Improve 'view data' view, add download links

datameta/api/metadatasets.py

@@ -18,7 +18,7 @@
 from pyramid.request import Request
 from typing import Optional, Dict
 from ..linting import validate_metadataset_record
-from .. import security, siteid, models
+from .. import security, siteid, models, resource
 from ..security import authz
 import datetime
 from ..resource import resource_by_id, get_identifier
@@ -29,25 +29,25 @@
 class MetaDataSetResponse(DataHolderBase):
     """MetaDataSetResponse container for OpenApi communication"""
     id: dict
-    record: dict
+    record: Dict[str, Optional[str]]
+    file_ids: Dict[str, Optional[Dict[str, str]]]
     user_id: str
     submission_id: Optional[str] = None
 
-def render_record_values(mdatum:Dict[str, models.MetaDatum], record:dict) -> dict:
+def render_record_values(metadata:Dict[str, models.MetaDatum], record:dict) -> dict:
     """Renders values of a metadataset record. Please note: the record should already have passed validation."""
     record_rendered = record.copy()
-    for field in mdatum:
+    for field in metadata:
         if not field in record_rendered.keys():
             # if field is not contained in record, add it as None to the record:
             record_rendered[field] = None
             continue
-        elif record_rendered[field] and mdatum[field].datetimefmt:
+        elif record_rendered[field] and metadata[field].datetimefmt:
             # if MetaDatum is a datetime field, render the value in isoformat
             record_rendered[field] = datetime.datetime.strptime(
                     record_rendered[field],
-                    mdatum[field].datetimefmt
+                    metadata[field].datetimefmt
                 ).isoformat()
-
     return record_rendered
 
 def formatted_mrec_value(mrec):
@@ -59,9 +59,9 @@ def formatted_mrec_value(mrec):
 def get_record_from_metadataset(mdata_set:models.MetaDataSet) -> dict:
     """ Construct a dict containing all records of that MetaDataSet"""
     return {
-        rec.metadatum.name: formatted_mrec_value(rec)
-        for rec in mdata_set.metadatumrecords
-    }
+            rec.metadatum.name : formatted_mrec_value(rec)
+            for rec in mdata_set.metadatumrecords
+            }
 
 def delete_staged_metadataset_from_db(mdata_id, db, auth_user, request):
     # Find the requested metadataset
@@ -124,8 +124,8 @@ def post(request:Request) -> MetaDataSetResponse:
     mdatum_query = db.query(models.MetaDatum).order_by(
         models.MetaDatum.order
     ).all()
-    mdatum = {mdat.name: mdat for mdat in mdatum_query }
-    record = render_record_values(mdatum, record)
+    metadata = {mdat.name: mdat for mdat in mdatum_query }
+    record = render_record_values(metadata, record)
 
     # construct new MetaDataSet:
     mdata_set = models.MetaDataSet(
@@ -139,18 +139,19 @@ def post(request:Request) -> MetaDataSetResponse:
     # construct new MetaDatumRecords
     for name, value in record.items():
         mdatum_rec = models.MetaDatumRecord(
-            metadatum_id = mdatum[name].id,
-            metadataset_id = mdata_set.id,
-            file_id = None,
-            value = value
+            metadatum_id     = metadata[name].id,
+            metadataset_id   = mdata_set.id,
+            file_id          = None,
+            value            = value
         )
         db.add(mdatum_rec)
 
     return MetaDataSetResponse(
-        id             = get_identifier(mdata_set),
-        record         = record,
-        user_id        = get_identifier(mdata_set.user),
-        submission_id  = get_identifier(mdata_set.submission) if mdata_set.submission else None,
+        id              = get_identifier(mdata_set),
+        record          = record,
+        file_ids        = { name : None for name, metadatum in metadata.items() if metadatum.isfile },
+        user_id         = get_identifier(mdata_set.user),
+        submission_id   = get_identifier(mdata_set.submission) if mdata_set.submission else None,
     )
 
 @view_config(
@@ -160,7 +161,7 @@ def post(request:Request) -> MetaDataSetResponse:
     openapi=True
 )
 def get_metadataset(request:Request) -> MetaDataSetResponse:
-    """Create new metadataset"""
+    """Get a metadataset by ID"""
     auth_user = security.revalidate_user(request)
     db = request.dbsession
     mdata_set = resource_by_id(db, models.MetaDataSet, request.matchdict['id'])
@@ -172,10 +173,11 @@ def get_metadataset(request:Request) -> MetaDataSetResponse:
         raise HTTPForbidden()
 
     return MetaDataSetResponse(
-        id=get_identifier(mdata_set),
-        record=get_record_from_metadataset(mdata_set),
-        user_id=get_identifier(mdata_set.user),
-        submission_id=get_identifier(mdata_set.submission) if mdata_set.submission else None,
+        id              = get_identifier(mdata_set),
+        record          = get_record_from_metadataset(mdata_set),
+        file_ids        = { mdrec.metadatum.name : resource.get_identifier_or_none(mdrec.file) for mdrec in mdata_set.metadatumrecords if mdrec.metadatum.isfile },
+        user_id         = get_identifier(mdata_set.user),
+        submission_id   = get_identifier(mdata_set.submission) if mdata_set.submission else None,
     )
 
 @view_config(

datameta/api/openapi.yaml

@@ -15,7 +15,7 @@
 openapi: 3.0.0
 info:
   description: DataMeta
-  version: 0.15.0
+  version: 0.16.0
   title: DataMeta
 
 servers:
@@ -1096,8 +1096,11 @@ components:
         record:
           type: object
           additionalProperties: true
-          # a free-form object,
-          # any property is allowed
+          # a free-form object, any property is allowed
+        fileIds:
+          type: object
+          additionalProperties: true
+          # a free-form object mapping the field names to file IDs
         id:
           $ref: "#/components/schemas/Identifier"
         submissionId:   

datameta/api/ui/view.py

@@ -27,7 +27,8 @@
 
 import pandas as pd
 
-from ... import security, samplesheet, errors
+from ... import security, samplesheet, errors, resource
+from ...security import authz
 from ...resource import get_identifier
 from ...models import MetaDatum, MetaDataSet, MetaDatumRecord, User, Group, Submission
 
@@ -40,6 +41,8 @@ class ViewTableResponse(MetaDataSetResponse):
     """Data class representing the JSON response returned by POST:/api/ui/view"""
     submission_label : Optional[str] = None
     group_id : Optional[dict] = None
+    group_name: Optional[str] = None
+    user_name: Optional[str] = None
 
 def metadata_index_to_name(db, idx):
     name = db.query(MetaDatum.name).order_by(MetaDatum.order).limit(1).offset(idx).scalar()
@@ -116,7 +119,7 @@ def post(request: Request):
         # search term with the metadataset and submission site_ids, the
         # submission label and the MetaDatumRecord value, using the table alias
         # that was constructed for the search term before.
-        search_clauses = [ or_(*( field.ilike(f"%{search}%") for field in [ User.site_id, Group.site_id, MetaDataSetFilter.site_id, Submission.site_id, Submission.label, MetaDatumRecordFilter.value ])) for search, MetaDatumRecordFilter in searches ]
+        search_clauses = [ or_(*( field.ilike(f"%{search}%") for field in [ User.site_id, User.fullname, Group.site_id, Group.name, MetaDataSetFilter.site_id, Submission.site_id, Submission.label, MetaDatumRecordFilter.value ])) for search, MetaDatumRecordFilter in searches ]
         and_filters += search_clauses
 
     # Finally, the filter query, which will be added to the main query as a
@@ -144,18 +147,16 @@ def post(request: Request):
 
     MetaDatumRecordOrder = aliased(MetaDatumRecord)
     mdata_name = None
-    if   sort_idx == 0: # The submission site ID
-        mdatasets_base_query = mdatasets_base_query.join(Submission).order_by(direction(Submission.site_id))
-    elif sort_idx == 1: # The submission label
+    if   sort_idx == 0: # The submission label
         mdatasets_base_query = mdatasets_base_query.join(Submission).order_by(direction(Submission.label))
-    elif sort_idx == 2: # The metadataset user site ID
-        mdatasets_base_query = mdatasets_base_query.join(User).order_by(direction(User.site_id))
-    elif sort_idx == 3: # The submission group site ID
-        mdatasets_base_query = mdatasets_base_query.join(Submission).join(Group).order_by(direction(Group.site_id))
-    elif sort_idx == 4: # The metadataset site ID
+    elif sort_idx == 1: # The user full name
+        mdatasets_base_query = mdatasets_base_query.join(User).order_by(direction(User.fullname)) # TODO FIX
+    elif sort_idx == 2: # The submission group name
+        mdatasets_base_query = mdatasets_base_query.join(Submission).join(Group).order_by(direction(Group.site_id)) # TODO FIX
+    elif sort_idx == 3: # The metadataset site ID
         mdatasets_base_query = mdatasets_base_query.order_by(direction(MetaDataSet.site_id))
     else: # Sorting by a metadatum value
-        mdata_name = metadata_index_to_name(db, sort_idx - 5)
+        mdata_name = metadata_index_to_name(db, sort_idx - 4)
         # [WARNING] The following JOIN assumes that an inner join between MetaDatumRecord
         # and MetaDatum does not result in a loss of rows if the JOIN is restricted to one
         # particular MetaDatum.name. Put differently, this query requires that we always
@@ -196,12 +197,15 @@ def post(request: Request):
     # Build the 'data' response
     data = [
             ViewTableResponse(
-                id               = get_identifier(mdata_set),
-                record           = get_record_from_metadataset(mdata_set),
-                user_id          = get_identifier(mdata_set.user),
-                group_id         = get_identifier(mdata_set.submission.group),
-                submission_id    = get_identifier(mdata_set.submission) if mdata_set.submission else None,
-                submission_label = mdata_set.submission.label
+                id                 = get_identifier(mdata_set),
+                record             = get_record_from_metadataset(mdata_set),
+                file_ids           = { mdrec.metadatum.name : resource.get_identifier_or_none(mdrec.file) for mdrec in mdata_set.metadatumrecords if mdrec.metadatum.isfile },
+                user_id            = get_identifier(mdata_set.user),
+                user_name          = mdata_set.user.fullname,
+                group_id           = get_identifier(mdata_set.submission.group),
+                group_name         = mdata_set.submission.group.name,
+                submission_id      = get_identifier(mdata_set.submission) if mdata_set.submission else None,
+                submission_label   = mdata_set.submission.label
                 )
             for mdata_set, _ in mdata_sets
             ]

datameta/resource.py

@@ -24,6 +24,12 @@ def get_identifier(db_obj):
         pass
     return ids
 
+def get_identifier_or_none(db_obj):
+    """Given a database object, return the identifying IDs as a dictionary or None if the objecft is None"""
+    if db_obj is None:
+        return None
+    return get_identifier(db_obj)
+
 def resource_query_by_id(db, model, idstring):
     """Returns a database query that returns an entity based on it's uuid or
     site_id as specified by idstring.

datameta/security/authz.py

@@ -30,6 +30,8 @@ def has_data_access(user, data_user_id, data_group_id=None, was_submitted=False)
         (not was_submitted and data_user_id and data_user_id == user.id)
     ))
 
+def view_mset_any(user):
+    return user.site_read
 
 def view_apikey(user, target_user):
     return user_is_target(user, target_user)
@@ -107,4 +109,4 @@ def update_user_name(user, target_user):
     return any((
         has_group_rights(user, target_user.group),
         user_is_target(user, target_user)
-    ))
+    ))

datameta/static/css/datameta.css

@@ -2,4 +2,13 @@
     color: inherit;
     text-decoration: inherit;
 }
+.text-accent {
+    color:#dc3545 !important;
+}
+.background-accent {
+    color:#ffc107 !important;
+}
+.border-accent {
+    border-color:#ffc107 !important;
+}
 

datameta/static/js/submit.js

@@ -226,7 +226,7 @@ DataMeta.submit.buildKeyColunns = function(fileKeys, keys) {
         if (fileKeys.includes(key)) {
             /* FILE VALUES */
             columns.push({ title:key, data:null, render:function(metadataset) {
-                var str = metadataset.record[key] === null ? '<span class="text-black-50"><i>empty</i></span>' : metadataset.record[key];
+                var str = metadataset.record[key].value === null ? '<span class="text-black-50"><i>empty</i></span>' : metadataset.record[key].value;
                 return '<span data-datameta-class="field-status" data-datameta-uuid="'+metadataset.id.uuid+'" data-datameta-field="'+key+'">' +
                     '<i class="bi bi-hdd-rack-fill text-secondary" data-datameta-class="status-none" style="display:inline"></i>' +
                     '<i class="bi bi-hdd-rack-fill text-danger" data-datameta-class="status-err" style="display:none"></i>' +
@@ -237,7 +237,7 @@ DataMeta.submit.buildKeyColunns = function(fileKeys, keys) {
         } else {
             /* NON-FILE VALUES */
             columns.push({ title:key, data:"record", render: function(record) {
-                var str = record[key] === null ? '<span class="text-black-50"><i>empty</i></span>' : record[key];
+                var str = record[key].value === null ? '<span class="text-black-50"><i>empty</i></span>' : record[key].value;
                 return str;
             }});
         }

datameta/static/js/view.js

@@ -19,13 +19,21 @@
 DataMeta.view = {}
 
 DataMeta.view.buildColumns = function(mdata_names) {
-  return mdata_names.map(function(mdata_name) {
-    return {
-      title : mdata_name,
-      data : null,
-      render : mdataset => mdataset.record[mdata_name] ? mdataset.record[mdata_name] : "<em>empty</em>"
-    };
-  });
+    return mdata_names.map(function(mdata_name) {
+        return {
+            title : mdata_name,
+            data : null,
+            render : function(mdataset, type, row, meta) {
+                console.log(mdataset)
+                // Special case NULL
+                if (mdataset.record[mdata_name] === null) return '<span class="text-black-50"><i>empty</i></span>';
+                // Speical case file
+                if (mdataset.fileIds[mdata_name]) return '<a class="link-bare" href="' + DataMeta.api('rpc/get-file-url/'+mdataset.fileIds[mdata_name].site) +'"><i class="bi bi-cloud-arrow-down-fill"></i> '+mdataset.record[mdata_name]+'</a>';
+                // All other cases
+                return mdataset.record[mdata_name];
+            }
+        };
+    });
 }
 
 DataMeta.view.initTable = function() {
@@ -44,11 +52,17 @@ DataMeta.view.initTable = function() {
     var mdata_names = json.map(record => record.name);
 
     var columns = [
-        { title: "Submission", data: "submissionId.site", className: "id_col"},
-        { title: "Label", data: "submissionLabel", className: "id_col"},
-        { title: "User", data: "userId.site", className: "id_col"},
-        { title: "Group", data: "groupId.site", className: "id_col"},
-        { title: "Metadataset", data: "id.site", className: "id_col"}
+        { title: "Submission", data: null, className: "id_col", render: function(data) {
+            var label = data.submissionLabel ? data.submissionLabel : '<span class="text-black-50"><i>empty</i></span>';
+            return '<div> <div class="large-super">' + label + '</div><div class="text-accent small-sub">' + data.submissionId.site + '</div></div>'
+        }},
+        { title: "User", data: null, className: "id_col", render: data =>
+            '<div> <div class="large-super">'+data.userName+'</div><div class="text-accent small-sub">'+data.userId.site+'</div></div>'
+        },
+        { title: "Group", data: null, className: "id_col", render: data =>
+            '<div> <div class="large-super">'+data.groupName+'</div><div class="text-accent small-sub">'+data.groupId.site+'</div></div>'
+        },
+        { title: "Metadataset", data: "id.site", className: "id_col", render: data => '<span class="text-accent">' + data + '</span>'}
       ].concat(DataMeta.view.buildColumns(mdata_names))
 
     // Build table based on field names

datameta/templates/layout.pt

@@ -97,7 +97,7 @@
     </head>
     <body class="d-flex flex-column h-100" onload=init_widescreen()>
 
-        <header class="sticky-top d-flex flex-column flex-md-row align-items-center p-3 px-md-4 mb-3 bg-body border-bottom border-warning">
+        <header class="sticky-top d-flex flex-column flex-md-row align-items-center p-3 px-md-4 mb-3 bg-body border-bottom border-accent">
             <div tal:replace="structure logo_html"></div>
 
             <nav class="my-2 my-md-0 me-md-3">

datameta/templates/view.pt

@@ -10,7 +10,16 @@
     <link href="${request.static_url('datameta:static/css/dataTables.bootstrap5.css')}" rel="stylesheet">
     <style>
     td.id_col {
-        background-color: #f7d4da;
+        padding-bottom:0pt;
+    }
+    .large-super {
+        line-height: 1.0;
+        margin-top: .25rem;
+    }
+    .small-sub {
+        line-height: 1.0;
+        font-size:6pt;
+        margin-top:0.1rem;
     }
     </style>
     </metal:block>