@sjcrh/proteinpaint-rust 2.167.0 → 2.170.0

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Files changed (7) hide show
  1. package/Cargo.toml +8 -4
  2. package/package.json +1 -1
  3. package/src/aichatbot.rs +307 -310
  4. package/src/manhattan_plot.rs +31 -16
  5. package/src/query_classification.rs +152 -0
  6. package/src/summary_agent.rs +201 -0
  7. package/src/test_ai.rs +81 -58
package/src/test_ai.rs CHANGED
@@ -5,6 +5,7 @@ fn main() {}
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5
 
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6
  #[cfg(test)]
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7
  mod tests {
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+ use crate::aichatbot::{AiJsonFormat, AnswerFormat, SummaryType, llm_backend, run_pipeline};
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  use serde_json;
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  use std::fs::{self};
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  use std::path::Path;
@@ -20,6 +21,7 @@ mod tests {
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  ollama_comp_model_name: String,
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  ollama_embedding_model_name: String,
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  genomes: Vec<Genomes>,
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+ aiRoute: String,
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  }
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26
 
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  #[derive(PartialEq, Debug, Clone, schemars::JsonSchema, serde::Serialize, serde::Deserialize)]
@@ -49,7 +51,7 @@ mod tests {
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51
 
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  // Parse the JSON data
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  let serverconfig: ServerConfig = serde_json::from_str(&data).expect("JSON not in serverconfig.json format");
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-
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+ let airoute = String::from("../../") + &serverconfig.aiRoute;
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  for genome in &serverconfig.genomes {
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  for dataset in &genome.datasets {
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  match &dataset.aifiles {
@@ -61,13 +63,13 @@ mod tests {
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  // Read the file
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  let ai_data = fs::read_to_string(ai_json_file).unwrap();
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  // Parse the JSON data
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- let ai_json: super::super::AiJsonFormat =
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+ let ai_json: AiJsonFormat =
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  serde_json::from_str(&ai_data).expect("AI JSON file does not have the correct format");
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  //println!("ai_json:{:?}", ai_json);
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  let genedb = String::from(&serverconfig.tpmasterdir) + &"/" + &ai_json.genedb;
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  let dataset_db = String::from(&serverconfig.tpmasterdir) + &"/" + &ai_json.db;
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  let llm_backend_name = &serverconfig.llm_backend;
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- let llm_backend_type: super::super::llm_backend;
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+ let llm_backend_type: llm_backend;
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73
 
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  if llm_backend_name != "ollama" && llm_backend_name != "SJ" {
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  panic!(
@@ -77,7 +79,7 @@ mod tests {
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  let ollama_host = &serverconfig.ollama_apilink;
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  let ollama_embedding_model_name = &serverconfig.ollama_embedding_model_name;
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  let ollama_comp_model_name = &serverconfig.ollama_comp_model_name;
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- llm_backend_type = super::super::llm_backend::Ollama();
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+ llm_backend_type = llm_backend::Ollama();
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  let ollama_client = super::super::ollama::Client::builder()
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  .base_url(ollama_host)
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  .build()
@@ -85,40 +87,45 @@ mod tests {
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  let embedding_model = ollama_client.embedding_model(ollama_embedding_model_name);
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  let comp_model = ollama_client.completion_model(ollama_comp_model_name);
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  for chart in ai_json.charts.clone() {
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- match chart {
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- super::super::Charts::Summary(testdata) => {
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- for ques_ans in testdata.TestData {
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- let user_input = ques_ans.question;
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- let llm_output = super::super::run_pipeline(
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- &user_input,
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- comp_model.clone(),
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- embedding_model.clone(),
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- llm_backend_type.clone(),
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- temperature,
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- max_new_tokens,
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- top_p,
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- &dataset_db,
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- &genedb,
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- &ai_json,
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- testing,
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- )
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- .await;
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- let mut llm_json_value: super::super::SummaryType = serde_json::from_str(&llm_output.unwrap()).expect("Did not get a valid JSON of type {action: summary, summaryterms:[{clinical: term1}, {geneExpression: gene}], filter:[{term: term1, value: value1}]} from the LLM");
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- let mut expected_json_value: super::super::SummaryType = serde_json::from_str(&ques_ans.answer).expect("Did not get a valid JSON of type {action: summary, summaryterms:[{clinical: term1}, {geneExpression: gene}], filter:[{term: term1, value: value1}]} from the LLM");
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- assert_eq!(
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- llm_json_value.sort_summarytype_struct(),
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- expected_json_value.sort_summarytype_struct()
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- );
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+ if chart.r#type == "Summary" {
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+ for ques_ans in chart.TestData {
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+ let user_input = ques_ans.question;
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+ let llm_output = run_pipeline(
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+ &user_input,
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+ comp_model.clone(),
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+ embedding_model.clone(),
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+ llm_backend_type.clone(),
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+ temperature,
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+ max_new_tokens,
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+ top_p,
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+ &dataset_db,
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+ &genedb,
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+ &ai_json,
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+ &airoute,
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+ testing,
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+ )
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+ .await;
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+ let llm_json_value: SummaryType = serde_json::from_str(&llm_output.unwrap()).expect("Did not get a valid JSON of type {action: summary, summaryterms:[{clinical: term1}, {geneExpression: gene}], filter:[{term: term1, value: value1}]} from the LLM");
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+ match ques_ans.answer {
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+ AnswerFormat::summary_type(sum) => {
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+ //println!("expected answer:{:?}", &sum);
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+ assert_eq!(
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+ llm_json_value.sort_summarytype_struct(),
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+ sum.sort_summarytype_struct()
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+ );
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+ }
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+ AnswerFormat::DE_type(_) => {
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+ panic!("DE type not valid for summary")
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+ }
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120
  }
113
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  }
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- super::super::Charts::DE(_testdata) => {} // To do
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  }
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  }
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  } else if *llm_backend_name == "SJ".to_string() {
118
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  let sjprovider_host = &serverconfig.sj_apilink;
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  let sj_embedding_model_name = &serverconfig.sj_embedding_model_name;
120
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  let sj_comp_model_name = &serverconfig.sj_comp_model_name;
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- llm_backend_type = super::super::llm_backend::Sj();
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+ llm_backend_type = llm_backend::Sj();
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  let sj_client = super::super::sjprovider::Client::builder()
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  .base_url(sjprovider_host)
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  .build()
@@ -127,37 +134,53 @@ mod tests {
127
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  let comp_model = sj_client.completion_model(sj_comp_model_name);
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135
 
129
136
  for chart in ai_json.charts.clone() {
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- match chart {
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- super::super::Charts::Summary(testdata) => {
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- for ques_ans in testdata.TestData {
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- let user_input = ques_ans.question;
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- if user_input.len() > 0 {
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- let llm_output = super::super::run_pipeline(
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- &user_input,
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- comp_model.clone(),
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- embedding_model.clone(),
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- llm_backend_type.clone(),
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- temperature,
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- max_new_tokens,
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- top_p,
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- &dataset_db,
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- &genedb,
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- &ai_json,
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- testing,
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- )
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- .await;
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- let mut llm_json_value: super::super::SummaryType = serde_json::from_str(&llm_output.unwrap()).expect("Did not get a valid JSON of type {action: summary, summaryterms:[{clinical: term1}, {geneExpression: gene}], filter:[{term: term1, value: value1}]} from the LLM");
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- let mut expected_json_value: super::super::SummaryType = serde_json::from_str(&ques_ans.answer).expect("Did not get a valid JSON of type {action: summary, summaryterms:[{clinical: term1}, {geneExpression: gene}], filter:[{term: term1, value: value1}]} from the LLM");
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- assert_eq!(
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- llm_json_value.sort_summarytype_struct(),
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- expected_json_value.sort_summarytype_struct()
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- );
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- } else {
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- panic!("The user input is empty");
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+ if chart.r#type == "Summary" {
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+ for ques_ans in chart.TestData {
139
+ let user_input = ques_ans.question;
140
+ if user_input.len() > 0 {
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+ let llm_output = run_pipeline(
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+ &user_input,
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+ comp_model.clone(),
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+ embedding_model.clone(),
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+ llm_backend_type.clone(),
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+ temperature,
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+ max_new_tokens,
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+ top_p,
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+ &dataset_db,
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+ &genedb,
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+ &ai_json,
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+ &airoute,
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+ testing,
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+ )
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+ .await;
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+ //println!("user_input:{}", user_input);
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+ //println!("llm_answer:{:?}", llm_output);
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+ //println!("expected answer:{:?}", &ques_ans.answer);
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+ let llm_json_value: SummaryType = serde_json::from_str(&llm_output.unwrap()).expect("Did not get a valid JSON of type {action: summary, summaryterms:[{clinical: term1}, {geneExpression: gene}], filter:[{term: term1, value: value1}]} from the LLM");
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+ //println!(
161
+ // "llm_answer:{:?}",
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+ // llm_json_value.clone().sort_summarytype_struct()
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+ //);
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+ //println!(
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+ // "expected answer:{:?}",
166
+ // &expected_json_value.clone().sort_summarytype_struct()
167
+ //);
168
+ match ques_ans.answer {
169
+ AnswerFormat::summary_type(sum) => {
170
+ //println!("expected answer:{:?}", &sum);
171
+ assert_eq!(
172
+ llm_json_value.sort_summarytype_struct(),
173
+ sum.sort_summarytype_struct()
174
+ );
175
+ }
176
+ AnswerFormat::DE_type(_) => {
177
+ panic!("DE type not valid for summary")
178
+ }
157
179
  }
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+ } else {
181
+ panic!("The user input is empty");
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182
  }
159
183
  }
160
- super::super::Charts::DE(_testdata) => {} // To do
161
184
  }
162
185
  }
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186
  }