Merge pull request #2 from refgenie/dev

Release 0.1.0
refgenie · Jun 17, 2021 · 3a362e8 · 3a362e8
2 parents f90ecf9 + ce9ee6b
commit 3a362e8
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Showing 7 changed files with 78 additions and 121 deletions.
diff --git a/docs/README.md b/docs/README.md
@@ -25,7 +25,7 @@ pip install refget
 ```python
 import refget
 
-rgc = RefGetClient("https://refget.herokuapp.com/sequence/")
+rgc = refget.RefGetClient("https://refget.herokuapp.com/sequence/")
 rgc.refget("6681ac2f62509cfc220d78751b8dc524", start=0, end=10)
 
 ```

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,6 +2,10 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
 
-## [0.0.1] - Unreleased
+## [0.1.0] - 2021-06-17
 
-First public version
+First public version, backed by henge version 0.1.1.
+
+## [0.0.1] - 2020-06-25
+
+Beta version for testing
diff --git a/docs_jupyter/tutorial.ipynb b/docs_jupyter/tutorial.ipynb
diff --git a/refget/_version.py b/refget/_version.py
@@ -1 +1 @@
-__version__ = "0.0.1"
+__version__ = "0.1.0"
diff --git a/refget/refget.py b/refget/refget.py
@@ -18,19 +18,14 @@
 
 sequence_schema = """description: "Schema for a single raw sequence"
 henge_class: sequence
-type: object
-properties:
-  sequence:
-    type: string
-    description: "Actual sequence content"
-required:
-  - sequence
+type: string
+description: "Actual sequence content"
 """
 
 
 
 class RefGetClient(henge.Henge):
-    def __init__(self, api_url_base=None, database={}, schemas=None, henges=None, checksum_function=henge.md5, suppress_connect=True):
+    def __init__(self, api_url_base=None, database={}, schemas=[], schemas_str=[], henges=None, checksum_function=henge.md5, suppress_connect=True):
         """
         A user interface to insert and retrieve decomposable recursive unique
         identifiers (DRUIDs).
@@ -49,10 +44,9 @@ def __init__(self, api_url_base=None, database={}, schemas=None, henges=None, ch
 
 
         # These are the item types that this henge can understand.
-        if not schemas:
-            schemas = [sequence_schema]
-        print(schemas)
-        super(RefGetClient, self).__init__(database, schemas, henges=henges,
+        if len(schemas) ==0 and len(schemas_str) == 0:
+            schemas_str = [sequence_schema]
+        super(RefGetClient, self).__init__(database, schemas, schemas_str, henges=henges,
                                           checksum_function=checksum_function)
 
     def refget_remote(self, digest, start=None, end=None):
@@ -82,18 +76,18 @@ def refget_remote(self, digest, start=None, end=None):
     def refget(self, digest, start=None, end=None):
         full_data = None
         try:
-            full_data = self.retrieve(digest)
+            full_data = super(RefGetClient, self).retrieve(digest)
             if start is not None and end is not None:
-                result = full_data['sequence'][start:end]
+                result = full_data[start:end]
             else:
-                result = full_data['sequence']
+                result = full_data
 
             return result
         except henge.NotFoundException:
             return self.refget_remote(digest, start, end)
 
     def load_seq(self, seq):
-        checksum = self.insert({'sequence': seq}, "sequence")
+        checksum = self.insert(seq, "sequence")
         _LOGGER.debug("Loaded {}".format(checksum))
         return checksum
 

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -1,4 +1,4 @@
-henge
+henge==0.1.1
 pyfaidx
 requests
 yacman>=0.6.7

diff --git a/setup.py b/setup.py
@@ -39,7 +39,7 @@
         "Programming Language :: Python :: 3.6",
     ],
     keywords="genome, assembly, bioinformatics, reference, sequence",
-    url="https://github.com/databio/refget",
+    url="https://github.com/refgenie/refget",
     author=u"Nathan Sheffield, Michal Stolarczyk",
     author_email=u"nathan@code.databio.org", 
     license="BSD2",