A LOT wrapped up. all search approaches are now standardized and temp…

…lated. 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

@@ -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": { },

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
@@ -2545,38 +2507,61 @@ 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)
 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, '')

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,

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;
+}

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 }};

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>

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>

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">