From c49e62a5bceb1d9255d6ed4ecae579b55a14a4f3 Mon Sep 17 00:00:00 2001
From: Mingxun Wang <mwang87@gmail.com>
Date: Fri, 7 Feb 2020 18:34:29 -0800
Subject: [PATCH 1/4] adding proxi interface

---
 views.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/views.py b/views.py
index 7ff8965..6ab747e 100644
--- a/views.py
+++ b/views.py
@@ -373,6 +373,24 @@ def peak_json():
                      'precursor_mz': spectrum.precursor_mz}
     return flask.jsonify(spectrum_dict)
 
+@app.route('/api/proxi/v0.1/spectra')
+def peak_proxi_json():
+    spectrum, _ = parsing.parse_usi(flask.request.args.get('usi'))
+    
+    spectrum_dict = {'intensities': [str(intensity) for intensity in spectrum.intensity],
+                     'mzs' : [str(mz) for mz in spectrum.mz],
+                     'attributes': [
+                         {
+                             'accession' : "MS:1000827",
+                             'name' : 'isolation window target m/z',
+                             'value' : str(spectrum.precursor_mz)
+                         }
+                     ]}
+                     
+    spectrum_list = [spectrum_dict]
+
+    return flask.jsonify(spectrum_dict)
+
 
 @app.route('/csv/')
 def peak_csv():

From 53b308cd42c6c8138895d1d8257ae9e7997e3312 Mon Sep 17 00:00:00 2001
From: Mingxun Wang <mwang87@gmail.com>
Date: Thu, 19 Mar 2020 17:15:12 -0700
Subject: [PATCH 2/4] resolving comments

---
 views.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/views.py b/views.py
index 6ab747e..ba36a45 100644
--- a/views.py
+++ b/views.py
@@ -377,19 +377,24 @@ def peak_json():
 def peak_proxi_json():
     spectrum, _ = parsing.parse_usi(flask.request.args.get('usi'))
     
-    spectrum_dict = {'intensities': [str(intensity) for intensity in spectrum.intensity],
-                     'mzs' : [str(mz) for mz in spectrum.mz],
+    spectrum_dict = {'intensities': [
+        str(intensity) for intensity in spectrum.intensity
+        ],
+                     'mzs': [str(mz) for mz in spectrum.mz],
                      'attributes': [
                          {
-                             'accession' : "MS:1000827",
-                             'name' : 'isolation window target m/z',
+                             'accession' : "MS:1000744",
+                             'name' : 'selected ion m/z',
                              'value' : str(spectrum.precursor_mz)
+                         },
+                         {
+                             'accession' : "MS:1000041",
+                             'name' : 'precursor charge	',
+                             'value' : str(spectrum.precursor_charge)
                          }
                      ]}
-                     
-    spectrum_list = [spectrum_dict]
 
-    return flask.jsonify(spectrum_dict)
+    return flask.jsonify([spectrum_dict])
 
 
 @app.route('/csv/')

From 80be63419306c3d39def3cd8759a8a7ae620d8d1 Mon Sep 17 00:00:00 2001
From: Mingxun Wang <mwang87@gmail.com>
Date: Thu, 19 Mar 2020 17:17:46 -0700
Subject: [PATCH 3/4] integration testing

---
 test-production-integration/test_integration.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/test-production-integration/test_integration.py b/test-production-integration/test_integration.py
index 7b2a8cf..0b42922 100644
--- a/test-production-integration/test_integration.py
+++ b/test-production-integration/test_integration.py
@@ -35,4 +35,15 @@ def test_img():
 
         url = f"{PRODUCTION_URL}/png/?usi={quote(usi)}"
         r = requests.get(url)
-        r.raise_for_status()
\ No newline at end of file
+        r.raise_for_status()
+
+def test_json():
+    from urllib.parse import quote
+    for usi in test_usi_list:
+        url = f"{PRODUCTION_URL}/json/?usi={quote(usi)}"
+        r = requests.get(url)
+        r.raise_for_status()
+
+        url = f"{PRODUCTION_URL}/api/proxi/v0.1/spectra?usi={quote(usi)}"
+        r = requests.get(url)
+        r.raise_for_status()

From 5b8ff395ab84cc9be61e9ceae7214909395e7735 Mon Sep 17 00:00:00 2001
From: Wout <wout@bittremieux.be>
Date: Thu, 19 Mar 2020 18:54:10 -0700
Subject: [PATCH 4/4] Better formatting

---
 views.py | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/views.py b/views.py
index ba36a45..e53ef8a 100644
--- a/views.py
+++ b/views.py
@@ -373,26 +373,27 @@ def peak_json():
                      'precursor_mz': spectrum.precursor_mz}
     return flask.jsonify(spectrum_dict)
 
+
 @app.route('/api/proxi/v0.1/spectra')
 def peak_proxi_json():
     spectrum, _ = parsing.parse_usi(flask.request.args.get('usi'))
-    
-    spectrum_dict = {'intensities': [
-        str(intensity) for intensity in spectrum.intensity
-        ],
-                     'mzs': [str(mz) for mz in spectrum.mz],
-                     'attributes': [
-                         {
-                             'accession' : "MS:1000744",
-                             'name' : 'selected ion m/z',
-                             'value' : str(spectrum.precursor_mz)
-                         },
-                         {
-                             'accession' : "MS:1000041",
-                             'name' : 'precursor charge	',
-                             'value' : str(spectrum.precursor_charge)
-                         }
-                     ]}
+
+    spectrum_dict = {
+        'intensities': [str(intensity) for intensity in spectrum.intensity],
+        'mzs': [str(mz) for mz in spectrum.mz],
+        'attributes': [
+            {
+                'accession': 'MS:1000744',
+                'name': 'selected ion m/z',
+                'value': str(spectrum.precursor_mz)
+            },
+            {
+                'accession': 'MS:1000041',
+                'name': 'precursor charge',
+                'value': str(spectrum.precursor_charge)
+            }
+        ]
+    }
 
     return flask.jsonify([spectrum_dict])