biocypher 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

biocypher/__init__.py

@@ -21,10 +21,11 @@ __all__ = [
     "log",
     "Driver",
     "BioCypher",
-    "Resource",
+    "FileDownload",
+    "APIRequest",
 ]
 
-from ._get import Resource
+from ._get import APIRequest, FileDownload
 from ._core import BioCypher
 from ._config import config, module_data
 from ._logger import log, logger, logfile

biocypher/_get.py

@@ -228,13 +228,12 @@ class Downloader:
             paths = []
             for url in file_download.url_s:
                 fname = url[url.rfind("/") + 1 :].split("?")[0]
-                paths.append(
-                    self._retrieve(
-                        url=url,
-                        fname=fname,
-                        path=os.path.join(self.cache_dir, file_download.name),
-                    )
+                path = self._retrieve(
+                    url=url,
+                    fname=fname,
+                    path=os.path.join(self.cache_dir, file_download.name),
                 )
+                paths.append(path)
         else:
             paths = []
             fname = file_download.url_s[

biocypher/_metadata.py

@@ -19,7 +19,7 @@ import importlib.metadata
 
 import toml
 
-_VERSION = "0.6.0"
+_VERSION = "0.6.2"
 
 
 def get_metadata():

biocypher/output/write/_batch_writer.py

@@ -18,6 +18,16 @@ from biocypher.output.write._writer import _Writer
 class _BatchWriter(_Writer, ABC):
     """Abstract batch writer class"""
 
+    @abstractmethod
+    def _quote_string(self, value: str) -> str:
+        """
+        Abstract method to quote a string. Escaping is handled by the database-specific writer.
+        """
+
+        raise NotImplementedError(
+            "Database writer must override '_quote_string'"
+        )
+
     @abstractmethod
     def _get_default_import_call_bin_prefix(self):
         """
@@ -626,7 +636,7 @@ class _BatchWriter(_Writer, ABC):
                         if isinstance(p, list):
                             plist.append(self._write_array_string(p))
                         else:
-                            plist.append(f"{self.quote}{str(p)}{self.quote}")
+                            plist.append(self._quote_string(str(p)))
 
                 line.append(self.delim.join(plist))
             line.append(labels)
@@ -861,7 +871,7 @@ class _BatchWriter(_Writer, ABC):
                     if isinstance(p, list):
                         plist.append(self._write_array_string(p))
                     else:
-                        plist.append(self.quote + str(p) + self.quote)
+                        plist.append(self._quote_string(str(p)))
 
             entries = [e.get_source_id()]
 

biocypher/output/write/graph/_neo4j.py

@@ -45,6 +45,13 @@ class _Neo4jBatchWriter(_BatchWriter):
 
         return "bin/"
 
+    def _quote_string(self, value: str) -> str:
+        """
+        Quote a string. Quote character is escaped by doubling it.
+        """
+
+        return f"{self.quote}{value.replace(self.quote, self.quote * 2)}{self.quote}"
+
     def _write_array_string(self, string_list):
         """
         Abstract method to output.write the string representation of an array into a .csv file
@@ -57,7 +64,7 @@ class _Neo4jBatchWriter(_BatchWriter):
             str: The string representation of an array for the neo4j admin import
         """
         string = self.adelim.join(string_list)
-        return f"{self.quote}{string}{self.quote}"
+        return self._quote_string(string)
 
     def _write_node_headers(self):
         """

biocypher/output/write/graph/_rdf.py

@@ -391,6 +391,13 @@ class _RDFWriter(_BatchWriter):
         """
         return ""
 
+    def _quote_string(self, value: str) -> str:
+        """
+        Quote a string.
+        """
+
+        return f"{self.quote}{value}{self.quote}"
+
     def _write_array_string(self, string_list):
         """
         Abstract method to write the string representation of an array into a .csv file

biocypher/output/write/relational/_postgresql.py

@@ -57,6 +57,13 @@ class _PostgreSQLBatchWriter(_BatchWriter):
             )
             return "VARCHAR"
 
+    def _quote_string(self, value: str) -> str:
+        """
+        Quote a string.
+        """
+
+        return f"{self.quote}{value}{self.quote}"
+
     def _write_array_string(self, string_list) -> str:
         """
         Abstract method to output.write the string representation of an array into a .csv file

{biocypher-0.6.0.dist-info → biocypher-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.6.0
+Version: 0.6.2
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT

{biocypher-0.6.0.dist-info → biocypher-0.6.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biocypher/__init__.py,sha256=ejNY53vH_pE3ZbIN8G_ZBYxxPG9aERovRLD0XhDvt4k,942
+biocypher/__init__.py,sha256=-vr7dGUv6QK7f_i9mmUK5WpMsZuFPflUEFC4oElJTCA,980
 biocypher/_config/__init__.py,sha256=fFHRFYxE2MtDAQWL6upe--MJ1vw3Z8CwIPhF2gW8cRU,3698
 biocypher/_config/biocypher_config.yaml,sha256=pusj0IjJM3uWRcm0N7U7mb1IX257HCV2reZV3YKFCk0,3037
 biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsXypt-A,119
@@ -8,10 +8,10 @@ biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6ROD
 biocypher/_core.py,sha256=m4o4Szv2xY2gl3PnNAA9m7Gg5Sgd8iR9THv3RDyZlQ8,22618
 biocypher/_create.py,sha256=vpUchUdEpWupZi1LgFLxAWMtqoBwnWbP7PwEDUCBS4A,10202
 biocypher/_deduplicate.py,sha256=BBvfpXzu6L5YDY5FdtXxnf8YlsbJpbCE8RdUoKsm0n0,4949
-biocypher/_get.py,sha256=mOfne16yeAkFQidvoFprrpQjN6CZgS68pQi2BbOJ_-U,13843
+biocypher/_get.py,sha256=1FHs4n2R2k7OVWtVe7euF2J5WpsUXsFAmnpdSYuhLvY,13817
 biocypher/_logger.py,sha256=NGXe3hZA79WSujfOgpcxHBf8N2QAfrmvM1LFDpsGK2U,3185
 biocypher/_mapping.py,sha256=ERSNH2Bg19145KytxbFE4BInPaiP-LWW7osOBot29Eo,9304
-biocypher/_metadata.py,sha256=A-d_UprHx3ljxyziSQFgk-ts7MsDOnXTGdMnSRERwcw,1657
+biocypher/_metadata.py,sha256=D4HcHz3EKz_aLJ709LEcSnv5K3Nj4kX6DShGeA7j2Po,1657
 biocypher/_misc.py,sha256=oKNfmj9mUKDYtmx-R6FCZxRa7AOut3VKZZm16KFimyY,6363
 biocypher/_ontology.py,sha256=G5k-bnzvPZUqhLPxtoOPFa4OSQ4JpufgozVakLTjwLg,31789
 biocypher/_translate.py,sha256=JafvhtVaFSpruRfYh9BzjVbvDF1Mhg7LLKMDZHWkRjg,16496
@@ -21,19 +21,19 @@ biocypher/output/connect/_neo4j_driver.py,sha256=jzF5sDhs_WnYEfXiSjQ1P3wNgoadl4C
 biocypher/output/in_memory/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biocypher/output/in_memory/_pandas.py,sha256=lsYQKjfxUy0O-ae4-YpsCJX-l85bxyc60WOj8gKfMfU,3080
 biocypher/output/write/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biocypher/output/write/_batch_writer.py,sha256=3pdS8ZLN4sBwATXaXFaSrfPQmejjFjo0avHkPQavFSU,36959
+biocypher/output/write/_batch_writer.py,sha256=Yev0Qpm6Tx2Z9Y89xAWPSy8rLuD1g3FbVKcG9R2D1yA,37239
 biocypher/output/write/_get_writer.py,sha256=AeQcHQTrz68ZvtxsZl4W0ymc8cOxe3Qfq5PJRY7kq_I,3736
 biocypher/output/write/_writer.py,sha256=v4-c8yME1UCJeqy8Lfmv7KtY7_B4QkWgADt5xkFNJFQ,7453
 biocypher/output/write/graph/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biocypher/output/write/graph/_arangodb.py,sha256=aUa_CNZyunFaPrJHc9RtVHRo0Fca9xJ-ZmRz4PxPO8c,8078
-biocypher/output/write/graph/_neo4j.py,sha256=ZINbfrv7gBAgHMT9uE4HCznosNRspT3SmPV83XXfhCw,11849
+biocypher/output/write/graph/_neo4j.py,sha256=rWCyxeajN3TCbE6W4L57c-CBrqtShVa8ufUkCjVZlGc,12067
 biocypher/output/write/graph/_networkx.py,sha256=EW2we3FlqQ8KfLv4l_2wE27KBUlhXJyD5ORvowSjlaA,2545
-biocypher/output/write/graph/_rdf.py,sha256=BtunVo0iaCVM9I2tWOYwGpB9itbngHBjP0RhwgcJUiM,17977
+biocypher/output/write/graph/_rdf.py,sha256=DdpStVXNEIdEvVHo23Qru63XY_IsUbfeAKjs9TPjHbo,18125
 biocypher/output/write/relational/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biocypher/output/write/relational/_csv.py,sha256=eyAtmwfCNYnuVbkpd0rUoo9KgG2KPgopZVA3X97tRLU,2919
-biocypher/output/write/relational/_postgresql.py,sha256=6sABZaELzmV7a2aUy2iRksf28WFsc3EA9mdQ2mShPeM,11959
+biocypher/output/write/relational/_postgresql.py,sha256=MRgDicNRW0KWene1nag4FgJ-nEUlpkulatG1S8D33s0,12107
 biocypher/output/write/relational/_sqlite.py,sha256=ozElhca1YCYq8R-VFh-LDsnPBaXVJm2cvEboBK2LVVY,2073
-biocypher-0.6.0.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
-biocypher-0.6.0.dist-info/METADATA,sha256=k1r_9Unas2OGWVwcnWQq5Fs6lWDeVU_ApevfEqx1ddM,10641
-biocypher-0.6.0.dist-info/WHEEL,sha256=Zb28QaM1gQi8f4VCBhsUklF61CTlNYfs9YAZn-TOGFk,88
-biocypher-0.6.0.dist-info/RECORD,,
+biocypher-0.6.2.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
+biocypher-0.6.2.dist-info/METADATA,sha256=ZJfAl8_BsK1mRwFFy0HJOlkLKGiAByTeEdlwHX3C8Ec,10641
+biocypher-0.6.2.dist-info/WHEEL,sha256=Zb28QaM1gQi8f4VCBhsUklF61CTlNYfs9YAZn-TOGFk,88
+biocypher-0.6.2.dist-info/RECORD,,