LIMS-538: Remove the 'Centring Method' column from creating an MX container (#908)

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>

Author: ndg63276

api/src/Page/Sample.php

@@ -1311,8 +1311,8 @@ function _handle_update_sample_full($a, $sid)
         $blSampleId = $samp['BLSAMPLEID'];
 
         $this->db->pq(
-            "UPDATE blsample set name=:1,comments=:2,code=:3,volume=:4,packingfraction=:5,dimension1=:6,dimension2=:7,dimension3=:8,shape=:9,looptype=:10 WHERE blsampleid=:11",
-            array($a['NAME'], $a['COMMENTS'], $a['CODE'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $blSampleId)
+            "UPDATE blsample set name=:1,comments=:2,code=:3,volume=:4,packingfraction=:5,dimension1=:6,dimension2=:7,dimension3=:8,shape=:9,looptype=:10,smiles=:11 WHERE blsampleid=:12",
+            array($a['NAME'], $a['COMMENTS'], $a['CODE'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SMILES'], $blSampleId)
         );
 
         if (array_key_exists('PROTEINID', $a)) {
@@ -1480,6 +1480,7 @@ function _prepare_sample_args($s = null)
             'LOOPTYPE',
             'ENERGY',
             'USERPATH',
+            'SMILES',
             'SCREENINGMETHOD',
             'SCREENINGCOLLECTVALUE',
             'SAMPLEGROUP',
@@ -1537,8 +1538,8 @@ function _do_add_sample($s)
         }
 
         $this->db->pq(
-            "INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype,source) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16,IFNULL(:17,CURRENT_USER)) RETURNING blsampleid INTO :id",
-            array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SOURCE'])
+            "INSERT INTO blsample (blsampleid,crystalid,diffractionplanid,containerid,location,comments,name,code,blsubsampleid,screencomponentgroupid,volume,packingfraction,dimension1,dimension2,dimension3,shape,looptype,smiles,source) VALUES (s_blsample.nextval,:1,:2,:3,:4,:5,:6,:7,:8,:9,:10,:11,:12,:13,:14,:15,:16,:17,IFNULL(:18,CURRENT_USER)) RETURNING blsampleid INTO :id",
+            array($crysid, $did, $a['CONTAINERID'], $a['LOCATION'], $a['COMMENTS'], $a['NAME'], $a['CODE'], $a['BLSUBSAMPLEID'], $a['SCREENCOMPONENTGROUPID'], $a['VOLUME'], $a['PACKINGFRACTION'], $a['DIMENSION1'], $a['DIMENSION2'], $a['DIMENSION3'], $a['SHAPE'], $a['LOOPTYPE'], $a['SMILES'], $a['SOURCE'])
         );
         $sid = $this->db->id();
 

client/src/js/app/store/modules/store.samples.js

@@ -39,6 +39,7 @@ const INITIAL_SAMPLE_STATE = {
   SCREENINGCOLLECTVALUE: '',
   THEORETICALDENSITY: '',
   SHAPE: '',
+  SMILES: '',
   SPACEGROUP: '',
   SYMBOL: '',
   USERPATH: '',

client/src/js/modules/types/mx/samples/mx-puck-samples-table.vue

@@ -290,19 +290,19 @@ export default {
           componentType: 'base-input-text',
           data: '',
           inputType: 'number'
-        }
+        },
+        {
+          key: 'SMILES',
+          title: 'SMILES Code',
+          className: 'tw-w-3/12',
+          componentType: 'base-input-text',
+          data: '',
+          inputType: 'text'
+        },
       ]
     },
     udcColumns() {
       return [
-        {
-          key: 'CENTRINGMETHOD',
-          title: 'Centring Method',
-          className: 'tw-w-24',
-          componentType: 'base-input-select',
-          data: this.centringMethodList,
-          inputType: 'select'
-        },
         {
           key: 'EXPERIMENTKIND',
           title: 'Experiment Kind',

client/src/js/modules/types/mx/samples/sample-table-mixin.js

@@ -65,16 +65,6 @@ export default {
     experimentKindList() {
       return this.$experimentKindList();
     },
-    centringMethodList() {
-      return this.$centringMethods().filter(method => method).reduce(
-        (acc, curr) => {
-          if (curr) acc.push({ value: curr, text: curr });
-
-          return acc;
-        },
-        []
-      ).sort(this.sortSelectField);
-    },
     spaceGroupList() {
       const spaceGroups = this.$spaceGroups().reduce((acc, item) => {
         acc.push({
@@ -159,6 +149,7 @@ export default {
       'SCREENINGMETHOD',
       'SCREENINGCOLLECTVALUE',
       'SHAPE',
+      'SMILES',
       'SPACEGROUP',
       'SYMBOL',
       'THEORETICALDENSITY',
@@ -311,7 +302,6 @@ export default {
   },
   inject: [
     "$spaceGroups",
-    "$centringMethods",
     "$anomalousList",
     "$experimentKindList",
     "$sampleLocation",

client/src/js/modules/types/mx/samples/tabbed-columns-view.vue

@@ -266,26 +266,18 @@
           </extended-validation-provider>
         </div>
       </div>
-    </div>
 
-    <div
-      v-show="currentTab === 'unattended'"
-      class="tw-w-full tw-flex tw-items-center"
-    >
       <extended-validation-provider
-        :ref="`sample_${sampleIndex}_centring_method`"
-        class-names="tw-px-2 tw-w-24"
-        :name="`Sample ${sampleIndex + 1} Centring Method`"
-        :rules="sample['PROTEINID'] > -1 && queueForUDC ? 'required' : ''"
-        :vid="`sample ${sampleIndex + 1} centring method`"
+        :ref="`sample_${sampleIndex}_smiles`"
+        class-names="tw-px-2 tw-w-3/12"
+        :name="`Sample ${sampleIndex + 1} SMILES Code`"
+        :rules="sample['PROTEINID'] > -1 ? { regex: /^[A-Za-z0-9.:%=#$@+\-\[\]\(\)\/\\\\]+$/ } : ''"
+        :vid="`sample ${sampleIndex + 1} smiles`"
       >
         <template #default="{errors, inputChanged }">
-          <base-input-select
-            v-model="CENTRINGMETHOD"
-            :is-disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
-            :options="centringMethodList"
-            option-value-key="value"
-            option-text-key="text"
+          <base-input-text
+            v-model="SMILES"
+            :disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
             input-class="tw-w-full tw-h-8"
             :quiet="true"
             :error-message="errors[0]"
@@ -295,6 +287,12 @@
         </template>
       </extended-validation-provider>
 
+    </div>
+
+    <div
+      v-show="currentTab === 'unattended'"
+      class="tw-w-full tw-flex tw-items-center"
+    >
       <extended-validation-provider
         :ref="`sample_${sampleIndex}_experiment_kind`"
         class-names="tw-px-2 tw-w-32"
@@ -322,7 +320,7 @@
         :ref="`sample_${sampleIndex}_energy`"
         class-names="tw-px-2 tw-w-20"
         :name="`Sample ${sampleIndex + 1} Energy`"
-        :rules="sample['PROTEINID'] > -1 ? `required_if:sample ${sampleIndex + 1} experiment kind,SAD|non_zero_numeric` : ''"
+        :rules="sample['PROTEINID'] > -1 ? `required_if:sample ${sampleIndex + 1} experiment kind,SAD|min_value:1501` : ''"
         :vid="`sample ${sampleIndex + 1} energy`"
       >
         <template #default="{errors, inputChanged }">

client/src/js/modules/types/mx/shipment/views/container-mixin.js

@@ -1,7 +1,6 @@
 import Users from 'collections/users'
 import ProcessingPipelines from 'collections/processingpipelines'
 import SpaceGroups from 'collections/spacegroups.js'
-import CentringMethodList from 'utils/centringmethods.js'
 import AnomalousList from 'utils/anoms.js'
 import ExperimentKindsList from 'utils/experimentkinds.js'
 import DistinctProteins from 'modules/shipment/collections/distinctproteins'
@@ -35,7 +34,6 @@ export default {
     return {
       anomalousList: AnomalousList.list,
 
-      centringMethods: CentringMethodList.list,
       containerType: {},
       containerTypes: [],
       containerTypesCollection: new ContainerTypes(),
@@ -541,7 +539,6 @@ export default {
   provide() {
     return {
       $spaceGroups: () => this.spaceGroups,
-      $centringMethods: () => this.centringMethods,
       $anomalousList: () => this.anomalousList,
       $experimentKindList: () => this.experimentKindList,
       $sampleLocation: () => this.sampleLocation,

client/src/js/modules/types/mx/shipment/views/mx-container-add.vue

@@ -696,10 +696,6 @@ export default {
       let samples
       if (newVal) {
         samples = this.samples.map(sample => {
-          if (!sample.CENTRINGMETHOD) {
-            sample.CENTRINGMETHOD = 'diffraction'
-          }
-
           if (!sample.EXPERIMENTKIND) {
             sample.EXPERIMENTKIND = 'Ligand binding'
           }

client/src/js/utils/experimentkinds.js

@@ -32,11 +32,11 @@ define([], function() {
             'native': 'OSC',
             'phasing': 'SAD',
             'ligand': 'Ligand binding',
-            'stepped': 'Stepped transmission',
         },
 
         staff: {
-            'commissioning': 'Commissioning'
+            'stepped': 'Stepped transmission',
+            'commissioning': 'Commissioning',
         }
     }
 })