fix(pppdb): update xlsx and fixes relative to condition/properties va…

…lues (#32)

* fix(pppdb): update chi.xslx with valid BigSMILES

Single quotes where removed.

* fix(pppdb): ambiguous log

An "other" could be logged as "solvent".

* feat(pppdb): add FetchPubChemResult type

* fix(pppdb): temperature could have undefined value

* fix(pppdb): interaction_param for Type-1

* doc(pppdb): update comments

* doc(pppdb): update comments

scripts/typescript/src/pppdb/pppdb-loader.ts

@@ -299,34 +299,38 @@ export class PPPDBLoader {
 
  // shared conditions
  {
- if( !chi_row.chimax ) {
-
- // single temperature value
- if( !chi_row.tempmax ) {
- this.validate_and_push_condition( shared_by_all_properties, {
- node: ['Condition'],
- key: 'temperature',
- type: 'value',
- value: chi_row.temperature,
- unit: chi_row.tempunit
- });
-
- // min/max temperature values
- } else if ( chi_row.temperature ) {
- this.validate_and_push_condition( shared_by_all_properties, {
- node: ['Condition'],
- key: 'temperature',
- type: 'min',
- value: chi_row.temperature, // temperature is considered as min in such case
- unit: chi_row.tempunit
- });
- this.validate_and_push_condition( shared_by_all_properties, { 
- node: ['Condition'],
- key: 'temperature',
- type: 'max',
- value: chi_row.tempmax,
- unit: chi_row.tempunit
- });
+ if( chi_row.chimax === undefined ) {
+ if( chi_row.temperature !== undefined) {
+
+ // When we have no "tempmax", we store "temperature" as value.
+ if( chi_row.tempmax === undefined ) {
+ this.validate_and_push_condition( shared_by_all_properties, {
+ node: ['Condition'],
+ key: 'temperature',
+ type: 'value',
+ value: chi_row.temperature,
+ unit: chi_row.tempunit
+ });
+
+ // Otherwise, we store "temperature" as "min", and "tempmax" as "max".
+ } else {
+ this.validate_and_push_condition( shared_by_all_properties, {
+ node: ['Condition'],
+ key: 'temperature',
+ type: 'min',
+ value: chi_row.temperature, // temperature is considered as min in such case
+ unit: chi_row.tempunit
+ });
+ this.validate_and_push_condition( shared_by_all_properties, {
+ node: ['Condition'],
+ key: 'temperature',
+ type: 'max',
+ value: chi_row.tempmax,
+ unit: chi_row.tempunit
+ });
+ }
+ } else {
+ this.logger.warning(`Unable to add condition, "temperature" column is undefined`)
  }
 
  if( chi_row.refvolume ) {
@@ -378,40 +382,47 @@ export class PPPDBLoader {
  switch( chi_row.type ) {
  case "Type 1":
 
- if( !chi_row.chimax ) {
-
- this.validate_and_push_property(combined_material, {
- node: ['Property'],
- key: 'interaction_param',
- type: 'value',
- value: chi_row.chinumber,
- uncertainty: chi_row.chierror,
- unit: null,
- ...shared_by_all_properties,
- } satisfies IProperty);
-
- } else if (chi_row.chinumber && chi_row.chimax) {
-
- // interaction param (min)
- this.validate_and_push_property( combined_material, {
- node: ['Property'],
- key: 'interaction_param',
- type: 'min',
- value: chi_row.chinumber,
- unit: null,
- ...shared_by_all_properties,
- });
-
- // interaction param (max)
- this.validate_and_push_property( combined_material, {
- node: ['Property'],
- key: 'interaction_param',
- type: 'max',
- value: chi_row.chimax,
- unit: null,
- ...shared_by_all_properties,
- });
+ if( chi_row.chinumber !== undefined ) {
+
+ // If "chimax" is not defined, we interpret "chinumber" as "interaction_param" ("value")
+ if( chi_row.chimax === undefined ) {
+ this.validate_and_push_property(combined_material, {
+ node: ['Property'],
+ key: 'interaction_param',
+ type: 'value',
+ value: chi_row.chinumber,
+ uncertainty: chi_row.chierror,
+ unit: null,
+ ...shared_by_all_properties,
+ } satisfies IProperty);
+
+ // Otherwise, we interpret "chinumber" - "interaction_param - "min" and "chimax" as "max".
+ } else {
+
+ // interaction param (min)
+ this.validate_and_push_property( combined_material, {
+ node: ['Property'],
+ key: 'interaction_param',
+ type: 'min',
+ value: chi_row.chinumber,
+ unit: null,
+ ...shared_by_all_properties,
+ });
+
+ // interaction param (max)
+ this.validate_and_push_property( combined_material, {
+ node: ['Property'],
+ key: 'interaction_param',
+ type: 'max',
+ value: chi_row.chimax,
+ unit: null,
+ ...shared_by_all_properties,
+ });
+ }
+ } else if ( chi_row.chimax ) {
+ this.logger.warning(`chinumber is undefined but chimax is defined, interaction_param skipped`)
  }
+
  break;
 
  case 'Type 3':
@@ -534,6 +545,12 @@ export class PPPDBLoader {
  */
  validate_and_push_condition(node_with_condition: { condition: ICondition[]}, condition: ICondition) {
  this.validator.validate_or_throw(condition);
+
+ // Add a manual check on value (validtion does not detect it)
+ if( condition.value === undefined ) {
+ throw new Error(`Condition has an undefined value!`)
+ }
+
  node_with_condition.condition.push(condition);
  }
 
@@ -542,6 +559,12 @@ export class PPPDBLoader {
  */
  validate_and_push_property(node_with_property: { property: IProperty[] }, property: IProperty): void | never {
  this.validator.validate_or_throw(property);
+
+ // Add a manual check on value (validation does not detect it)
+ if( property.value === undefined ) {
+ throw new Error(`Property has an undefined value!`)
+ }
+
  node_with_property.property.push(property);
  }