Prettyfied json dump

uparma/styles.json

@@ -1 +1,45 @@
-{'msgfplus_style_1': {'name': 'MS-GF+', 'version': ['v2018.01.30', 'v2018.06.28', 'v2018.09.12'], 'reference': "Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, 'Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search."}, 'msfragger_style_1': {'name': 'MSFragger', 'version': ['20170103'], 'reference': 'Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nature Methods 14'}, 'ursgal_style_1': {'name': 'Ursgal', 'version': ['0.6.0', '0.6.1'], 'reference': 'Kremer, L. P. M., Leufken, J., Oyunchimeg, P., Schulze, S. & Fufezan, C. (2016) Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis. J. Proteome res. 15, 788-794.'}, 'searchgui_style_1': {}, 'searchgui_style_2': {}, 'psi_ms_style_1': {}, 'xtandem_style_1': {'name': 'X!Tandem', 'version': ['vengeance', 'alanine'], 'reference': ''}, 'masamanda_style_1': {'name': 'MS Amanda', 'version': ['2_0_0_9695', '2_0_0_9706', '2_0_0_10695']}}
+{
+  "masamanda_style_1": {
+    "name": "MS Amanda",
+    "version": [
+      "2_0_0_9695",
+      "2_0_0_9706",
+      "2_0_0_10695"
+    ]
+  },
+  "msfragger_style_1": {
+    "name": "MSFragger",
+    "reference": "Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nature Methods 14",
+    "version": [
+      "20170103"
+    ]
+  },
+  "msgfplus_style_1": {
+    "name": "MS-GF+",
+    "reference": "Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, 'Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.",
+    "version": [
+      "v2018.01.30",
+      "v2018.06.28",
+      "v2018.09.12"
+    ]
+  },
+  "psi_ms_style_1": {},
+  "searchgui_style_1": {},
+  "searchgui_style_2": {},
+  "ursgal_style_1": {
+    "name": "Ursgal",
+    "reference": "Kremer, L. P. M., Leufken, J., Oyunchimeg, P., Schulze, S. & Fufezan, C. (2016) Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis. J. Proteome res. 15, 788-794.",
+    "version": [
+      "0.6.0",
+      "0.6.1"
+    ]
+  },
+  "xtandem_style_1": {
+    "name": "X!Tandem",
+    "reference": "",
+    "version": [
+      "vengeance",
+      "alanine"
+    ]
+  }
+}

uparma/uparma.py

@@ -46,7 +46,13 @@ def __init__(self, refresh_jsons=False, source_style="ursgal_style_1"):
             if refresh_jsons is True:
                 with requests.get(url) as req:
                     with open(full_path, 'w') as j:
-                        print(req.json(), file=j)
+                        print(
+                            json.dumps(
+                                req.json(),
+                                indent=2,
+                                sort_keys=True
+                            ), file=j
+                        )
                     self.jsons[url_id] = req.json()
             else:
                 for url_id, url in URLS.items():
@@ -70,6 +76,7 @@ def _parse_jsons(self):
             if json_type != 'parameters':
                 continue
             for uparma_entry in self.jsons[url_id]:
+                print(uparma_entry)
                 _id = uparma_entry['_id']
                 self.parameters[_id] = uparma_entry