feat(api): fix csv parsing logic and ensure feature/ai randomization

answer_config.json

@@ -0,0 +1,24 @@
+[
+  {
+    "type": "Text",
+    "title": "What is your diagnosis based on the information you currently have?",
+    "required": true
+  },
+  {
+    "type": "Paragraph",
+    "title": "What additional information do you require to make a final diagnosis?",
+    "required": true
+  },
+  {
+    "type": "SingleChoice",
+    "title": "What is your confidence?",
+    "options": ["High Confidence", "Medium Confidence", "Low Confidence"],
+    "required": false
+  },
+  {
+    "type": "MultipleChoice",
+    "title": "What medical field are you interested in?",
+    "options": ["Cardiology", "Neurology", "Orthopedics", "Radiology"],
+    "required": true
+  }
+]

page_config.json

@@ -0,0 +1,7 @@
+{
+  "Background":           { "concept_ids": [] },
+  "Chief Complaint":      { "concept_ids": [] },
+  "Physical Examination": { "concept_ids": [] },
+  "Vitals":               { "concept_ids": [] },
+  "Labs":                 { "concept_ids": [] }
+}

script/assign_cases/generate_config.sh

@@ -0,0 +1,338 @@
+#!/usr/bin/env sh
+
+# ---------------------------------------------------------------------------------------------------------------
+# generate_config.sh
+#
+# A Shell script to generate a configuration file for assigning cases to users in a database.
+# This script connects to a PostgreSQL database and retrieves a specified number of users and cases,
+# then generates a CSV file with the assigned cases and features for each user.
+#
+# This script requires the following parameters:
+# 1. Database host
+# 2. Database port (default is 5432)
+# 3. Database name
+# 4. Database user
+# 5. Number of users to select
+# 6. Number of cases per user
+# 7. Number of AI cases per user
+# 8. Output CSV file path (default is "config.csv", which is in the same directory as this script)
+#
+# It will create a CSV file for N users sampled from your public.user table, assigns each 24 random person-cases,
+# randomly flags 12 of them for AI (“RISK ASSESSMENT.CRC risk assessments”), and writes out one row per
+# (User, Case No., Path) in exactly the lab’s OMOP format.
+# You can then use this CSV file to configure the assignment of cases to users in your application. Specifically,
+# use it with Postman and the `https://augmed1.dhep.org/admin/config/upload` endpoint to upload the configuration
+# CSV for case assignments. The backend will then use this configuration to assign cases to users.
+#
+# To run:
+# 1. Change directory to the script's location: cd script/assign_cases
+# 1. Run: chmod +x generate_config.sh
+# 2. Run the script: (Remember to remove the # symbols at the beginning of each line)
+#   ./generate_config.sh \
+#     <db_host> \
+#     <db_port> \
+#     <db_name> \
+#     <db_user> \
+#     <number_of_users> \
+#     <cases_per_user> \
+#     <ai_per_user> \
+#     <output_file.csv>
+#
+# Example:
+#   ./generate_config.sh \
+#     localhost \
+#     5433 \
+#     aimaheaddev \
+#     aim_ahead \
+#     6 \
+#     20 10 \
+#     config.csv
+#
+# (Enter your database password when prompted)
+#
+# ---------------------------------------------------------------------------------------------------------------
+
+set -eu
+
+DB_HOST="$1"
+DB_PORT="$2"
+DB_NAME="$3"
+DB_USER="$4"
+NUM_USERS="$5"
+CASES_PER_USER="$6"
+RISK_CASES_PER_USER="$7"
+OUT="$8"
+
+# 1) Print a single header line.  (The CSV parser expects exactly these columns.)
+printf 'User,Case No.,Path,Collapse,Highlight,Top\n' > "$OUT"
+
+# 2) Run one big psql‐COPY that:
+#    • Picks N random users
+#    • Picks M random cases per user (only person_ids that exist in visit_occurrence)
+#    • For each sampled (user,case_id), fetch all leaf‐observations but filter them at random() < 0.5
+#      → emit only those chosen leaves, with Collapse=FALSE, Highlight=TRUE
+#    • Separately, pick K random “risk cases” per user → emit exactly one "CRC risk assessments" row for each
+#      of those, again with Collapse=FALSE, Highlight=TRUE
+psql -h "$DB_HOST" \
+     -p "$DB_PORT" \
+     -U "$DB_USER" \
+     -d "$DB_NAME" \
+     -A -F',' -t <<SQL >> "$OUT"
+WITH
+  -- STEP A: Pick N random users
+  users AS (
+    SELECT email
+    FROM public."user"
+    ORDER BY random()
+    LIMIT $NUM_USERS
+  ),
+
+  -- STEP B: All person_ids that actually have at least one visit (so get_case_by_user won't blow up)
+  valid_persons AS (
+    SELECT DISTINCT person_id
+    FROM public.visit_occurrence
+  ),
+
+  -- STEP C: Cross‐join to pick M random cases/user + K random “risk cases”/user
+  picks AS (
+    SELECT
+      u.email,
+      vp.person_id           AS case_no,
+      ROW_NUMBER() OVER (PARTITION BY u.email ORDER BY random()) AS rn_case,
+      ROW_NUMBER() OVER (PARTITION BY u.email ORDER BY random()) AS rn_risk
+    FROM users u
+    CROSS JOIN valid_persons vp
+  ),
+
+  sample_cases AS (
+    SELECT email, case_no
+    FROM picks
+    WHERE rn_case <= $CASES_PER_USER
+  ),
+
+  risk_cases AS (
+    SELECT email, case_no
+    FROM picks
+    WHERE rn_risk <= $RISK_CASES_PER_USER
+  ),
+
+  -- STEP D: Gather *all* leaf‐level observation rows for each (user,case_id)
+  all_leaves AS (
+    -- BACKGROUND.Family History (4167217)
+    SELECT
+      s.email,
+      s.case_no,
+      'BACKGROUND.Family History.' || o.value_as_string AS path
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4167217
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- BACKGROUND.Social History.Smoke (4041306)
+    SELECT
+      s.email,
+      s.case_no,
+      'BACKGROUND.Social History.Smoke.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4041306
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- BACKGROUND.Social History.Alcohol (4238768)
+    SELECT
+      s.email,
+      s.case_no,
+      'BACKGROUND.Social History.Alcohol.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4238768
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- BACKGROUND.Social History.Drug use (4038710)
+    SELECT
+      s.email,
+      s.case_no,
+      'BACKGROUND.Social History.Drug use.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4038710
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- BACKGROUND.Social History.Sexual behavior (4283657, 4314454)
+    SELECT
+      s.email,
+      s.case_no,
+      'BACKGROUND.Social History.Sexual behavior.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id IN (4283657, 4314454)
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- BACKGROUND.Medical History (1008364)
+    SELECT
+      s.email,
+      s.case_no,
+      'BACKGROUND.Medical History.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 1008364
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PATIENT COMPLAINT.Chief Complaint (38000282)
+    SELECT
+      s.email,
+      s.case_no,
+      'PATIENT COMPLAINT.Chief Complaint.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 38000282
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PATIENT COMPLAINT.Current Symptoms (38000280, 38000281, 44814721, 38000276)
+    SELECT
+      s.email,
+      s.case_no,
+      'PATIENT COMPLAINT.Current Symptoms.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id IN (38000280, 38000281, 44814721, 38000276)
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PHYSICAL EXAMINATION.Abdomen (4152368)
+    SELECT
+      s.email,
+      s.case_no,
+      'PHYSICAL EXAMINATION.Abdomen.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4152368
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PHYSICAL EXAMINATION.Respiratory (4090320)
+    SELECT
+      s.email,
+      s.case_no,
+      'PHYSICAL EXAMINATION.Respiratory.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4090320
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PHYSICAL EXAMINATION.Vital Signs (4263222)
+    SELECT
+      s.email,
+      s.case_no,
+      'PHYSICAL EXAMINATION.Vital Signs.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4263222
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PHYSICAL EXAMINATION.Neurological (4154954)
+    SELECT
+      s.email,
+      s.case_no,
+      'PHYSICAL EXAMINATION.Neurological.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4154954
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PHYSICAL EXAMINATION.Ophthalmology (4080843)
+    SELECT
+      s.email,
+      s.case_no,
+      'PHYSICAL EXAMINATION.Ophthalmology.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4080843
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PHYSICAL EXAMINATION.Cardiovascular (36717771)
+    SELECT
+      s.email,
+      s.case_no,
+      'PHYSICAL EXAMINATION.Cardiovascular.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 36717771
+     AND o.value_as_string IS NOT NULL
+
+    UNION ALL
+    -- PHYSICAL EXAMINATION.Physical Characteristics (4086988)
+    SELECT
+      s.email,
+      s.case_no,
+      'PHYSICAL EXAMINATION.Physical Characteristics.' || o.value_as_string
+    FROM sample_cases s
+    JOIN public.observation o
+      ON o.person_id = s.case_no
+     AND o.observation_concept_id = 4086988
+     AND o.value_as_string IS NOT NULL
+  ),
+
+  -- STEP E: From all_leaves, randomly pick ~50% to “show” (WHERE random()<0.5)
+  shown_leaves AS (
+    SELECT email, case_no, path
+    FROM all_leaves
+    WHERE random() < 0.5
+  ),
+
+  -- STEP F: Emit exactly one CSV‐row for each chosen leaf, with Collapse=FALSE,Highlight=TRUE
+  leaf_rows AS (
+    SELECT
+      sl.email    AS "User",
+      sl.case_no  AS "Case No.",
+      sl.path     AS Path,
+      'FALSE'     AS Collapse,
+      'TRUE'      AS Highlight,
+      ''          AS Top
+    FROM shown_leaves sl
+  ),
+
+  -- STEP G: Emit one “CRC risk assessments” row for each (user,case_no) in risk_cases
+  risk_rows AS (
+    SELECT
+      rc.email   AS "User",
+      rc.case_no AS "Case No.",
+      'RISK ASSESSMENT.CRC risk assessments' AS Path,
+      'FALSE'    AS Collapse,
+      'TRUE'     AS Highlight,
+      ''         AS Top
+    FROM risk_cases rc
+  )
+
+-- UNION together leaf_rows + risk_rows
+SELECT * FROM leaf_rows
+UNION ALL
+SELECT * FROM risk_rows;
+SQL
+
+echo "Wrote $OUT"