deriva 1.7.0__tar.gz → 1.7.3__tar.gz

deriva-1.7.3/CHANGELOG.md

@@ -0,0 +1,18 @@
+# CHANGE LOG
+
+## 1.6.5
+
+DataPath feature enhancements and changes:
+* new `denormalize()` method that uses a `visible-columns` "context" or a heuristic function to denormalize a path expression.
+* new `limit()` method as a chaining operation so that clients don't need to explicity `fetch()` results with limits.
+* subtle change to `link()` method for how it determines whether an alias name has been "bound" to the path. Now, it more explicitly checks if an alias object is found in the path's bound table instances. This change also relaxes the alias naming constraint to allow for automatic conflict resolution by appending an incremental numeric disambiguator if the given alias name is already in use. This could result in some `link()` methods now succeeding where they would have failed in the past.
+
+## 1.0.0
+Feature release. 
+* Refactored catalog configuration API.
+* Support for aggregate functions and binning in DataPath API.
+* Various bug fixes.
+* Complete change list [here](https://github.com/informatics-isi-edu/deriva-py/compare/v0.9.0...v1.0.0). 
+
+Change lists for previous releases can be found on the GitHub releases 
+page [here](https://github.com/informatics-isi-edu/deriva-py/releases).

{deriva-1.7.0/deriva.egg-info → deriva-1.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deriva
-Version: 1.7.0
+Version: 1.7.3
 Summary: Python APIs and CLIs (Command-Line Interfaces) for the DERIVA platform.
 Home-page: https://github.com/informatics-isi-edu/deriva-py
 Author: USC Information Sciences Institute, Informatics Systems Research Division
@@ -29,7 +29,7 @@ Requires-Dist: certifi
 Requires-Dist: pika
 Requires-Dist: urllib3<3,>=1.26
 Requires-Dist: portalocker>=1.2.1
-Requires-Dist: bdbag>=1.7.2
+Requires-Dist: bdbag>=1.7.3
 Requires-Dist: globus_sdk<4,>=3
 Requires-Dist: fair-research-login>=0.3.1
 Requires-Dist: fair-identifiers-client>=0.5.1

{deriva-1.7.0 → deriva-1.7.3}/deriva/config/annotation_config.py

@@ -33,7 +33,7 @@ class AttrSpecList(BaseSpecList):
             return None
         new = []
         for item in orig_list:
-            new.append(unicode(item))
+            new.append(item)
         return new
 
     def add_list(self, dictlist):
@@ -85,7 +85,7 @@ class AttrConfig:
         self.toplevel_config = ConfigUtil.find_toplevel_node(self.catalog.getCatalogModel(), schema_name, table_name)
 
     def make_speclist(self, name):
-        d = self.config.get(unicode(name))
+        d = self.config.get(name)
         if d is None:
             d = [dict()]
         return AttrSpecList(self.known_attrs, d)

{deriva-1.7.0 → deriva-1.7.3}/deriva/core/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.7.0"
+__version__ = "1.7.3"
 
 from deriva.core.utils.core_utils import *
 from deriva.core.base_cli import BaseCLI, KeyValuePairArgs

{deriva-1.7.0 → deriva-1.7.3}/deriva/core/catalog_cli.py

@@ -55,21 +55,21 @@ class DerivaCatalogCLI (BaseCLI):
 
         # parent arg parser
         self.remove_options(['--config-file', '--credential-file'])
-        self.parser.add_argument("--protocol", choices=["http", "https"], default='https',
+        self.parser.add_argument("-p", "--protocol", choices=["http", "https"], default='https',
                                  help="transport protocol: 'http' or 'https'")
         subparsers = self.parser.add_subparsers(title='sub-commands', dest='subcmd')
 
         # exists parser
         exists_parser = subparsers.add_parser('exists', help="Check if catalog exists.")
-        exists_parser.add_argument("id", metavar="<id>", type=str, help="catalog id")
+        exists_parser.add_argument("id", metavar="<id>", type=str, help="Catalog ID")
         exists_parser.set_defaults(func=self.catalog_exists)
 
         # create parser
         create_parser = subparsers.add_parser('create', help="Create a new catalog.")
-        create_parser.add_argument("--id", metavar="<id>", type=str, help="catalog id")
-        create_parser.add_argument("--owner", metavar="<owner> <owner> ...",
+        create_parser.add_argument("--id", metavar="<id>", type=str, help="Catalog ID")
+        create_parser.add_argument("-o", "--owner", metavar="<owner> <owner> ...",
                                    nargs="+", help="List of quoted user or group identifier strings.")
-        create_parser.add_argument("--auto-configure", action="store_true",
+        create_parser.add_argument("-a", "--auto-configure", action="store_true",
                                    help="Configure the new catalog with a set of baseline defaults")
         create_parser.add_argument("--configure-args", metavar="[key=value key=value ...]",
                                    nargs='+', action=KeyValuePairArgs, default={},
@@ -80,11 +80,12 @@ class DerivaCatalogCLI (BaseCLI):
 
         # get parser
         get_parser = subparsers.add_parser('get', help="Send a HTTP GET request to the catalog.")
-        get_parser.add_argument("id", metavar="<id>", type=str, help="catalog id")
+        get_parser.add_argument("id", metavar="<id>", type=str, help="Catalog ID")
         get_parser.add_argument("path", metavar="<request-path>", help="The ERMRest API path.")
-        get_parser.add_argument("--output-file", metavar="<output file path>", help="Path to output file.")
-        get_parser.add_argument("--output-format", choices=["json", "json-stream", "csv"], default="json")
-        get_parser.add_argument("--auto-delete", action="store_true",
+        get_parser.add_argument("-o", "--output-file", metavar="<output file path>", help="Path to output file.")
+        get_parser.add_argument("-f", "--output-format", choices=["json", "json-stream", "csv"], default="json",
+                                help="The output file format. Defaults to 'json'")
+        get_parser.add_argument("-a", "--auto-delete", action="store_true",
                                 help="Automatically delete output file if no results are returned.")
         get_parser.add_argument("--headers", metavar="[key=value key=value ...]",
                                 nargs='+', action=KeyValuePairArgs, default={},
@@ -95,10 +96,12 @@ class DerivaCatalogCLI (BaseCLI):
 
         # put parser
         put_parser = subparsers.add_parser('put', help="Send a HTTP PUT request to the catalog.")
-        put_parser.add_argument("id", metavar="<id>", type=str, help="catalog id")
+        put_parser.add_argument("id", metavar="<id>", type=str, help="Catalog ID")
         put_parser.add_argument("path", metavar="<request-path>", help="The ERMRest API path.")
-        put_parser.add_argument("--input-file", metavar="<output file path>", help="Path to input file.")
-        put_parser.add_argument("--input-format", choices=["json", "json-stream", "csv"], default="json")
+        put_parser.add_argument("input-file", metavar="<input file path>",
+                                help="Path to an input file containing the request message body.")
+        put_parser.add_argument("-f", "--input-format", choices=["json", "json-stream", "csv"], default="json",
+                                help="The input file format. Defaults to 'json'")
         put_parser.add_argument("--headers", metavar="[key=value key=value ...]",
                                 nargs='+', action=KeyValuePairArgs, default={},
                                 help="Variable length of whitespace-delimited key=value pair arguments used for "
@@ -108,10 +111,12 @@ class DerivaCatalogCLI (BaseCLI):
 
         # post parser
         post_parser = subparsers.add_parser('post', help="Send a HTTP POST request to the catalog.")
-        post_parser.add_argument("id", metavar="<id>", type=str, help="catalog id")
+        post_parser.add_argument("id", metavar="<id>", type=str, help="Catalog ID")
         post_parser.add_argument("path", metavar="<request-path>", help="The ERMRest API path.")
-        post_parser.add_argument("--input-file", metavar="<input file path>", help="Path to input file.")
-        post_parser.add_argument("--input-format", choices=["json", "json-stream", "csv"], default="json")
+        post_parser.add_argument("input-file", metavar="<input file path>",
+                                 help="Path to an input file containing the request message body.")
+        post_parser.add_argument("-f", "--input-format", choices=["json", "json-stream", "csv"], default="json",
+                                 help="The input file format. Defaults to 'json'")
         post_parser.add_argument("--headers", metavar="[key=value key=value ...]",
                                  nargs='+', action=KeyValuePairArgs, default={},
                                  help="Variable length of whitespace-delimited key=value pair arguments used for "
@@ -122,7 +127,7 @@ class DerivaCatalogCLI (BaseCLI):
         # delete parser
         del_parser = subparsers.add_parser('delete', help="Send a HTTP DELETE request to the catalog. "
                                                           "Use the 'drop' command to delete the entire catalog.")
-        del_parser.add_argument("id", metavar="<id>", type=str, help="catalog id")
+        del_parser.add_argument("id", metavar="<id>", type=str, help="Catalog ID")
         del_parser.add_argument("path", metavar="<request-path>", help="The ERMRest API path.")
         del_parser.add_argument("--headers", metavar="[key=value key=value ...]",
                                 nargs='+', action=KeyValuePairArgs, default={},
@@ -133,12 +138,12 @@ class DerivaCatalogCLI (BaseCLI):
 
         # drop parser
         drop_parser = subparsers.add_parser('drop', help="Delete a catalog.")
-        drop_parser.add_argument("id", metavar="<id>", type=str, help="catalog id")
+        drop_parser.add_argument("id", metavar="<id>", type=str, help="Catalog ID")
         drop_parser.set_defaults(func=self.catalog_drop)
 
         # clone parser
         clone_parser = subparsers.add_parser('clone', help="Clone a source catalog to a new destination catalog.")
-        clone_parser.add_argument("id", metavar="<id>", type=str, help="catalog id")
+        clone_parser.add_argument("id", metavar="<id>", type=str, help="Catalog ID")
         clone_parser.add_argument("--no-copy-data", action="store_false",
                                   help="Do not copy table contents.")
         clone_parser.add_argument("--no-copy-annotations", action="store_false",
@@ -154,8 +159,8 @@ class DerivaCatalogCLI (BaseCLI):
         # create_alias parser
         create_alias_parser = subparsers.add_parser('create-alias', help="Create a new catalog alias")
         create_alias_parser.add_argument("--id", metavar="<id>", type=str, help="The alias id.")
-        create_alias_parser.add_argument("--alias-target", metavar="<alias>", help="The target catalog id.")
-        create_alias_parser.add_argument("--owner", metavar="<owner> <owner> ...",
+        create_alias_parser.add_argument("-t", "--alias-target", metavar="<alias>", help="The target catalog id.")
+        create_alias_parser.add_argument("-o", "--owner", metavar="<owner> <owner> ...",
                                          nargs="+", help="List of quoted user or group identifier strings.")
         create_alias_parser.set_defaults(func=self.catalog_alias_create)
 
@@ -167,10 +172,10 @@ class DerivaCatalogCLI (BaseCLI):
         # update_alias parser
         update_alias_parser = subparsers.add_parser('update-alias', help="Update an existing catalog alias")
         update_alias_parser.add_argument("--id", metavar="<id>", type=str, help="The alias id.")
-        update_alias_parser.add_argument("--alias-target", metavar="<alias>", nargs='?', default=nochange, const=None,
+        update_alias_parser.add_argument("-t", "--alias-target", metavar="<alias>", nargs='?', default=nochange, const=None,
                                          help="The target catalog id. If specified without a catalog id as an argument "
                                               "value, the existing alias target will be cleared ")
-        update_alias_parser.add_argument("--owner", metavar="<owner> <owner> ...", nargs='+', default=nochange,
+        update_alias_parser.add_argument("-o", "--owner", metavar="<owner> <owner> ...", nargs='+', default=nochange,
                                          help="List of quoted user or group identifier strings.")
         update_alias_parser.set_defaults(func=self.catalog_alias_update)
 
@@ -194,9 +199,29 @@ class DerivaCatalogCLI (BaseCLI):
         self.id = args.id
         self.server = DerivaServer(self.protocol,
                                    args.host,
-                                   credentials=DerivaCatalogCLI._get_credential(self.host,
-                                                                                token=args.token,
-                                                                                oauth2_token=args.oauth2_token))
+                                   credentials=DerivaCatalogCLI._get_credential(
+                                       self.host,
+                                       token=args.token,
+                                       oauth2_token=args.oauth2_token))
+
+    @staticmethod
+    def _decorate_headers(headers, file_format, method="get"):
+
+        header_format_map = {
+            "json": "application/json",
+            "json-stream": "application/x-json-stream",
+            "csv": "text/csv"
+        }
+
+        format_type = header_format_map.get(file_format)
+        if format_type is None:
+            raise UsageException("Unsupported format: %s" % file_format)
+        if str(method).lower() in ["get", "head"]:
+            headers["accept"] = format_type
+        elif str(method).lower() in ["post", "put"]:
+            headers["content-type"] = format_type
+        else:
+            raise UsageException("Unsupported method: %s" % method)
 
     def catalog_exists(self, args):
         """Implements the catalog_exists sub-command.
@@ -250,16 +275,7 @@ class DerivaCatalogCLI (BaseCLI):
         """
         headers = DEFAULT_HEADERS.copy()
         headers.update(args.headers)
-
-        if args.output_format == "json":
-            headers["accept"] = "application/json"
-        elif args.output_format == "json-stream":
-            headers["accept"] = "application/x-json-stream"
-        elif args.output_format == "csv":
-            headers["accept"] = "text/csv"
-        else:
-            raise UsageException("Unsupported output format: %s" % args.output_format)
-
+        self._decorate_headers(headers, args.output_format)
         catalog = self.server.connect_ermrest(args.id)
         try:
             if args.output_file:
@@ -278,13 +294,41 @@ class DerivaCatalogCLI (BaseCLI):
                 os.remove(args.output_file)
             raise
 
-    # TODO: implement PUT at some point
     def catalog_put(self, args):
-        raise NotImplementedError
+        """Implements the catalog_put sub-command.
+        """
+        headers = DEFAULT_HEADERS.copy()
+        headers.update(args.headers)
+        self._decorate_headers(headers, args.input_format, "put")
+        try:
+            catalog = self.server.connect_ermrest(args.id)
+            with open(args.input_file, "rb") as input_file:
+                resp = catalog.put(args.path, data=input_file, headers=headers)
+                if not args.quiet:
+                    pp(resp.json())
+        except HTTPError as e:
+            if e.response.status_code == requests.codes.not_found:
+                raise ResourceException('Catalog not found', e)
+            else:
+                raise e
 
-    # TODO: implement POST at some point
     def catalog_post(self, args):
-        raise NotImplementedError
+        """Implements the catalog_post sub-command.
+        """
+        headers = DEFAULT_HEADERS.copy()
+        headers.update(args.headers)
+        self._decorate_headers(headers, args.input_format, "post")
+        try:
+            catalog = self.server.connect_ermrest(args.id)
+            with open(args.input_file, "rb") as input_file:
+                resp = catalog.post(args.path, data=input_file, headers=headers)
+                if not args.quiet:
+                    pp(resp.json())
+        except HTTPError as e:
+            if e.response.status_code == requests.codes.not_found:
+                raise ResourceException('Catalog not found', e)
+            else:
+                raise e
 
     def catalog_delete(self, args):
         """Implements the catalog_delete sub-command.