Merge pull request #19 from ccaitlingo/remove-error-import

Remove error import
biocommons · Jul 5, 2023 · 6f49b97 · 6f49b97
2 parents ae09fad + 1dbd86a
commit 6f49b97
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Showing 7 changed files with 106 additions and 24 deletions.
diff --git a/README.md b/README.md
@@ -19,16 +19,16 @@ Read the official cdot documentation [here](https://github.com/SACGF/cdot).
 | Data Provider Function    | uta       | cdot      |
 | ------------------------- |-----------| ----------|
 | get_seq                   |           |
-| get_acs_for_protein       | *         | *
+| get_acs_for_protein_seq   |           | Not implemented (note in hgvs to drop this method)
 | get_gene_info             | Includes datetime of when transcript was added  |
 | get_tx_exons              | Includes the following additional fields: hgnc, tx_aseq, alt_aseq, test_exon_set_id, aes_exon_set_id, tx_exon_id, alt_exon_id, exon_aln_id
 | get_tx_for_gene           | *         | *
 | get_tx_for_region         |
-| get_alignments_for_region |           | Not implemented
+| get_alignments_for_region |           |
 | get_tx_identity_info      |
-| get_tx_info               |           | Does not perform alignments (does not use the alt_c argument) when fetching transcripts
+| get_tx_info               |           |
 | get_tx_mapping_options    |
-| get_similar_transcripts   |
+| get_similar_transcripts   |           | Not implemented (hgvs does not use this function)
 | get_pro_ac_for_tx_ac      |
 | get_assembly_map          |
 
@@ -47,7 +47,7 @@ In python:
 Assign any of the following supported clients to your hgvs data provider.
 
     >>> hdp = utaclients.uta.connect()
-    >>> hdp = utaclients.uta_rest.connect()
+    >>> hdp = utaclients.utarest.connect()
     >>> hdp = utaclients.cdot.connect()
 
 Then you can get started using all the functionalities of hgvs.

diff --git a/src/uta_clients/cdot.py b/src/uta_clients/cdot.py
@@ -1,4 +1,4 @@
-from cdot.hgvs.dataproviders import RESTDataProvider
+from cdot.hgvs.dataproviders import HGVSDataNotAvailableError, RESTDataProvider
 
 
 def connect():

diff --git a/src/uta_clients/uta.py b/src/uta_clients/uta.py
@@ -1 +1 @@
-from hgvs.dataproviders.uta import connect
+from hgvs.dataproviders.uta import HGVSDataNotAvailableError, HGVSError, connect
diff --git a/tests/cassettes/test_cdot_alignments_for_region_e.yaml b/tests/cassettes/test_cdot_alignments_for_region_e.yaml
@@ -0,0 +1,46 @@
+interactions:
+- request:
+    body: null
+    headers:
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      User-Agent:
+      - python-requests/2.31.0
+    method: GET
+    uri: https://cdot.cc/transcripts/region/NC_000007.13/splign/0/50
+  response:
+    body:
+      string: '{"results": []}'
+    headers:
+      Access-Control-Allow-Origin:
+      - http://203.101.229.44
+      Cache-Control:
+      - max-age=86400
+      Connection:
+      - keep-alive
+      Content-Length:
+      - '15'
+      Content-Type:
+      - application/json
+      Cross-Origin-Opener-Policy:
+      - same-origin
+      Date:
+      - Wed, 05 Jul 2023 17:05:31 GMT
+      Expires:
+      - Thu, 06 Jul 2023 17:05:31 GMT
+      Referrer-Policy:
+      - same-origin
+      Server:
+      - gunicorn
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - DENY
+    status:
+      code: 200
+      message: OK
+version: 1
diff --git a/tests/cassettes/test_cdot_alignments_for_region_ne.yaml b/tests/cassettes/test_cdot_alignments_for_region_ne.yaml
@@ -0,0 +1,41 @@
+interactions:
+- request:
+    body: null
+    headers:
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      User-Agent:
+      - python-requests/2.31.0
+    method: GET
+    uri: https://cdot.cc/transcripts/region/fake/splign/0/50
+  response:
+    body:
+      string: "\n<!doctype html>\n<html lang=\"en\">\n<head>\n  <title>Server Error
+        (500)</title>\n</head>\n<body>\n  <h1>Server Error (500)</h1><p></p>\n</body>\n</html>\n"
+    headers:
+      Connection:
+      - keep-alive
+      Content-Length:
+      - '145'
+      Content-Type:
+      - text/html
+      Cross-Origin-Opener-Policy:
+      - same-origin
+      Date:
+      - Wed, 05 Jul 2023 17:03:03 GMT
+      Referrer-Policy:
+      - same-origin
+      Server:
+      - gunicorn
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - DENY
+    status:
+      code: 500
+      message: Internal Server Error
+version: 1
diff --git a/tests/cassettes/test_cdot_tx_info_ne.yaml b/tests/cassettes/test_cdot_tx_info_ne.yaml
@@ -39,9 +39,9 @@ interactions:
       Cross-Origin-Opener-Policy:
       - same-origin
       Date:
-      - Thu, 15 Jun 2023 23:36:27 GMT
+      - Wed, 05 Jul 2023 16:54:44 GMT
       Expires:
-      - Fri, 16 Jun 2023 23:06:23 GMT
+      - Thu, 06 Jul 2023 16:54:44 GMT
       Referrer-Policy:
       - same-origin
       Server:

diff --git a/tests/test_cdot_vs_uta.py b/tests/test_cdot_vs_uta.py
@@ -1,10 +1,9 @@
 import datetime
 from typing import Dict, List
 
-import hgvs.dataproviders.uta as uta
 import pytest
 
-import src.uta_clients.cdot as cdot
+from src.uta_clients import cdot, uta
 
 
 def just_values(dictionaries: List[Dict]) -> List[List]:
@@ -63,7 +62,7 @@ def test_cdot_seq_e_indices():
     assert u == c
 
 
-@pytest.mark.skip(reason="cdot has different transcripts than uta")
+@pytest.mark.skip(reason="not implemented in cdot")
 # @pytest.mark.vcr
 def test_cdot_acs_for_protein_seq_e():
     """Existing seq."""
@@ -72,7 +71,7 @@ def test_cdot_acs_for_protein_seq_e():
     assert u == c
 
 
-@pytest.mark.skip(reason="cdot has different transcripts than uta")
+@pytest.mark.skip(reason="not implemented in cdot")
 # @pytest.mark.vcr
 def test_cdot_acs_for_protein_seq_ne():
     """Nonexisting seq."""
@@ -81,7 +80,7 @@ def test_cdot_acs_for_protein_seq_ne():
     assert u == c
 
 
-@pytest.mark.skip(reason="error not implemented in cdot")
+@pytest.mark.skip(reason="not implemented in cdot")
 # @pytest.mark.vcr
 def test_cdot_acs_for_protein_seq_ne_nonalphabetical():
     """Non-alphabetic character seq."""
@@ -200,26 +199,23 @@ def test_cdot_tx_for_region_ne_params():
         uta.connect().get_tx_for_region("fake", "splign")
 
 
-@pytest.mark.skip(reason="not implemented in cdot")
-# @pytest.mark.vcr
+@pytest.mark.vcr
 def test_cdot_alignments_for_region_e():  # Need example
     """Existing region."""
     u = uta.connect().get_alignments_for_region("NC_000007.13", 0, 50)
     c = cdot.connect().get_alignments_for_region("NC_000007.13", 0, 50)
     assert u == c
 
 
-@pytest.mark.skip(reason="not implemented in cdot")
-# @pytest.mark.vcr
+@pytest.mark.vcr
 def test_cdot_alignments_for_region_ne():
     """Nonexisting region"""
     u = uta.connect().get_alignments_for_region("fake", 0, 50)
     c = cdot.connect().get_alignments_for_region("fake", 0, 50)
     assert u == c
 
 
-@pytest.mark.skip(reason="not implemented in cdot")
-# @pytest.mark.vcr
+@pytest.mark.vcr
 def test_cdot_alignments_region_e_params():
     """Existing region with only some params."""
     with pytest.raises(TypeError):
@@ -228,8 +224,7 @@ def test_cdot_alignments_region_e_params():
         uta.connect().get_alignments_for_region("NC_000007.13")
 
 
-@pytest.mark.skip(reason="not implemented in cdot")
-# @pytest.mark.vcr
+@pytest.mark.vcr
 def test_cdot_alignments_region_ne_params():
     """Existing region with only some params."""
     with pytest.raises(TypeError):
@@ -262,11 +257,11 @@ def test_cdot_tx_info_e():
     assert u == c
 
 
-@pytest.mark.xfail
 @pytest.mark.vcr
 def test_cdot_tx_info_ne():
     """Nonexisting seq."""
-    assert cdot.connect().get_tx_info("NM_199425.2", "fake", "splign") == None
+    with pytest.raises(cdot.HGVSDataNotAvailableError):
+        cdot.connect().get_tx_info("NM_199425.2", "fake", "splign")
     with pytest.raises(uta.HGVSDataNotAvailableError):
         uta.connect().get_tx_info("NM_199425.2", "fake", "splign")
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		from hgvs.dataproviders.uta import connect
		from hgvs.dataproviders.uta import HGVSDataNotAvailableError, HGVSError, connect