Update matrix

src/soa_builder/web/app.py

@@ -91,6 +91,7 @@
     soa_exists,
     load_epoch_type_map,
     table_has_columns as _table_has_columns,
+    iso_duration_to_days,
 )
 
 # Audit functions
@@ -3569,12 +3570,49 @@ def ui_edit(request: Request, soa_id: int):
     cur_inst = conn_inst.cursor()
     cur_inst.execute(
         """
-        SELECT i.id,i.name,i.instance_uid,
-        (SELECT t.name from schedule_timelines t WHERE t.schedule_timeline_uid=i.member_of_timeline AND t.soa_id=i.soa_id) as timeline_name,
-        (SELECT v.name from visit v WHERE v.encounter_uid=i.encounter_uid and v.soa_id=i.soa_id) as encounter_name,
-        (SELECT e.name FROM epoch e WHERE e.epoch_uid=i.epoch_uid AND e.soa_id=i.soa_id) as epoch_name
-        FROM instances i WHERE soa_id=?
-        ORDER BY member_of_timeline,length(instance_uid),instance_uid
+        SELECT i.id,
+               i.name,
+               i.instance_uid,
+               i.label,
+               (SELECT t.name
+                  FROM schedule_timelines t
+                 WHERE t.schedule_timeline_uid = i.member_of_timeline
+                   AND t.soa_id = i.soa_id) AS timeline_name,
+               (SELECT v.name
+                  FROM visit v
+                 WHERE v.encounter_uid = i.encounter_uid
+                   AND v.soa_id = i.soa_id) AS encounter_name,
+               (SELECT e.name
+                  FROM epoch e
+                 WHERE e.epoch_uid = i.epoch_uid
+                   AND e.soa_id = i.soa_id) AS epoch_name,
+               (SELECT tm.window_label
+                  FROM visit v
+                  JOIN timing tm
+                    ON tm.id = v.scheduledAtId
+                   AND tm.soa_id = v.soa_id
+                 WHERE v.encounter_uid = i.encounter_uid
+                   AND v.soa_id = i.soa_id
+                 LIMIT 1) AS window_label,
+                 (SELECT tm.label
+                  FROM visit v
+                  JOIN timing tm
+                    ON tm.id = v.scheduledAtId
+                   AND tm.soa_id = v.soa_id
+                 WHERE v.encounter_uid = i.encounter_uid
+                   AND v.soa_id = i.soa_id
+                 LIMIT 1) AS timing_label,
+                 (SELECT tm.value
+                  FROM visit v
+                  JOIN timing tm
+                    ON tm.id = v.scheduledAtId
+                   AND tm.soa_id = v.soa_id
+                 WHERE v.encounter_uid = i.encounter_uid
+                   AND v.soa_id = i.soa_id
+                 LIMIT 1) AS study_day
+        FROM instances i
+        WHERE soa_id=?
+        ORDER BY member_of_timeline, length(instance_uid), instance_uid
         """,
         (soa_id,),
     )
@@ -3583,9 +3621,13 @@ def ui_edit(request: Request, soa_id: int):
             "id": r[0],
             "name": r[1],
             "instance_uid": r[2],
-            "timeline_name": r[3],
-            "encounter_name": r[4],
-            "epoch_name": r[5],
+            "label": r[3],
+            "timeline_name": r[4],
+            "encounter_name": r[5],
+            "epoch_name": r[6],
+            "window_label": r[7],
+            "timing_label": r[8],
+            "study_day": iso_duration_to_days(r[9]),
         }
         for r in cur_inst.fetchall()
     ]

src/soa_builder/web/templates/edit.html

@@ -188,15 +188,66 @@ <h2>Editing SoA {{ soa_id }}</h2>
 <hr />
 <h3>Matrix</h3>
 <table class="matrix">
+  <tr class="matrix-scheduled-instance-row">
+    <th></th>
+    <th style="text-align:right;font-size:0.50em;">Timeline Name:-></th>
+    {% for inst in instances %}
+      <th style="text-align:center;font-size:0.50em;">
+        {% if inst.timeline_name %}{{ inst.timeline_name }}{% endif %}
+      </th>
+    {% endfor %}
+  </tr>
+  <tr class="matrix-encounter-row">
+    <th></th>
+    <th style="text-align:right;font-size:0.50em;">Encounter Name:-></th>
+    {% for inst in instances %}
+    <th style="text-align:center;font-size:0.50em;">
+      {% if inst.encounter_name %}{{ inst.encounter_name }}{% endif %}
+    </th>
+    {% endfor %}
+  </tr>
+  <tr class="matrix-epoch-row">
+    <th></th>
+    <th style="text-align:right;font-size:0.50em;">Epoch:-></th>
+    {% for inst in instances %}
+    <th style="text-align:center;font-size:0.50em;">
+      {% if inst.epoch_name %}{{ inst.epoch_name }}{% endif %}
+    </th>
+    {% endfor %}
+  </tr>
+  <tr class="matrix-timing-label-row">
+    <th></th>
+    <th style="text-align:right;font-size:0.50em;">Timing Label:-></th>
+    {% for inst in instances %}
+    <th style="text-align:center;font-size:0.50em;">
+      {% if inst.timing_label %}{{ inst.timing_label }}{% endif %}
+    </th>
+    {% endfor %}
+  </tr>
+  <tr class="matrix-study-day-row">
+    <th></th>
+    <th style="text-align:right;font-size:0.50em;">Study Day:-></th>
+    {% for inst in instances %}
+    <th style="text-align:center;font-size:0.50em;">
+      {% if inst.study_day %}{{ inst.study_day }}{% endif %}
+    </th>
+    {% endfor %}
+  </tr>
+  <tr class="matrix-visit-window-row">
+    <th></th>
+    <th style="text-align:right;font-size:0.50em;">Visit Window:-></th>
+    {% for inst in instances %}
+    <th style="text-align:center;font-size:0.50em;">
+        {% if inst.window_label %}{{ inst.window_label }}{% endif %}
+    </th>
+    {% endfor %}
+  </tr>
   <tr>
     <th>Activity</th>
     <th>Concepts</th>
     {% for inst in instances %}
     <th style="min-width: 70px; vertical-align: top;" data-instance-id="{{ inst.id }}" data-visit-id="{{ inst.id }}">
-      <div style="font-size:0.65em;color:#555;line-height:1.1;text-align:left;">{% if inst.timeline_name %}{{ inst.timeline_name or '' }}{% endif %}</div>
-      <div>{{ inst.name }}</div>
-      <div style="font-size:0.65em;color:#555;line-height:1.1;text-align:left;">{% if inst.encounter_name %}{{ inst.encounter_name }}{% endif %}</div>
-      <div style="font-size:0.65em;color:#555;line-height:1.1;text-align:left;">{% if inst.epoch_name %}{{ inst.epoch_name }}{% endif %}</div>
+      <div style="color: #1976d2;" {%if inst.label %}title="Scheduled Activity Instance: {{ inst.label }}"{% endif %}>{{ inst.name }}</div>
     </th>
     {% endfor %}
   </tr>

src/soa_builder/web/templates/elements.html

@@ -88,8 +88,9 @@ <h2>Elements for SoA {{ soa_id }}</h2>
     <tr>
       <td colspan="8" style="padding:6px;color:#777;">No elements yet.</td>
     </tr>
+    {% endfor %}
 </table>
-{% endfor %}
+
 
 
 

src/soa_builder/web/templates/instances.html

@@ -20,7 +20,7 @@ <h2>Scheduled Activity Instances for SoA {{ soa_id }}</h2>
         <div style="display: flex;flex-direction: column;gap:2px;">
             <label><strong>Default Condition ID</strong></label>
             <select name="default_condition_uid">
-                <option name="">-- Select Activity Instance --</option>
+                <option value="">-- Select Activity Instance --</option>
                 {% for name, instance_uid in (instance_options or {}).items() %}
                     <option value="{{ instance_uid }}">{{ name }}: [{{ instance_uid }}]</option>
                 {% endfor %}

src/soa_builder/web/templates/rules.html

@@ -58,6 +58,7 @@ <h2>Transition Rules for SoA {{ soa_id }}</h2>
     <tr>
       <td colspan="7" style="padding:6px;color:#777;">No rules yet.</td>
     </tr>
+    {% endfor %}
 </table>
-{% endfor %}
+
 {% endblock %}

src/soa_builder/web/utils.py

@@ -1,5 +1,6 @@
 from typing import Any, Dict, List
 import os
+import re
 import requests
 import time
 from .db import _connect
@@ -29,6 +30,64 @@
 _CONTACT_MODE_CACHE_TTL = 60 * 60  # 1 hour
 
 
+# Constants for the helper function
+_ISO_DURATION_RE = re.compile(
+    r"^P"  # starts with 'P'
+    r"(?:(?P<years>\d+)Y)?"  # years
+    r"(?:(?P<months>\d+)M)?"  # months (date part)
+    r"(?:(?P<weeks>\d+)W)?"  # weeks
+    r"(?:(?P<days>\d+)D)?"  # days
+    r"(?:T"  # time part
+    r"(?:(?P<hours>\d+)H)?"
+    r"(?:(?P<minutes>\d+)M)?"
+    r"(?:(?P<seconds>\d+)S)?"
+    r")?$"
+)
+
+
+# Helper function to convert ISO-8601 duration/period strings
+# to days, using these common approximations for years and months
+"""
+    1 year = 365 days
+    1 month = 30 days
+    1 week = 7 days
+    1 hour = 1/24 day
+    1 minute = 1/(24*60) day
+    1 second = 1/(24*3600) day
+"""
+
+
+def iso_duration_to_days(iso_duration: str) -> float:
+    """
+    Convert an ISO-8601 duration (e.g. 'P1D', 'P2W', 'P1Y2M3D', 'P1DT12H')
+    into a number of days (float).
+
+    Uses approximations: 1Y=365d, 1M=30d.
+    Returns:
+        float: Number of days represented by the duration.
+        None: If the input is empty or not a valid ISO-8601 duration string.
+    """
+    if not iso_duration:
+        return None
+
+    m = _ISO_DURATION_RE.match(iso_duration)
+    if not m:
+        return None
+
+    parts = {k: int(v) if v is not None else 0 for k, v in m.groupdict().items()}
+
+    days = 0.0
+    days += parts["years"] * 365
+    days += parts["months"] * 30
+    days += parts["weeks"] * 7
+    days += parts["days"]
+    days += parts["hours"] / 24.0
+    days += parts["minutes"] / (24.0 * 60.0)
+    days += parts["seconds"] / (24.0 * 3600.0)
+
+    return days
+
+
 def get_cdisc_api_key():
     return os.environ.get("CDISC_API_KEY")
 

src/usdm/generate_study_timings.py

@@ -157,7 +157,7 @@ def build_usdm_timings(
                 "id": type,
                 "extensionAttributes": [],
                 "code": t_code[0],
-                "codeSystem": t_codeSystem[0],
+                "codeSystem": "db://" + t_codeSystem[0],
                 "codeSystemVersion": t_codeSystemVersion[0],
                 "decode": t_decode[0],
                 "instanceType": "Code",
@@ -168,7 +168,7 @@ def build_usdm_timings(
                 "id": relative_to_from,
                 "extensionAttributes": [],
                 "code": rtf_code[0],
-                "codeSystem": rtf_codeSystem[0],
+                "codeSystem": "db://" + rtf_codeSystem[0],
                 "codeSystemVersion": rtf_codeSystemVersion[0],
                 "decode": rtf_decode[0],
                 "instanceType": "Code",