Merge pull request #238 from AberystwythSystemsBiology/feature/csv-im…

…port1

Feature/csv import1

services/web/app/sample/api/queries.py

@@ -44,14 +44,17 @@
     SampleConsent,
     DonorToSample,
     SampleToCustomAttributeData,
+    TemporaryStore,
 )
 
 from ..views import (
     new_fluid_sample_schema,
     new_cell_sample_schema,
     new_molecular_sample_schema,
     new_sample_protocol_event_schema,
+    sample_protocol_event_schema,
 )
+from ...tmpstore.views import new_store_schema
 from ..enums import SampleSource
 
 
@@ -540,6 +543,104 @@ def func_deep_remove_subsampletosample_children(
     return (success, msgs)
 
 
+def func_root_sample_acquision_protocol_event(sample_id):
+    sample = Sample.query.filter_by(id=sample_id).first()
+    pe_acq = None
+    if sample is None:
+        success = False
+        msg = "Sample (id=%d) not found" % sample_id
+        return pe_acq, msg
+
+    while sample.source != "NEW":
+        sample = SubSampleToSample.query.filter_by(subsample_id=sample.id).first()
+        if sample is None:
+            success = False
+            msg = "Root sample (id=%d) not found" % sample_id
+            return pe_acq, msg
+
+    pe_acq = SampleProtocolEvent.query.filter_by(sample_id=sample.id).join(
+        ProtocolTemplate, ProtocolTemplate.type == "ACQ"
+    )
+
+    if pe_acq is None:
+        msg = "Root sample (id=%d) acquisition event found!" % sample.id
+    else:
+        msg = "Root sample acquisition event found!"
+    return pe_acq, msg
+
+
+# def func_update_sample_tmpstore_info(uuid=None, sample=None, tokenuser: UserAccount):
+#     # Update temporarystore
+#     if uuid:
+#         if sample is None:
+#             sample = Sample.query.filter_by(uuid=uuid).first()
+#         elif sample.uuid != uuid:
+#             return {"success": False, "message": "sample and uuid not matched!"}
+#     elif not sample:
+#         return not_found("Sample object or uuid!")
+#     else:
+#         uuid = sample.uuid
+#
+#     # Update sample collection date
+#     pe_acq, msg = func_root_sample_acquision_protocol_event(sample.id)
+#     if not pe_acq:
+#         return not_found("Sample acquisition event for sample %s" %uuid)
+#
+#     info = sample_protocol_event_schema.dump(pe_acq)
+#     return info
+
+# @api.route("/sample/<uuid>/extra", methods=["DELETE", "GET", "POST"])
+# @token_required
+# def sample_update_sample_tmpstore_info(uuid: str, tokenuser: UserAccount):
+#     # if uuid:
+#     #     if sample is None:
+#     #         sample = Sample.query.filter_by(uuid=uuid).first()
+#     #     elif sample.uuid != uuid:
+#     #         return {"success": False, "message": "sample and uuid not matched!"}
+#     # elif not sample:
+#     #     return not_found("Sample object or uuid!")
+#     # else:
+#     #     uuid = sample.uuid
+#     if uuid:
+#         sample = Sample.query.filter_by(uuid=uuid).first()
+#         if not sample:
+#             return not_found("sample %s " % uuid)
+#
+#     tmpstore = temporarystore.query.filter_by(uuid=uuid, type='smp').first()
+#     if tmpstore:
+#         # Update entry
+#         tmpstore.data["root_sample_collection_date"] = info
+#         tmpstore.update({"editor_id": tokenuser.id})
+#     else:
+#         # new entry
+#         values = {}
+#         values["uuid"] = uuid
+#         values["type"] = 'smp'
+#
+#         try:
+#             result = new_store_schema.load(values)
+#         except ValidationError as err:
+#             return validation_error_response(err)
+#
+#         tmpstore = TemporaryStore(**result)
+#         tmpstore.author_id = tokenuser.id
+#
+#     return {"success": True, "tempstore": tmpstore}
+#
+#     (success, msgs) = func_remove_sample(sample, tokenuser, [])
+#     if not success:
+#         return msgs[-1]
+#
+#     try:
+#         db.session.commit()
+#         msgs.append("Committed successfully!")
+#         message = " | ".join(msgs)
+#         return success_with_content_message_response(uuid, message)
+#     except Exception as err:
+#         db.session.rollback()
+#         return transaction_error_response(err)
+
+
 @api.route("/sample/<uuid>/remove", methods=["DELETE", "GET", "POST"])
 @token_required
 def sample_remove_sample(uuid: str, tokenuser: UserAccount):

services/web/app/sample/routes/shipment.py

@@ -297,7 +297,8 @@ def shipment_new_step_one():
     sites_ext = [[0, "None"]]
 
     sites_response = requests.get(
-        url_for("api.site_home", _external=True), headers=get_internal_api_header()
+        url_for("api.site_home", _external=True),
+        headers=get_internal_api_header(),
     )
     external_sites_response = requests.get(
         url_for("api.site_external_home", _external=True),
@@ -313,6 +314,8 @@ def shipment_new_step_one():
     addresses = {}
     if external_sites_response.status_code == 200:
         for site in external_sites_response.json()["content"]:
+            if site["is_locked"]:
+                continue
             sites_ext.append(
                 [site["id"], "LIMBSIT-%i: %s" % (site["id"], site["name"])]
             )
@@ -322,6 +325,8 @@ def shipment_new_step_one():
 
     if sites_response.status_code == 200:
         for site in sites_response.json()["content"]:
+            if site["is_locked"]:
+                continue
             sites.append([site["id"], "LIMBSIT-%i: %s" % (site["id"], site["name"])])
             address = site["address"]
             addresses[site["id"]] = [[address["id"], address_label(address)]]

services/web/app/static/js/donor/index.js

@@ -46,7 +46,7 @@ function calc_age(date0, date1) {
     date0 = new Date(date0 + "Z");
     date1 = new Date(date1 + "Z");
     var timeDiff = Math.abs(date0.getTime() - date1.getTime());
-    var age = Math.ceil(timeDiff / (1000 * 3600 * 24)/ 365);
+    var age = Math.floor(timeDiff / (1000 * 3600 * 24)/ 365.25);
     return age;
 }
 
@@ -62,7 +62,7 @@ function render_table(query) {
         buttons: [ 'print', 'csv', 'colvis' ],
         columnDefs: [
             {targets: '_all', defaultContent: '-'},
-            {targets: [2, 3, 4, 6, 7, 12, 13,  16], visible: false, "defaultContent": "-"},
+            {targets: [0, 2, 3, 4, 6, 7, 12, 13,  16], visible: false, "defaultContent": "-"},
             //{width: 200, targets: 6 }
         ],
         //fixedColumns: true,

services/web/app/static/js/donor/view.js

@@ -79,7 +79,7 @@ function fill_sample_table(samples) {
 
         columnDefs: [
             {targets: '_all', defaultContent: ''},
-            {targets: [2, 3, 6], visible: false, "defaultContent": ""},
+            {targets: [2, 3, 6, 11], visible: false, "defaultContent": ""},
             {
                 targets:  -1,
                  orderable: false,
@@ -207,6 +207,14 @@ function fill_sample_table(samples) {
                 }
             },
 
+            {
+                "mData": {},
+                "mRender": function (data, type, row) {
+                    //console.log("--", data)
+                    return data["collected_on"];
+                }
+            },
+
             {
                 "mData": {},
                 "mRender": function (data, type, row) {

services/web/app/static/js/sample/aliquot/derive.js

@@ -324,6 +324,7 @@ function generate_container_select(indx) {
     return select_html;
 }
 
+
 function generate_fixation_select(indx) {
     var cbt = containerbasetypes[0][0]; //"PRM"
     var fixation_list = containertypes[cbt]["fixation_type"];
@@ -463,7 +464,7 @@ function make_new_form(indx) {
     lastvals = {sample_basetype: $("#samplebasetype_select_"+ indx).val(),
                 sample_type: $("#sampletype_select_"+ indx).val(),
                 container_basetype: $("#containerbasetype_select_"+indx).val(),
-                container_type: $("#containertye_select_" + indx).val(),
+                container_type: $("#containertype_select_" + indx).val(),
                 volume: $("#volume_" + indx).val()
     }
 

services/web/app/static/js/storage/rack/sampletorack_view.js

@@ -620,10 +620,9 @@ function dragndrop_rack_view() {
        $("#submit_sampletorack").fadeTo(1000, 0.3, function() { $(this).fadeTo(500, 1.0); });
        $("#submit_sampletorack").show();
 
-
-
         var dispopt = $("input[name='dispopt']:checked").val();
         var changed = [];
+
         document.ondragstart = function (event) {
             //event.dataTransfer.setData("text/plain", event.target.id);
             event.dataTransfer.setData('target_id', event.target.id);
@@ -814,6 +813,15 @@ $(document).ready(function () {
         var new_rack = false;
     }
 
+    if ("update_storage" in sampletostore) {
+        var update_storage = sampletostore["update_storage"];
+    } else {
+        var update_storage = true;
+    }
+
+    if (update_storage == false) {
+        $("#submit_sampletorack").text("Update Sample in Rack");
+    }
 
     $("input[id='qr_on']").attr('hidden', true);
 
@@ -829,17 +837,21 @@ $(document).ready(function () {
         render_subtitle(rack_information);
         render_information(rack_information);
     }
+
+
     var dispopt = $("input[name='dispopt']:checked").val();
 
     if (from_file==true) {
         //console.log("rack_information[view]", rack_information["view"]);
         var samples = render_view_from_file(rack_information["view"],
             rack_information["_links"]["assign_sample"], dispopt);
+
     } else {
         var samples = render_view(rack_information["view"],
             rack_information["_links"]["assign_sample"], dispopt);
     }
 
+
     $("input[name='dispopt']").change(function(){
         var dispopt = $("input[name='dispopt']:checked").val();
         $("#view_area").empty()
@@ -855,8 +867,9 @@ $(document).ready(function () {
     render_sample_table(samples);
 
 
-    if (from_file==true)
+    if (from_file == true) {
         $("#cancel_change").show();
+    }
     else {
         $("#cancel_change").show();
         dragndrop_rack_view();
@@ -874,8 +887,12 @@ $(document).ready(function () {
 
     });
 
+    if (update_storage) {
+        alert("Note: Please check the storage info before pressing STORE-SAMPLE-TO-RACK button to confirm!!")
+    } else {
+        alert("Note: Please check the storage info before pressing UPDATE-SAMPLE-IN-RACK button to confirm!!")
+    }
 
-    alert("Note: Please check the storage info before pressing STORE-SAMPLE-TO-RACK button to confirm!!")
 
     $("#submit_sampletorack").click(function (event) {
         if (from_file) {
@@ -884,6 +901,13 @@ $(document).ready(function () {
 
             else
                 var api_url = window.location.origin + "/storage/rack/refill_with_samples";
+
+                if (update_storage) {
+                        var api_url = window.location.origin + "/storage/rack/refill_with_samples";
+                } else {
+                        var api_url = window.location.origin + "/storage/rack/update_sample_info";
+                }
+
         }
         else if (!update_only)
             var api_url = window.location.origin + "/storage/rack/fill_with_samples"

services/web/app/static/js/storage/rack/view.js

@@ -423,6 +423,11 @@ $(document).ready(function () {
     var sampletostore = fill_sample_pos(api_url, rack_id, {}, commit=false)
     })
 
+    $("#update-sample-from-file-btn").click(function() {
+    var api_url = window.location.href = rack_information["_links"]["update_sample_info"];
+    var sampletostore = fill_sample_pos(api_url, rack_id, {}, commit=false)
+    })
+
     $("#loading-screen").fadeOut();
     $("#content").delay(500).fadeIn();