From ba07be2fd9dfd71fe4bde15a38a7ae015cd5c082 Mon Sep 17 00:00:00 2001
From: Lan Le <lan.le@kit.edu>
Date: Tue, 28 May 2024 10:29:13 +0200
Subject: [PATCH] feat: store scan rate and spectrum direction

---
 README.md                                            |  1 +
 chem_spectra/lib/composer/ni.py                      | 12 ++++++++++++
 environment.yml                                      |  2 +-
 requirements.txt                                     |  2 +-
 .../cyclicvoltammetry/RCV_LSH-R444_full+Fc.jdx       |  1 +
 tests/test_cyclic_volta.py                           |  2 ++
 tests/test_ms.py                                     |  2 --
 7 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 3b38b631..f5ad640f 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,7 @@
 
 This backend web service provides NMR/IR/MS processing for jcamp/RAW/mzML files.
 
+![GitHub release (release name instead of tag name)](https://img.shields.io/github/v/release/ComPlat/chem-spectra-app?include_prereleases&label=version)
 ![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)
 ![Testing](https://github.com/ComPlat/chem-spectra-app/actions/workflows/unit_test.yml/badge.svg)
 
diff --git a/chem_spectra/lib/composer/ni.py b/chem_spectra/lib/composer/ni.py
index 80269c0a..b448736d 100644
--- a/chem_spectra/lib/composer/ni.py
+++ b/chem_spectra/lib/composer/ni.py
@@ -148,6 +148,17 @@ def __get_xy_of_peak(self, peak):
         y = peak['y'] or ''
         return x, y
 
+    def __gen_cyclic_voltammetry_medadata(self):
+        scan_rate = self.core.dic.get('SCANRATE', [0.1])[0]
+        x_values = self.core.xs
+        spectrum_direction = ''
+        if len(x_values) > 2:
+            spectrum_direction = 'NEGATIVE' if x_values[0] > x_values[1] else 'POSITIVE'
+        return [
+            f"##$CSSCANRATE={scan_rate}\n",
+            f"##$CSSPECTRUMDIRECTION={spectrum_direction}\n"
+        ]
+
     def __gen_cyclic_voltammetry_data_peaks(self):
         content = ['##$CSCYCLICVOLTAMMETRYDATA=\n']
         if self.core.is_cyclic_volta:
@@ -226,6 +237,7 @@ def __compose(self):
         meta.extend(self.gen_simulation_info())
         if self.core.is_cyclic_volta:
             meta.extend(self.__gen_header_cyclic_voltammetry())
+            meta.extend(self.__gen_cyclic_voltammetry_medadata())
             meta.extend(self.__gen_cyclic_voltammetry_data_peaks())
         meta.extend(self.gen_ending())
 
diff --git a/environment.yml b/environment.yml
index 5addf1f1..288f61bb 100644
--- a/environment.yml
+++ b/environment.yml
@@ -76,7 +76,7 @@ dependencies:
       - pytz==2023.3
       - rdkit==2023.9.1
       - regex==2019.4.9
-      - requests==2.31.0
+      - requests==2.32.0
       - scipy==1.7.3
       - six==1.11.0
       - tomli==2.0.1
diff --git a/requirements.txt b/requirements.txt
index 73621146..69711403 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -35,7 +35,7 @@ pytest==7.2.0
 python-dateutil==2.8.2
 pytz==2023.3
 regex==2019.4.9
-requests==2.31.0
+requests==2.32.0
 scipy==1.7.3
 six==1.11.0
 urllib3==1.26.18
diff --git a/tests/fixtures/source/cyclicvoltammetry/RCV_LSH-R444_full+Fc.jdx b/tests/fixtures/source/cyclicvoltammetry/RCV_LSH-R444_full+Fc.jdx
index ea3f8943..703eed7b 100644
--- a/tests/fixtures/source/cyclicvoltammetry/RCV_LSH-R444_full+Fc.jdx
+++ b/tests/fixtures/source/cyclicvoltammetry/RCV_LSH-R444_full+Fc.jdx
@@ -4,6 +4,7 @@
 ##DATA CLASS=XYPOINTS
 ##ORIGIN=
 ##OWNER=
+##SCAN_RATE=0.09
 ##FIRSTX=1.49048
 ##LASTX=1.50049
 ##MINX=-1.9005
diff --git a/tests/test_cyclic_volta.py b/tests/test_cyclic_volta.py
index 4cb60356..8539dac1 100644
--- a/tests/test_cyclic_volta.py
+++ b/tests/test_cyclic_volta.py
@@ -28,4 +28,6 @@ def test_cv_compose():
     nicv = JcampNIConverter(jbcv)
     nicmpsr = NIComposer(nicv)
     assert "$$ === CHEMSPECTRA CYCLIC VOLTAMMETRY ===\n" in nicmpsr.meta
+    assert "##$CSSCANRATE=0.09\n" in nicmpsr.meta
+    assert "##$CSSPECTRUMDIRECTION=NEGATIVE\n" in nicmpsr.meta
     assert "##$CSCYCLICVOLTAMMETRYDATA=\n" in nicmpsr.meta
diff --git a/tests/test_ms.py b/tests/test_ms.py
index 6e1c4ab7..bfb210d2 100644
--- a/tests/test_ms.py
+++ b/tests/test_ms.py
@@ -21,8 +21,6 @@ def test_ms_mzml_converter_composer():
 
     lines = mscp.tf_jcamp().read()[:800] \
                 .decode('utf-8', errors='ignore').split('\n')
-    
-    print(lines)
 
     assert '##$CSSCANAUTOTARGET=24' in lines
     assert '##$CSSCANEDITTARGET=24' in lines