_lower.equals("host_org_scientific_name") && class_name.equalsIgnoreCase("EntityExperimentalSrc"))
+							buffw.write("\t\t\t\t\tif (!set_string_host_org_scientific_name(list[0], \"" + method_name + "\", \"" + nil_method_name + "\", " + required + ", rset.getString(\"" + column_name + "\"), conn_tax, ncbi_taxonomy_id, logw))\n\t\t\t\t\t\tcontinue;\n");
 
 						// item='database_code', category='BMRBx:natural_source_db'
 						else if (attr_name_lower.equals("database_code") && class_name.equalsIgnoreCase("NaturalSourceDb"))
@@ -3748,8 +3774,8 @@ else if (attr_name_lower.equals("stereo_config") && class_name.equalsIgnoreCase(
 							buffw.write("\t\tif (val_name != null)\n");
 							buffw.write("\t\t\tval_name = " + file_prefix + "_" + BMSxTool_DOM.util_chemcompbond + ".getAromaticFlag(val_name);\n\n");
 
-						}		
-						
+						}
+
 						// item='type'
 						if (attr_name_lower.equals("type")) {