From 39358c1d622affd0b574fd1e282e59ead44c4acf Mon Sep 17 00:00:00 2001
From: John Major <daylily@daylilyinformatics.com>
Date: Wed, 7 Aug 2024 04:34:54 -0700
Subject: [PATCH] A LOT wrapped up.  all search approaches are now standardized
 and templated. files and file sets look good.  admin WYSIWYG config editor
 works, as does improved detail view property editor.  general style tidying.
 some performance improvements. code housekeeping.  Basically, this is ready
 to roll.  remaining big nice todos: automate pulling in xcures files, play
 with superset integration.  One real to-do is a proper larger instance stress
 test with 100s of k of database records at the least (large file slogging
 harder and costly to test).  I'm pleased

---
 bloom_lims/config/file/file_set.json   |   2 +-
 main.py                                | 138 +++++++++++--------------
 setup.py                               |   2 +-
 static/skins/bloom.css                 |  22 ++++
 templates/dewey.html                   |  14 +++
 templates/file_search.html             |   4 +-
 templates/file_set_search_results.html |   4 +-
 templates/search_file_sets.html        |  47 +++++++--
 templates/search_results.html          |  86 ++++++++++++++-
 9 files changed, 225 insertions(+), 94 deletions(-)

diff --git a/bloom_lims/config/file/file_set.json b/bloom_lims/config/file/file_set.json
index d8b755b..8cc30f9 100644
--- a/bloom_lims/config/file/file_set.json
+++ b/bloom_lims/config/file/file_set.json
@@ -20,7 +20,7 @@
         {"property_key":"tag","form_label":"Tag", "required": false, "value_type":"uid-interactive"},
         {"property_key":"tags","form_label":"Tags", "required": false, "value_type":"list"},
         {"property_key": "creating_user", "form_label":"Creating User", "required":false, "value_type":"uid-static"},
-        {"property_key": "ref_type", "form_label":"Ref Type", "required":false, "value_type":"query-only-uid-statuc"},
+        {"property_key": "ref_type", "form_label":"Ref Type", "required":false, "value_type":"uid-static"},
         {"property_key": "comments", "form_label": "Comments", "required": false, "value_type": "string"}       
       ],
       "controlled_properties": { },
diff --git a/main.py b/main.py
index dd973ab..7ccc473 100644
--- a/main.py
+++ b/main.py
@@ -2298,73 +2298,34 @@ async def search_files(
     created_datetime_end: str = Form(None),
     creating_user: List[str] = Form(None),
 ):
-    search_criteria = {}
-
-    if euid:
-        search_criteria["euid"] = euid
-
-    if patient_id:
-        if len(patient_id) == 1 and patient_id[0] == ".na":
-            patient_id = ""        
-        
-        if len(patient_id) == 1 and patient_id[0] == "":
-            pass
-        else:   
-            search_criteria["patient_id"] = patient_id
-
-    if clinician_id:   
-        if len(clinician_id) == 1 and clinician_id[0] == ".na": 
-            clinician_id = ""
-        if len(clinician_id) == 1 and clinician_id[0] == "":
-            pass
-        else:
-            search_criteria["clinician_id"] = clinician_id
     
+    form_data = {
+    "euid": euid,
+    "patient_id": patient_id,
+    "clinician_id": clinician_id,
+    "lab_code": lab_code,
+    "purpose": purpose,
+    "purpose_subtype": purpose_subtype,
+    "category": category,
+    "sub_category": sub_category,
+    "sub_category_2": sub_category_2,
+    "study_id": study_id,
+    "comments": comments,
+    "creating_user": creating_user,
+    }
+    
+    search_fields = [
+        "euid", "patient_id", "clinician_id", "lab_code", "purpose", "purpose_subtype", 
+        "category", "sub_category", "sub_category_2", "study_id", "comments", "creating_user"
+    ]
+    
+    search_criteria = create_search_criteria(form_data, search_fields)
+        
     if relevant_datetime_start or relevant_datetime_end:
         search_criteria["relevant_datetime"] = {
             "start": relevant_datetime_start,
             "end": relevant_datetime_end
         }
-    
-    if lab_code:
-        if len(lab_code) == 1 and lab_code[0] == ".na":
-            lab_code = ""
-        
-        if len(lab_code) == 1 and lab_code[0] == "":
-            pass
-        else:
-            search_criteria["lab_code"] = lab_code
-    
-    if purpose:
-        search_criteria["purpose"] = purpose
-    if purpose_subtype:
-        search_criteria["purpose_subtype"] = purpose_subtype
-    if category:
-        search_criteria["category"] = category
-    if sub_category:
-        search_criteria["sub_category"] = sub_category
-    if sub_category_2:
-        search_criteria["sub_category_2"] = sub_category_2
-    if study_id:
-        if len(study_id) == 1 and study_id[0] == ".na":
-            study_id = ""
-        
-        if len(study_id) == 1 and study_id[0] == "":
-            pass
-        else:   
-            search_criteria["study_id"] = study_id
-    
-    if comments:
-        search_criteria["comments"] = comments
-    
-    if creating_user:
-        if len(creating_user) == 1 and creating_user[0] == ".na":
-            creating_user = ""
-        
-        if len(creating_user) == 1 and creating_user[0] == "":
-            pass
-        else:
-            search_criteria["creating_user"] = creating_user
 
     greedy = is_greedy == "yes"
 
@@ -2511,7 +2472,8 @@ async def create_file_set(
             "comments": comments,
             "ref_type": ref_type,
             "duration": duration,
-            "rclone_config": rclone_config
+            "rclone_config": rclone_config,
+            "creating_user": request.session["user_data"]["email"],
         }
 
         # Create the file set
@@ -2545,6 +2507,27 @@ async def create_file_set(
 
     except Exception as e:
         raise (e)
+    
+    
+def create_search_criteria(form_data, fields):
+    search_criteria = {}
+    for field in fields:
+        field_value = form_data.get(field)
+        if field_value:
+            if isinstance(field_value, list):
+                if len(field_value) == 1 and field_value[0] in [".na"]:
+                    field_value = ""
+                if len(field_value) == 1 and field_value[0] in [""]:
+                    continue
+                search_criteria[field] = field_value
+            else:
+                if field_value in [".na"]:
+                    field_value = ""
+                if field_value in [""]:
+                    continue
+                search_criteria[field] = field_value
+    return search_criteria
+
 
 # The following is very redundant to the file_search and <s>probably</s> should be refactored
 @app.post("/search_file_sets", response_class=HTMLResponse)
@@ -2552,31 +2535,33 @@ async def search_file_sets(
     request: Request,
     name: str = Form(None),
     description: str = Form(None),
-    tag: str = Form(None),
+    tag: List[str] = Form(None),
     comments: str = Form(None),
     file_euids: str = Form(None),
     is_greedy: str = Form("yes"),
-    ref_type: str = Form(None),
+    ref_type: List[str] = Form(None),
+    creating_user: List[str] = Form(None),
 ):
-    search_criteria = {}
 
-    if name:
-        search_criteria["name"] = name
-    if description:
-        search_criteria["description"] = description
-    if tag:
-        search_criteria["tag"] = tag
-    if comments:
-        search_criteria["comments"] = comments
+    form_data = {
+            "name": name,
+            "description": description,
+            "tag": tag,
+            "comments": comments,
+            "file_euids": file_euids,
+            "ref_type": ref_type,
+            "creating_user": creating_user,
+        }
 
-    q_ds = {"properties": search_criteria}
+    search_fields = ["name", "description", "tag", "comments", "ref_type", "creating_user"]
+    search_criteria = create_search_criteria(form_data, search_fields)
 
     greedy = is_greedy == "yes"
 
     try:
         bfs = BloomFileSet(BLOOMdb3(app_username=request.session["user_data"]["email"]))
         file_sets = bfs.search_objs_by_addl_metadata(
-            q_ds, greedy, "file_set", super_type="file"
+            {'properties':search_criteria}, greedy, "file_set", super_type="file"
         )
 
         # Fetch details for each EUID
@@ -2609,12 +2594,14 @@ async def search_file_sets(
         user_data = request.session.get("user_data", {})
         style = {"skin_css": user_data.get("style_css", "static/skins/bloom.css")}
 
+        num_results = len(table_data)
         content = templates.get_template("file_set_search_results.html").render(
             request=request,
             table_data=table_data,
             columns=columns,
             style=style,
             udat=user_data,
+            num_results=num_results,
         )
         return HTMLResponse(content=content)
 
@@ -2798,7 +2785,6 @@ def generate_ui_form_fields(ui_form_properties: List[Dict], controlled_propertie
                         required=required
                     ))
             else:
-                #from IPython import embed; embed()
                 unique_values = sorted(bobject.get_unique_property_values(property_key, super_type=super_type, btype=btype, b_sub_type=b_sub_type, version=version))
                 if '' not in unique_values:
                     unique_values.insert(0, '')
diff --git a/setup.py b/setup.py
index b6c494b..b6a35b9 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name="bloom_lims",
-    version="0.10.4",
+    version="0.10.5",
     packages=find_packages(),
     install_requires=[
         # Add dependencies here,
diff --git a/static/skins/bloom.css b/static/skins/bloom.css
index 14b279c..78a8643 100644
--- a/static/skins/bloom.css
+++ b/static/skins/bloom.css
@@ -53,4 +53,26 @@
 }
 
 
+input[type="date" i] {
+    font-family: inherit;
+    padding-inline-start: 1px;
+    cursor: default;
+    padding: inherit;
+    border: inherit;
+    overflow: hidden;
+}
 
+input[type="file" i] {
+    font-family: inherit;
+    appearance: none;
+    background-color: inherit;
+    cursor: default;
+    align-items: baseline;
+    color: inherit;
+    text-overflow: ellipsis;
+    text-align: start !important;
+    padding: initial;
+    border: inherit;
+    white-space: pre;
+    overflow: hidden !important;
+}
\ No newline at end of file
diff --git a/templates/dewey.html b/templates/dewey.html
index f34542d..871a6a4 100644
--- a/templates/dewey.html
+++ b/templates/dewey.html
@@ -35,6 +35,20 @@
             color: var(--text-color);
             border-color: var(--button-border-color);
         }
+
+        .div.selectize-input {
+            padding: inherit;
+            border: inherit;
+            margin: inherit;
+            position: inherit;
+        }
+        .selectize-input {
+            padding: inherit;
+            border: inherit;
+            margin: inherit;
+            position: inherit;
+            background-color: var(--form-in-bg-color);
+        }
     </style>
     <script>
         const controlledProperties = {{ controlled_properties | tojson | safe }};
diff --git a/templates/file_search.html b/templates/file_search.html
index 2a3c13c..257eb9c 100644
--- a/templates/file_search.html
+++ b/templates/file_search.html
@@ -2,8 +2,8 @@
     <ul>
         <h3>Search Files</h3>
         <table>
-            <tr>
-                <td style="align:top;">
+            <tr style="vertical-align: top;">
+                <td style="align:top; width:22%;">
                     <!-- New form for querying by EUIDs -->
                     <form id="queryByEuidsForm" action="query_by_euids" method="post" enctype="multipart/form-data">
                         <label for="file_euids">File EUIDs (one per line):</label>
diff --git a/templates/file_set_search_results.html b/templates/file_set_search_results.html
index caa47f1..bd8eb93 100644
--- a/templates/file_set_search_results.html
+++ b/templates/file_set_search_results.html
@@ -12,7 +12,7 @@
 <body>
     {% include 'bloom_header.html' %}
 
-    <h1>Search Results</h1>
+    <h1>{{ num_results }} Results</h1>
 
     <table id="results-table" border="1">
         <thead>
@@ -27,7 +27,9 @@ <h1>Search Results</h1>
             {% for row in table_data %}
             <tr>
                 <td>
+                    {% if row['ref_type'] == 'presigned_url' %}
                     <a href="/file_set_urls?fs_euid={{ row['EUID'] }}" target="_blank">View Presigned URLSs</a>
+                    {% endif %}
                 </td> <!-- New cell with the link -->
                 {% for column in columns %}
                 <td>
diff --git a/templates/search_file_sets.html b/templates/search_file_sets.html
index ab3df5b..f6372d5 100644
--- a/templates/search_file_sets.html
+++ b/templates/search_file_sets.html
@@ -2,20 +2,47 @@
     <ul>
         <h3>Search File Sets By</h3>
         <form id="searchFileSetForm" action="search_file_sets" method="post" enctype="multipart/form-data">
-            <label for="file_set_name">Name: </label>
-            <input type="text" id="file_set_name" name="file_set_name" value=""><br><br>
 
-            <label for="file_set_description">Description: </label>
-            <input type="text" id="file_set_description" name="file_set_description" value=""><br><br>
 
-            <label for="file_set_tag">Tag: </label>
-            <input type="text" id="file_set_tag" name="file_set_tag" value=""><br><br>
 
-            <label for="comments">Comments: </label>
-            <input type="text" id="comments" name="comments" value=""><br><br>
+            {% for field in ui_search_fields_fset %}
+            <div>
+                {% if field.name in ["tags",  "xxx"] %}
+
+                {% else %}
+                
+                  {% if field.type == "select" and field.multiple %}
+                    
+                    <label for="{{ field.name }}">{{ field.label }}</label>          
+                    <div class="option-buttons" data-select-id="{{ field.name }}">
+                        <select class="no-selectize" name="{{ field.name }}" id="{{ field.name }}" multiple style="display: none;">
+                            <option value="" selected></option> <!-- Placeholder for blank state -->
+                            <option value=".na">isnull</option>
+                            {% for option in field.options %}
+                                <option value="{{ option }}">{{ option }}</option>
+                            {% endfor %}
+                        </select>
+                    </div>
+                    {% elif field.type == "select" %}
+                    <label for="{{ field.name }}">{{ field.label }}</label>          
+                    <select class="no-selectize" name="{{ field.name }}" id="{{ field.name }}">
+                            <option value="" selected></option> <!-- Placeholder for blank state -->
+                            <option value=".na">isnull</option>
+                            {% for option in field.options %}
+                                <option value="{{ option }}">{{ option }}</option>
+                            {% endfor %}
+                        </select>
+                    {% else %}
+                        {% if not field.name.endswith('_datetime') %}
+                        <label for="{{ field.name }}">{{ field.label }}</label>
+                        <input type="{{ field.type }}" name="{{ field.name }}" id="{{ field.name }}" />
+                        {% endif %}
+                    {% endif %}
+            {% endif %}
+            </div>
+
+            {% endfor %}
 
-            <label for="file_euids">File EUIDs (not working presently): </label>
-            <input type="text" id="file_euids" name="file_euids" value=""><br><br>
 
             <label for="is_greedy">Greedy Search: </label>
             <select name="is_greedy">
diff --git a/templates/search_results.html b/templates/search_results.html
index e556661..6f73e67 100644
--- a/templates/search_results.html
+++ b/templates/search_results.html
@@ -11,6 +11,10 @@
     <link rel="stylesheet" type="text/css" href="{{ style.skin_css }}">
     <link rel="stylesheet" type="text/css" href="static/style.css">
     <script src="static/action_buttons.js"></script>
+
+    <script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
+    <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.13.3/css/selectize.css" />
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.13.3/js/standalone/selectize.min.js"></script>
     <script>
         function toggleSelectAll(checkboxClass, masterCheckboxId) {
             const checkboxes = document.querySelectorAll(checkboxClass);
@@ -119,6 +123,67 @@
             header.classList.toggle('descending', isAscending);
         }
     </script>
+
+
+    <script>
+        
+        function updateDependentFields(formContext) {
+            function populateSelectField(selectFieldId, options) {
+                const selectField = $(`[data-form=${formContext}] #${selectFieldId}`);
+                selectField.empty();
+                options.forEach(function(option) {
+                    selectField.append(new Option(option, option));
+                });
+                selectField.trigger('change');
+            }
+
+            function handleFieldChange(field, dependentField, enumObj, formContext) {
+                $(`[data-form=${formContext}] #${field}`).change(function() {
+                    const selectedValue = $(this).val();
+                    const dependentOptions = enumObj[selectedValue] || [];
+                    populateSelectField(dependentField, dependentOptions, formContext);
+                });
+            }
+
+            Object.keys(controlledProperties).forEach(function(prop) {
+                if (controlledProperties[prop].type === "dependent string") {
+                    const dependentField = controlledProperties[prop].on;
+                    const enumObj = controlledProperties[prop].enum;
+                    handleFieldChange(dependentField, prop, enumObj, formContext);
+                }
+            });
+        }
+
+        function filterOptions(event) {
+            const input = event.target.value.toLowerCase();
+            const selectField = event.target;
+            const options = selectField.options;
+
+            for (let i = 0; i < options.length; i++) {
+                const optionText = options[i].text.toLowerCase();
+                if (optionText.includes(input) || options[i].value === "") {
+                    options[i].style.display = "";
+                } else {
+                    options[i].style.display = "none";
+                }
+            }
+        }
+
+        $(document).ready(function() {
+            $('#tag').selectize({
+                create: true,
+                sortField: [{ field: 'value', direction: 'asc' }],
+                placeholder: 'Select or type to add...',
+                persist: false,
+                render: {
+                    option_create: function(data, escape) {
+                        return '<div class="create">Create: <strong>' + escape(data.input) + '</strong>&hellip;</div>';
+                    }
+                }
+            });
+        });
+
+    </script>
     <style>
         .floating-button {
             position: fixed;
@@ -194,13 +259,27 @@
         th.descending::after {
             content: ' \25BC'; /* Down arrow */
         }
+
+        .div.selectize-input {
+            padding: inherit;
+            border: inherit;
+            margin: inherit;
+            position: inherit;
+        }
+        .selectize-input {
+            padding: inherit;
+            border: inherit;
+            margin: inherit;
+            position: inherit;
+            background-color: var(--form-in-bg-color);
+        }
     </style>
 </head>
 <body>
     {% include 'bloom_header.html' %}
 
     <h1>{{ n_results }} File Search Results</h1>
-    <form id="fileSetForm" action="/create_file_set" method="post">
+    <form id="fileSetForm" action="/create_file_set" method="post"  >
         <div style="display: flex;">
             <div class="form-section" style="background-color: rgba(255, 204, 204, 0.1);">
                 <div class="form-group">
@@ -235,8 +314,8 @@ <h1>{{ n_results }} File Search Results</h1>
                             
                               
                             <label for="{{ field.name }}">{{ field.label }}</label>
-        
-                            <select name="{{ field.name }}" id="{{ field.name }}" class="select-filter">
+                            
+                            <select data-form="create-fs" name="{{ field.name }}" id="{{ field.name }}" class="select-filter">
                                 <option value="" selected></option> <!-- Placeholder for blank state -->
                                 {% for option in field.options %}
                                     <option value="{{ option }}">{{ option }}</option>
@@ -446,5 +525,6 @@ <h1>{{ n_results }} File Search Results</h1>
     });
 </script>
 
+    {% include 'pre_body_close.html' %}
 </body>
 </html>