small corrections after rebase of the branch

Author: mhsarmiento

astroquery/gaia/core.py

@@ -11,8 +11,7 @@
 European Space Agency (ESA)
 
 Created on 30 jun. 2016
-Modified on 1 jun. 2021 by mhsarmiento
-Version: gaia-astroquery-1.0
+
 
 """
 from requests import HTTPError
@@ -173,9 +172,12 @@ def load_data(self, ids, data_release=None, data_structure='INDIVIDUAL', retriev
             By default, it takes the current default one.
         data_structure: str, optional, default 'INDIVIDUAL'
             it can be 'INDIVIDUAL', 'COMBINED', 'RAW':
-            'INDIVIDUAL' means...
-            'COMBINED' means...
-            'RAW' means...
+            'INDIVIDUAL' products are provided in separate files for each sourceId. All files are zipped in a single
+                bundle, even if only one source/file is considered
+            'COMBINED' products are provided in a single file concatenating the data of all sourceIds together.
+                How this is organised depends on the chosen format
+            'RAW' products are provided following a Data Model similar to that used in the MDB, meaning in
+                particular that parameters stored as arrays will remain as such. Like in the COMBINED structure, a single file is provided for the data of all sourceIds together, but in this case there will be always be one row per sourceId
         retrieval_type : str, optional, default 'ALL'
             retrieval type identifier. It can be either 'epoch_photometry'
             for compatibility reasons or 'ALL' to retrieve all data from
@@ -194,7 +196,7 @@ def load_data(self, ids, data_release=None, data_structure='INDIVIDUAL', retriev
             By default, this value will be set to False. If it is set to 'true'
             the Datalink items tags will not be checked.
         format : str, optional, default 'votable'
-            loading format
+            loading format. Other available formats are 'csv' and 'fits'
         output_file : string, optional, default None
             file where the results are saved.
             If it is not provided, the http response contents are returned.
@@ -903,23 +905,20 @@ def launch_job_async(self, query, name=None, output_file=None,
 
     def rename_table(self, table_name=None, new_table_name=None, new_column_names_dict={},
                      verbose=False):
-        """ This new method allows you to update the column names of a user table.
-
-        Parameters
-        ----------
-        table_name: str, required
-            old name of the user's table
-        new_table_name: str, required
-            new name of the user's table
-        new_column_names_dict: dict str:str, required
-            dict with pairs "old_column1_name:new_column1_name"
-        verbose : bool, optional, default 'False'
-            flag to display information about the process
-
-        Example
-        -------
-        TapPlus.rename_table.rename_table(table_name=old_table_name, new_table_name=new_table_name,
-        new_column_names_dict=[old_column1:new_column1, old_column2:new_column2, ...])
+        """
+            This new method allows to update the column names of a user table.
+            header example: rename_table(table_name=old_table_name, new_table_name=new_table_name -optional-
+             , new_column_names_dict=[old_column1:new_column1, old_column2:new_colum2...])
+            Parameters
+            ----------
+            table_name: str, required
+                old name of the user's table
+            new_table_name: str, required
+                new name of the user's table
+            new_column_names_dict: dict str:str, required
+                dict with pairs "old_column1_name:new_column1_name"
+            verbose : bool, optional, default 'False'
+                flag to display information about the process
         """
         return TapPlus.rename_table(self, table_name=table_name, new_table_name=new_table_name,
                                     new_column_names_dict=new_column_names_dict, verbose=verbose)

astroquery/utils/tap/conn/tapconn.py

@@ -87,7 +87,7 @@ def __init__(self, ishttps,
         self.__connPort = port
         self.__connPortSsl = sslport
         if server_context is not None:
-            if (server_context.startswith("/")):
+            if(server_context.startswith("/")):
                 self.__serverContext = server_context
             else:
                 self.__serverContext = f"/{server_context}"
@@ -107,7 +107,7 @@ def __init__(self, ishttps,
 
     def __create_context(self, context):
         if (context is not None and context != ""):
-            if (str(context).startswith("/")):
+            if(str(context).startswith("/")):
                 return f"{self.__serverContext}{context}"
             else:
                 return f"{self.__serverContext}/{context}"
@@ -125,7 +125,7 @@ def __interna_init(self):
         self.__postHeaders = {
             "Content-type": CONTENT_TYPE_POST_DEFAULT,
             "Accept": "text/plain"
-        }
+            }
         self.__getHeaders = {}
         self.__cookie = None
         self.__currentStatus = 0
@@ -414,6 +414,9 @@ def execute_table_tool(self, data,
         context = self.__get_table_edit_context()
         return self.__execute_post(context, data, content_type, verbose)
 
+
+
+
     def __execute_post(self, context, data,
                        content_type=CONTENT_TYPE_POST_DEFAULT,
                        verbose=False):
@@ -599,7 +602,7 @@ def get_file_from_header(self, headers):
         if content_disposition is not None:
             p = content_disposition.find('filename="')
             if p >= 0:
-                filename = content_disposition[p + 10:len(content_disposition) - 1]
+                filename = content_disposition[p+10:len(content_disposition)-1]
                 content_encoding = self.find_header(headers, 'Content-Encoding')
                 if content_encoding is not None:
                     if "gzip" == content_encoding.lower():
@@ -733,7 +736,7 @@ def encode_multipart(self, fields, files):
 
     def __str__(self):
         return f"\tHost: {self.__connHost}\n\tUse HTTPS: {self.__isHttps}" \
-               f"\n\tPort: {self.__connPort}\n\tSSL Port: {self.__connPortSsl}"
+            f"\n\tPort: {self.__connPort}\n\tSSL Port: {self.__connPortSsl}"
 
 
 class ConnectionHandler:

astroquery/utils/tap/core.py

@@ -1245,7 +1245,7 @@ def get_datalinks(self, ids, verbose=False):
             print("Retrieving datalink.")
         if ids is None:
             raise ValueError("Missing mandatory argument 'ids'")
-        if isinstance(ids, str):
+        if isinstance(ids, str):
             ids_arg = f"ID={ids}"
         else:
             if isinstance(ids, int):
@@ -1368,7 +1368,7 @@ def login(self, user=None, password=None, credentials_file=None,
                 user = ins.readline().strip()
                 password = ins.readline().strip()
         if user is None:
-            user = input("User: ")
+            user = input("User: ")
             if user is None:
                 print("Invalid user name")
                 return
@@ -2059,7 +2059,7 @@ def login(self, user=None, password=None, credentials_file=None,
                 user = ins.readline().strip()
                 password = ins.readline().strip()
         if user is None:
-            user = input("User: ")
+            user = input("User: ")
             if user is None:
                 log.info("Invalid user name")
                 return
@@ -2165,4 +2165,4 @@ def __changesContainFlag(changes=None, flag=None, verbose=False):
         return c
 
     def __getconnhandler(self):
-        return self._Tap__connHandler
+        return self._Tap__connHandler

astroquery/utils/tap/tests/data/job_1.vot

@@ -1,7 +1,7 @@
 <VOTABLE version="1.3" xmlns="http://www.ivoa.net/xml/VOTable/v1.3">
 <RESOURCE type="results">
 <INFO name="QUERY_STATUS" value="OK"/>
-<INFO name="ADQL_QUERY" value="select * from user_mhenar.table_test_update" />
+<INFO name="ADQL_QUERY" value="select * from user_test.table_test_update" />
 <INFO name="CAPTION" value="If you use public Gaia DR1 data in your paper, please take note of our guide on how to acknowledge and cite Gaia DR1: http://gaia.esac.esa.int/documentation/GDR1/Miscellaneous/sec_credit_and_citation_instructions.html" />
 <TABLE>
 <FIELD datatype="double" name="ra">
@@ -14,7 +14,7 @@
 <DESCRIPTION>source_id</DESCRIPTION>
 </FIELD>
 <FIELD datatype="int" name="table1_oid">
-<DESCRIPTION>table_test_update_oid</DESCRIPTION>
+<DESCRIPTION>table1_oid</DESCRIPTION>
 </FIELD>
 <DATA>
 <BINARY2>

astroquery/utils/tap/tests/data/table_test_rename.vot

@@ -1,7 +1,7 @@
 <VOTABLE version="1.3" xmlns="http://www.ivoa.net/xml/VOTable/v1.3">
 <RESOURCE type="results">
 <INFO name="QUERY_STATUS" value="OK"/>
-<INFO name="ADQL_QUERY" value="select * from user_mhenar.table_test_update" />
+<INFO name="ADQL_QUERY" value="select * from user_test.table_test_update" />
 <INFO name="CAPTION" value="If you use public Gaia DR1 data in your paper, please take note of our guide on how to acknowledge and cite Gaia DR1: http://gaia.esac.esa.int/documentation/GDR1/Miscellaneous/sec_credit_and_citation_instructions.html" />
 <TABLE>
 <FIELD datatype="double" name="ra">

astroquery/utils/tap/tests/data/test_table_rename.xml

@@ -7,7 +7,7 @@
         <name>user_mhenar</name>
         <description/>
         <table type="base_table" esatapplus:size="3" esatapplus:flags="0">
-            <name>user_mhenar.table1</name>
+            <name>user_test.table1</name>
             <description>
             <![CDATA[ Uploaded from disk ]]>
             </description>

astroquery/utils/tap/tests/test_tap.py

@@ -205,13 +205,13 @@ def test_launch_sync_job():
     results = job.get_results()
     assert len(results) == 3
     __check_results_column(results,
-                           'alpha',
-                           'alpha',
+                           'ra',
+                           'ra',
                            None,
                            np.float64)
     __check_results_column(results,
-                           'delta',
-                           'delta',
+                           'dec',
+                           'dec',
                            None,
                            np.float64)
     __check_results_column(results,
@@ -308,13 +308,13 @@ def test_launch_sync_job_redirect():
     results = job.get_results()
     assert len(results) == 3
     __check_results_column(results,
-                           'alpha',
-                           'alpha',
+                           'ra',
+                           'ra',
                            None,
                            np.float64)
     __check_results_column(results,
-                           'delta',
-                           'delta',
+                           'dec',
+                           'dec',
                            None,
                            np.float64)
     __check_results_column(results,
@@ -404,13 +404,13 @@ def test_launch_async_job():
     results = job.get_results()
     assert len(results) == 3
     __check_results_column(results,
-                           'alpha',
-                           'alpha',
+                           'ra',
+                           'ra',
                            None,
                            np.float64)
     __check_results_column(results,
-                           'delta',
-                           'delta',
+                           'dec',
+                           'dec',
                            None,
                            np.float64)
     __check_results_column(results,
@@ -954,8 +954,8 @@ def test_update_user_table():
 
 
 def test_rename_table():
-    tableName = 'user_mhenar.table_test_rename'
-    newTableName = 'user_mhenar.table_test_rename_new'
+    tableName = 'user_test.table_test_rename'
+    newTableName = 'user_test.table_test_rename_new'
     newColumnNames = {'ra': 'alpha', 'dec': 'delta'}
     connHandler = DummyConnHandler()
     tap = TapPlus("http://test:1111/tap", connhandler=connHandler)
@@ -997,8 +997,6 @@ def test_rename_table():
     tap.rename_table(table_name=tableName, new_table_name=newTableName, new_column_names_dict=newColumnNames)
 
 
-# __end_of_Test
-
 def __find_table(schemaName, tableName, tables):
     qualifiedName = f"{schemaName}.{tableName}"
     for table in (tables):

docs/gaia/gaia.rst

@@ -849,7 +849,7 @@ will be able to access to your shared table in a query.
   >>> from astroquery.gaia import Gaia
   >>> Gaia.login()
   >>> Gaia.share_table(group_name="my_group",
-  ...                  table_name="user_<user_loign_name>.my_table",
+  ...                  table_name="user_<user_login_name>.my_table",
   ...                  description="description")
 
 
@@ -862,26 +862,6 @@ will be able to access to your shared table in a query.
   >>> Gaia.login()
   >>> Gaia.share_table_stop(table_name="user_<user_login_name>.my_table", group_name="my_group")
 
-2.7.8. Rename Table
-~~~~~~~~~~~~~~~~~~~~
-
-This query allows the user to rename a table and/or its columns names. For this method it is only mandatory
-to provide the old name of the table and at least one of the following parameters: new table name and/or
-new columns names. Here is an example:
-
-
-.. code-block:: python
-
-    >>>from astroquery.gaia import Gaia, GaiaClass
-    >>>from astroquery.utils.tap.model.tapcolumn import TapColumn
-    >>>from astroquery.utils.tap.core import TapPlus, TAP_CLIENT_ID
-    >>>from astroquery.utils.tap import taputils
-    >>>gaia = GaiaClass(gaia_tap_server='https://<env>.esac.esa.int/', gaia_data_server='https://<env>.esac.esa.int/')
-    >>>gaia.login()
-    >>>tableName = 'user_<user_login_name>.my_old_table_name'
-    >>>newTableName = 'user_<user_login_name>.my_new_table_name'
-    >>>newColumnNames = {'old_col_name1': 'new_col_name1', 'old_col_name2': 'new_col_name2'}
-    >>>gaia.rename_table(table_name=tableName, new_table_name=newTableName, new_column_names_dict=newColumnNames,verbose=True)
 
 Reference/API
 =============