Merge pull request #114 from neuroscout/example_ridge

FIX: Fetch utils, and sorting of uploads
neuroscout · Oct 5, 2023 · c5a388b · c5a388b
2 parents dc65808 + 94636af
commit c5a388b
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Showing 22 changed files with 399 additions and 674 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -7,7 +7,7 @@ build:
 
 python:
   install:
-    - requirements: requirements.txt
+    - requirements: docs/requirements.txt
     - method: pip
       path: .
 

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,4 @@
+{
+    "python.linting.flake8Enabled": true,
+    "python.linting.enabled": true
+}
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,9 @@
+pytest>=4.2.0
+betamax>=0.8.1
+betamax_serializers>=0.2.0
+tqdm>=4.30.0
+altair>=4.0.0
+vega>=2.6.0
+pyjwt~=1.7.1
+requests>=2.21
+sphinx-rtd-theme
diff --git a/pyns/api.py b/pyns/api.py
@@ -137,10 +137,12 @@ def _authorize(self, email=None, password=None):
             self._api_token = rv['access_token']
 
             iat = datetime.utcfromtimestamp(
-                jwt.decode(self._api_token, verify=False)['iat'])
+                jwt.decode(self._api_token, verify=False, 
+                           options={'verify_signature': False})['iat'])
             adj = iat - datetime.now()
             self._api_token_exp = datetime.utcfromtimestamp(
-                jwt.decode(self._api_token, verify=False)['exp']) - adj
+                jwt.decode(self._api_token, verify=False, 
+                           options={'verify_signature': False})['exp']) - adj
 
     def _check_expiry(self):
         if self._api_token is not None:

diff --git a/pyns/endpoints/analysis.py b/pyns/endpoints/analysis.py
@@ -529,6 +529,11 @@ def get_uploads(self, id, select='latest', **kwargs):
         uploads = self.get(id=id, sub_route='upload')
 
         # Sort by date
+        # Strip off seconds if they are there
+        for u in uploads:
+            if u['uploaded_at'].count(':') > 1:
+                u['uploaded_at'] = u['uploaded_at'][:-3]
+
         uploads = sorted(uploads, key=lambda x: datetime.datetime.strptime(
                 x['uploaded_at'], '%Y-%m-%dT%H:%M'),
                          reverse=(select == 'latest'))

diff --git a/pyns/fetch_utils.py b/pyns/fetch_utils.py
@@ -7,7 +7,7 @@
 try:
     from bids.variables import SparseRunVariable, BIDSRunVariableCollection
     from bids.variables.entities import RunInfo
-    from bids.layout import BIDSLayout
+    from bids.layout import BIDSLayout, BIDSLayoutIndexer
 except ImportError:
     SparseRunVariable = None
     BIDSRunVariableCollection = None
@@ -90,7 +90,7 @@ def fetch_predictors(predictor_names, dataset_name, return_type='df', rescale=Fa
         Scale(collection, predictor_names)
 
     if resample:
-        collection = collection.to_dense().resample('TR')
+        collection = collection.to_dense('TR')
 
     if return_type == 'df':
         collection = collection.to_df()
@@ -177,7 +177,7 @@ def install_dataset(dataset_dir, preproc_address, no_get=False):
     return preproc_dir
 
 
-def fetch_images(dataset_name, data_dir, no_get=False, datalad_jobs=-1, 
+def fetch_images(dataset_name, data_dir, no_get=False, datalad_jobs='auto', 
     preproc_address=None, **kwargs):
     """ Fetch preprocessed images from a Neuroscout dataset.
     Installs dataset using DataLad if not already installed.

diff --git a/tests/cassettes/analysis.json b/tests/cassettes/analysis.json
@@ -1,7 +1,7 @@
 {
   "http_interactions": [
     {
-      "recorded_at": "2022-07-26T00:02:45",
+      "recorded_at": "2023-10-05T20:35:16",
       "request": {
         "body": {
           "encoding": "utf-8",
@@ -15,7 +15,7 @@
             "gzip, deflate, br"
           ],
           "Authorization": [
-            "JWT eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJleHAiOjE2NTkzOTg1NTIsImlhdCI6MTY1ODc5Mzc1MiwibmJmIjoxNjU4NzkzNzUyLCJpZGVudGl0eSI6MX0.55A1Lj_YkR1rnvtVxXnDkHuyMbY8I5xRYvD38Rh9NXY"
+            "JWT eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJleHAiOjE2OTcxNDI5MDMsImlhdCI6MTY5NjUzODEwMywibmJmIjoxNjk2NTM4MTAzLCJpZGVudGl0eSI6MX0.hHABEu1rQp90CjzyOR4_lNzu9NFmGMYqo8tTE3tnlDA"
           ],
           "Connection": [
             "keep-alive"
@@ -35,7 +35,7 @@
       },
       "response": {
         "body": {
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+          "base64_string": "H4sIAAAAAAAAA31Sy2rDMBC89zP2rIDtkEJ8C00DhaaHxIdCCEaR10SNJQs9Qo3xv3dlN6U9pD55R5rZmV31ICxyj1XJPeSQJdl8liazZFFkST4HBhX33KEvZQX5kkp0wkrjZash16FpGJy5O4/HIJSxijhNKy5IQM0bhwxUW2EDeQ8v2gQff3aB2If0yGAfTh8oCDyAlVUSvxQIL7i7kGIja4SBwRtXSKXpPDpfcs2bzklHrfYejSN2D0+t9pY7HysSWAelul9YD0VnooaPeq94jZZGIwy2N4Pv0YcziOIMR7pWWK5d3VrFY+BReWD9fe3N83b1W/6W7l/SH0PradwwxPY0OFnL+7vR96air6VogyZWwsBwi3pa4LQwY7GS4jsRwA/Q2pgwzZbJ4hhBeaWHAbm3gZZow5g/mz/SmfPch0he71abghRcOCnpb89oahMcWrqCn1yZBsuxHB6+AGVJPhBxAgAA",
           "encoding": "utf-8",
           "string": ""
         },
@@ -53,7 +53,7 @@
             "application/json"
           ],
           "Date": [
-            "Tue, 26 Jul 2022 00:02:45 GMT"
+            "Thu, 05 Oct 2023 20:35:16 GMT"
           ],
           "Server": [
             "nginx/1.21.6"

diff --git a/tests/cassettes/analysis_object.json b/tests/cassettes/analysis_object.json
diff --git a/tests/cassettes/auth.json b/tests/cassettes/auth.json
@@ -1,7 +1,7 @@
 {
   "http_interactions": [
     {
-      "recorded_at": "2022-07-26T00:02:32",
+      "recorded_at": "2023-10-05T20:35:03",
       "request": {
         "body": {
           "encoding": "utf-8",
@@ -32,7 +32,7 @@
       },
       "response": {
         "body": {
-          "base64_string": "H4sIAAAAAAAAAxWM0Q6CIAAA3/sMP8BJZavenDaDEpepg15cEktArWWZ0vr36PG2u/tYZ8Z41xXPm+Kttbb4iBxOPBELtMvBQex9VJUh+zPMNARYoJVtpJpvjSQ3U5wqHadXgFPYwaauLj5cRCkFccDcSDMQibcoG9RAeRuwzOZYK411Nprx/RTmr0tYO/xoGuLYruuBvSyoSsCj7Z/5QNpAbV9jVNIldIeE9sFsmVQrTKj1nfwA8qMS37wAAAA=",
+          "base64_string": "H4sIAAAAAAAAAxWM0Q6CIAAA3/sMP6BpacveSEyhwFXotBdXxiaIWakraf179njb3X2Mc1Hwts27puI3Y2XwAZs8BSISeJtYe7HzcHkJij+jWCOLCuxOR0nxcJSkP4tY8aYQOQSSFtWqvHpoQVjmUBnrCPovMrzEpcY1ks2bympGGbEJA3oc309B0l8DZfLj2KTmtAzB2u+t5/7ump7UQ3Swc0V179JNHZDs0Sw75s+7m4LA+E5+szv14bwAAAA=",
           "encoding": "utf-8",
           "string": ""
         },
@@ -50,7 +50,7 @@
             "application/json"
           ],
           "Date": [
-            "Tue, 26 Jul 2022 00:02:32 GMT"
+            "Thu, 05 Oct 2023 20:35:03 GMT"
           ],
           "Server": [
             "nginx/1.21.6"

diff --git a/tests/cassettes/dataset.json b/tests/cassettes/dataset.json
diff --git a/tests/cassettes/get_analysis.json b/tests/cassettes/get_analysis.json
@@ -1,7 +1,7 @@
 {
   "http_interactions": [
     {
-      "recorded_at": "2022-07-26T00:02:45",
+      "recorded_at": "2023-10-05T20:35:17",
       "request": {
         "body": {
           "encoding": "utf-8",
@@ -15,7 +15,7 @@
             "gzip, deflate, br"
           ],
           "Authorization": [
-            "JWT eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJleHAiOjE2NTkzOTg1NTIsImlhdCI6MTY1ODc5Mzc1MiwibmJmIjoxNjU4NzkzNzUyLCJpZGVudGl0eSI6MX0.55A1Lj_YkR1rnvtVxXnDkHuyMbY8I5xRYvD38Rh9NXY"
+            "JWT eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJleHAiOjE2OTcxNDI5MDMsImlhdCI6MTY5NjUzODEwMywibmJmIjoxNjk2NTM4MTAzLCJpZGVudGl0eSI6MX0.hHABEu1rQp90CjzyOR4_lNzu9NFmGMYqo8tTE3tnlDA"
           ],
           "Connection": [
             "keep-alive"
@@ -25,11 +25,11 @@
           ]
         },
         "method": "GET",
-        "uri": "https://neuroscout.org/api/analyses/o8sbu"
+        "uri": "https://neuroscout.org/api/analyses/cmprm"
       },
       "response": {
         "body": {
-          "base64_string": "H4sIAAAAAAAAA31Sy2rDMBC89zP2rIDj0rTxLTQNFJoeEh8KIRjFXhM1siT0CDXG/96V3ZT0kPrkHWlmZ3bVQWmRe6wK7iGDNEnTSfI4SWd5kmQJMKi45w59ISrI5lSiK60wXmgFmQpSMjhydxyOQT+5QyCO1OUJCai5dMig0RVKyDp4VSb4+LMJxN5N9wy24fCJJYE7sKJK4jcFwnPuTqQoRY3QM3jnDVJpWo/OF1xx2TrhqNXWo3HE7uBZK2+587EigWVomvYK6yBvTdTwUe8Nz9HSYITB+mLwI/pwBrE8wp6u5ZYrV2vb8Bh4UO5Zd1t79bJeXMtf0v1L+mNoOY4b+tieBidqcXs36tZU1LkodVDEShgYblGNCxwXZixWovxJBPALaBsTTtN58rCPoDjTw4DM20BLtGHIn97P6Mx57kMkLzeLVU4KLhwa4S/PaGwTHFq6gl+8MRKLoezvvgEbyNMlcQIAAA==",
+          "base64_string": "H4sIAAAAAAAAA31Sy2rDMBC89zP2rIDtkEJ8C00DhaaHxIdCCEaR10SNJQs9Qo3xv3dlN6U9pD55R5rZmV31ICxyj1XJPeSQJdl8liazZFFkST4HBhX33KEvZQX5kkp0wkrjZash16FpGJy5O4/HIJSxijhNKy5IQM0bhwxUW2EDeQ8v2gQff3aB2If0yGAfTh8oCDyAlVUSvxQIL7i7kGIja4SBwRtXSKXpPDpfcs2bzklHrfYejSN2D0+t9pY7HysSWAelul9YD0VnooaPeq94jZZGIwy2N4Pv0YcziOIMR7pWWK5d3VrFY+BReWD9fe3N83b1W/6W7l/SH0PradwwxPY0OFnL+7vR96air6VogyZWwsBwi3pa4LQwY7GS4jsRwA/Q2pgwzZbJ4hhBeaWHAbm3gZZow5g/mz/SmfPch0he71abghRcOCnpb89oahMcWrqCn1yZBsuxHB6+AGVJPhBxAgAA",
           "encoding": "utf-8",
           "string": ""
         },
@@ -47,7 +47,7 @@
             "application/json"
           ],
           "Date": [
-            "Tue, 26 Jul 2022 00:02:45 GMT"
+            "Thu, 05 Oct 2023 20:35:17 GMT"
           ],
           "Server": [
             "nginx/1.21.6"
@@ -66,11 +66,11 @@
           "code": 200,
           "message": "OK"
         },
-        "url": "https://neuroscout.org/api/analyses/o8sbu"
+        "url": "https://neuroscout.org/api/analyses/cmprm"
       }
     },
     {
-      "recorded_at": "2022-07-26T00:02:46",
+      "recorded_at": "2023-10-05T20:35:17",
       "request": {
         "body": {
           "encoding": "utf-8",
@@ -84,7 +84,7 @@
             "gzip, deflate, br"
           ],
           "Authorization": [
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+            "JWT eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJleHAiOjE2OTcxNDI5MDMsImlhdCI6MTY5NjUzODEwMywibmJmIjoxNjk2NTM4MTAzLCJpZGVudGl0eSI6MX0.hHABEu1rQp90CjzyOR4_lNzu9NFmGMYqo8tTE3tnlDA"
           ],
           "Connection": [
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@@ -116,7 +116,7 @@
             "application/json"
           ],
           "Date": [
-            "Tue, 26 Jul 2022 00:02:46 GMT"
+            "Thu, 05 Oct 2023 20:35:17 GMT"
           ],
           "Server": [
             "nginx/1.21.6"
@@ -139,7 +139,7 @@
       }
     },
     {
-      "recorded_at": "2022-07-26T00:02:46",
+      "recorded_at": "2023-10-05T20:35:17",
       "request": {
         "body": {
           "encoding": "utf-8",
@@ -153,7 +153,7 @@
             "gzip, deflate, br"
           ],
           "Authorization": [
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+            "JWT eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJleHAiOjE2OTcxNDI5MDMsImlhdCI6MTY5NjUzODEwMywibmJmIjoxNjk2NTM4MTAzLCJpZGVudGl0eSI6MX0.hHABEu1rQp90CjzyOR4_lNzu9NFmGMYqo8tTE3tnlDA"
           ],
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@@ -185,7 +185,7 @@
             "application/json"
           ],
           "Date": [
-            "Tue, 26 Jul 2022 00:02:46 GMT"
+            "Thu, 05 Oct 2023 20:35:17 GMT"
           ],
           "Server": [
             "nginx/1.21.6"