Merge branch 'main' of https://github.com/NFDI4Chem/nmrxiv into prod-…

…helm-deploy
NFDI4Chem · Nov 16, 2023 · f57e3aa · f57e3aa
2 parents 4d514b1 + d4b3ae0
commit f57e3aa
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Showing 35 changed files with 2,331 additions and 190 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,15 @@
 # Changelog
 
+## [1.0.1-rc.10](https://github.com/NFDI4Chem/nmrxiv/compare/v1.0.0-rc.10...v1.0.1-rc.10) (2023-11-16)
+
+
+### Bug Fixes
+
+* added molecular search ([8dfcc4a](https://github.com/NFDI4Chem/nmrxiv/commit/8dfcc4a0a2b218ee68e7d39d8916ac44e93af508))
+* enable listing of files with missing flag at root and title udpates ([05adf74](https://github.com/NFDI4Chem/nmrxiv/commit/05adf74dbf0161c38475821f7c5528597d717a4a))
+* molecules filtering and other bug fixes ([bb3d701](https://github.com/NFDI4Chem/nmrxiv/commit/bb3d7012123df556c63188443b9741e7a8ea2ab9))
+* updated molecular card link and studies filtering ([cf6763e](https://github.com/NFDI4Chem/nmrxiv/commit/cf6763e6f595285682cc870f5dd5c44bf6d0a3ef))
+
 ## [1.0.1-rc.9](https://github.com/NFDI4Chem/nmrxiv/compare/v1.0.0-rc.9...v1.0.1-rc.9) (2023-11-15)
 
 

diff --git a/app/Console/Commands/SanitizeMolecules.php b/app/Console/Commands/SanitizeMolecules.php
@@ -27,17 +27,17 @@ class SanitizeMolecules extends Command
      */
     public function handle()
     {
-        $molecules = Molecule::whereNull('CANONICAL_SMILES')->get();
+        $molecules = Molecule::whereNull('canonical_smiles')->get();
 
         foreach ($molecules as $molecule) {
             echo $molecule->id;
             echo "\r\n";
             $molecule->MOL = '
             '.$molecule->MOL;
-            $standardisedMOL = $this->standardizeMolecule($molecule->MOL);
-            $molecule->CANONICAL_SMILES = $standardisedMOL['canonical_smiles'];
-            $molecule->STANDARD_INCHI = $standardisedMOL['inchi'];
-            $molecule->INCHI_KEY = $standardisedMOL['inchikey'];
+            $standardisedMOL = $this->standardizeMolecule($molecule->sdf);
+            $molecule->canonical_smiles = $standardisedMOL['canonical_smiles'];
+            $molecule->standard_inchi = $standardisedMOL['inchi'];
+            $molecule->inchi_key = $standardisedMOL['inchikey'];
             $molecule->save();
         }
     }

diff --git a/app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php b/app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php
@@ -230,7 +230,7 @@ public function getMolecules($sample)
     {
         $molecules = [];
         foreach ($sample->molecules as &$molecule) {
-            $inchiKey = $molecule->INCHI_KEY;
+            $inchiKey = $molecule->inchi_key;
             $pubchemLink = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/'.$inchiKey.'/property/IUPACName/JSON';
             $json = json_decode(Http::get($pubchemLink)->body(), true);
             // $cid = $json['PropertyTable']['Properties'][0]['CID'];
@@ -240,14 +240,14 @@ public function getMolecules($sample)
             // $moleculeSchema['@id'] = $inchiKey;
             // $moleculeSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']);
             // $moleculeSchema['identifier'] = $inchiKey;
-            // $moleculeSchema->name($molecule->CAS_NUMBER);
+            // $moleculeSchema->name($molecule->cas);
             // $moleculeSchema->url('https://pubchem.ncbi.nlm.nih.gov/compound/'.$cid);
-            // $moleculeSchema->inChI('InChI='.$molecule->STANDARD_INCHI);
+            // $moleculeSchema->inChI('InChI='.$molecule->standard_inchi);
             // $moleculeSchema->inChIKey($inchiKey);
             // $moleculeSchema->iupacName($iupacName);
-            // $moleculeSchema->molecularFormula($molecule->FORMULA);
-            // $moleculeSchema->molecularWeight($molecule->MOLECULAR_WEIGHT);
-            // $moleculeSchema->smiles([$molecule->SMILES, $molecule->SMILES_CHIRAL, $molecule->CANONICAL_SMILES]);
+            // $moleculeSchema->molecularFormula($molecule->molecular_formula);
+            // $moleculeSchema->molecularWeight($molecule->molecular_weight);
+            // $moleculeSchema->smiles([$molecule->SMILES, $molecule->absolute_smiles, $molecule->canonical_smiles]);
             // $moleculeSchema->hasRepresentation($molecule->MOL);
             // $moleculeSchema->description('Percentage composition: '.$molecule->pivot->percentage_composition.'%');
             // array_push($molecules, $moleculeSchema);