a2p2 0.7.4__tar.gz → 0.7.5__tar.gz

{a2p2-0.7.4/a2p2.egg-info → a2p2-0.7.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: a2p2
-Version: 0.7.4
+Version: 0.7.5
 Author-email: JMMC Tech Group <jmmc-tech-group@jmmc.fr>
 License: OSI Approved :: GNU General Public License v3 (GPLv3)
 Project-URL: Homepage, https://www.jmmc.fr/a2p2
@@ -16,7 +16,9 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: appdirs
 Requires-Dist: astropy>=5.2.2
+Requires-Dist: pyvo>=1.6.1
 Requires-Dist: p2api
+Dynamic: license-file
 
 a2p2 |A2P2Badge|
 ================

{a2p2-0.7.4 → a2p2-0.7.5}/a2p2/jmmc/catalogs.py

@@ -4,6 +4,9 @@ __all__ = []
 
 import logging
 
+import pyvo
+import astropy.table.table
+
 from ..client import A2P2ClientPreferences
 
 from .utils import JmmcAPI
@@ -17,20 +20,36 @@ class Catalog():
         Credential can be explicitly given for method that require an authentication, else:
         - a2p2 preferences login will be used if present (see a2p2 -c)
         - or uses .netrc file
+        A where clause can be added to limit on rows of interest (adql syntax)
+        A joins list of dictionnary can be provided to combine this catalog to other ones ( format is: [{"name":"cattojoin","id":"commonkey"},...] )
     """
 
-    def __init__(self, catalogName, username=None, password=None, prod=False, apiUrl=None):
+    def __init__(self, catalogName, username=None, password=None, prod=False, apiUrl=None, tapUrl=None, where=None, joins=None):
         self.catalogName = catalogName
+        self.where = where
+        self.joins = joins
         self.prod = prod
+        self.colDelimiterName = "coldelimiter___"
 
         # Manage prod & preprod or user provided access points
         if apiUrl:
             self.apiUrl = apiUrl  # trust given url as catalogAPI if value is provided
-        elif self.prod:
-            self.apiUrl = "https://oidb.jmmc.fr/restxq/catalogs"
-        else:
-            self.apiUrl = "https://oidb-beta.jmmc.fr/restxq/catalogs"
-
+        if tapUrl:
+            self.tapUrl = tapUrl  # trust given url as TAP server if value is provided
+
+        if not(apiUrl):
+            if self.prod:
+                self.apiUrl = "https://oidb.jmmc.fr/restxq/catalogs"
+            else:
+                self.apiUrl = "https://oidb-beta.jmmc.fr/restxq/catalogs"
+
+        if not(tapUrl):
+            if self.prod:
+                self.tapUrl = "https://tap.jmmc.fr/vollt/tap"
+            else:
+                self.tapUrl = "https://tap-preprod.jmmc.fr/vollt/tap"
+
+        self.tap = pyvo.dal.TAPService(self.tapUrl)
         self.api = JmmcAPI(self.apiUrl, username, password)
 
         logger.info(f"Create catalog wrapper to access '{catalogName}' ({PRODLABEL[self.prod]} API at {self.api.rootURL})")
@@ -40,7 +59,7 @@ class Catalog():
         return self.api._get("")
 
     def metadata(self):
-        """ Get catalog metadata """
+        """ Get catalog metadata"""
         return self.api._get(f"/meta/{self.catalogName}")
 
     def pis(self):
@@ -66,12 +85,75 @@ class Catalog():
                 return pi["name"]
 
     def getRow(self, id):
-        """ Get a single catalog record for the given id.
+        """ Get a single catalog record for the given id on the main catalog.
 
             usage: cat.getRow(42)
         """
         return self.api._get(f"/{self.catalogName}/{id}")
 
+    def getTable(self, maxrec=10000):
+        """ Get an astropy table from the main catalog joined the other if provided in constructor.
+
+            usage: cat.getRows()
+        """
+        # using SELECT TOP N below to workarround astroquery.utils.tap BUG
+
+        clauses = []
+        if self.joins :
+            joinedCatalogNames = []
+            for join in self.joins:
+                joinedCatalogNames.append(join["name"] + ".*")
+
+            # colDelimiterName is added so we can keep the mainCatalog colnames for later updates (using rowsToDict)
+            clauses.append(f"SELECT TOP {maxrec} {self.catalogName}.*, '' as {self.colDelimiterName}, {', '.join(joinedCatalogNames)} FROM {self.catalogName}" )
+
+            for join in self.joins:
+                if "catalogKey" in join.keys():
+                    catalogKey=join["catalogKey"]
+                else:
+                    # we could use the (cached) metadata key, but this would add a additional remote call.A2P2ClientPreferences
+                    # let's try with this convention using the same key name
+                    catalogKey=join["id"]
+                name=join["name"]
+                id=join["id"]
+                # LEFT JOIN may be an option provided by join key ?
+                clauses.append (f" LEFT JOIN {name} ON {self.catalogName}.{catalogKey} = {name}.{id}")
+
+            if self.where:
+                clauses.append(f" WHERE {self.catalogName}.{self.where}")
+        else:
+            clauses.append(f"SELECT TOP {maxrec} * FROM {self.catalogName}")
+            if self.where:
+                clauses.append(f" WHERE {self.where}")
+
+        query = "  ".join(clauses)
+        logger.info(f"Queriing TAP : {query}")
+        return self.tap.search(query,maxrec=maxrec).to_table()
+
+
+    def tableToDict(self, table):
+        """ Convert table (astropy.table or row) to a list of dict so we can modify content and update remote catalog using updateRows().
+
+            usage: cat.tableToDict(table)
+        """
+        colnames = table.colnames
+        if "coldelimiter___" in colnames:
+            colnames = colnames[0:colnames.index("coldelimiter___")]
+        dicts=[]
+        # handle single row case
+        table = table if isinstance(table, astropy.table.table.Table ) else [table]
+        for row in table:
+            dict = {}
+            for colname in colnames:
+                v=row[colname]
+                if isinstance(v,str):
+                    dict[colname] = v
+                else:
+                    # avoid np.numeric type to make it json serializable
+                    dict[colname] = v.item()
+            dicts.append(dict)
+        return dicts
+
     def updateRow(self, id, values):
         """ Update record identified by given id and associated values.
 
@@ -87,6 +169,7 @@ class Catalog():
         """
 
         # We may check befere sending payload that we always provide an id for every record
+        # What is the behaviour if we provide various data assosiated to the same id ?
         return self.api._put(f"/{self.catalogName}", values)
 
     def addRows(self, values):
@@ -97,6 +180,7 @@ class Catalog():
         """
         return self.api._post(f"/{self.catalogName}", json=values)
 
+
     def getDelegations(self, pi=None):
         """ Get -all- delegations.
             A specific pi parameter may be given but requires admin priviledges. Else use current piname will be used by remote service.

{a2p2-0.7.4 → a2p2-0.7.5}/a2p2/version.py

@@ -1,4 +1,4 @@
-__version__ = "0.7.4"
+__version__ = "0.7.5"
 
 __release_notes__ = {
     # "0.1.6": {
@@ -23,7 +23,11 @@ __release_notes__ = {
 #          "Try to read OB in P2 and send them back to Aspro2 as a new obs",
 #      ],
 
-    "0.7.4": {
+    "0.7.5": {
+       "A2P2": [
+           "Add support for join and filter in a2p2.jmmc.Catalog wrapper",
+        ],
+    },"0.7.4": {
        "A2P2": [
            "Use pyproject.toml for python installation",
         ],"VLTI": [

{a2p2-0.7.4 → a2p2-0.7.5/a2p2.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: a2p2
-Version: 0.7.4
+Version: 0.7.5
 Author-email: JMMC Tech Group <jmmc-tech-group@jmmc.fr>
 License: OSI Approved :: GNU General Public License v3 (GPLv3)
 Project-URL: Homepage, https://www.jmmc.fr/a2p2
@@ -16,7 +16,9 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: appdirs
 Requires-Dist: astropy>=5.2.2
+Requires-Dist: pyvo>=1.6.1
 Requires-Dist: p2api
+Dynamic: license-file
 
 a2p2 |A2P2Badge|
 ================

{a2p2-0.7.4 → a2p2-0.7.5}/a2p2.egg-info/requires.txt

@@ -1,3 +1,4 @@
 appdirs
 astropy>=5.2.2
+pyvo>=1.6.1
 p2api

{a2p2-0.7.4 → a2p2-0.7.5}/pyproject.toml

@@ -30,6 +30,7 @@ classifiers = [
 dependencies = [
     "appdirs",
     "astropy>=5.2.2",
+    "pyvo>=1.6.1",
     "p2api",
 ]