From 3243eef54a4bd0a5cdcfb8bcb79ead3cd1a6300e Mon Sep 17 00:00:00 2001
From: Nico Vermaas <vermaas@astron.nl>
Date: Tue, 15 Dec 2020 08:46:48 +0100
Subject: [PATCH] remove atdb_interface package
---
README.md | 2 +
atdb/taskdatabase/models.py | 1 -
atdb/taskdatabase/serializers.py | 2 +-
.../templates/taskdatabase/index.html | 2 +-
atdb/taskdatabase/views.py | 1 -
atdb_interface_pip/README.rst | 34 -
.../atdb_interface.egg-info/PKG-INFO | 10 -
.../atdb_interface.egg-info/SOURCES.txt | 10 -
.../dependency_links.txt | 1 -
.../atdb_interface.egg-info/entry_points.txt | 3 -
.../atdb_interface.egg-info/requires.txt | 1 -
.../atdb_interface.egg-info/top_level.txt | 1 -
atdb_interface_pip/atdb_interface/__init__.py | 0
.../atdb_interface/atdb_interface.py | 825 ------------------
.../examples/arg00_post_new_dataproducts | 3 -
atdb_interface_pip/build.sh | 9 -
.../dist/atdb_interface-1.2.8.tar.gz | Bin 8316 -> 0 bytes
.../dist/atdb_interface-1.2.9.tar.gz | Bin 8549 -> 0 bytes
atdb_interface_pip/setup.py | 21 -
atdb_interface_pip/upload_to_nexus.sh | 35 -
20 files changed, 4 insertions(+), 957 deletions(-)
delete mode 100644 atdb_interface_pip/README.rst
delete mode 100644 atdb_interface_pip/atdb_interface.egg-info/PKG-INFO
delete mode 100644 atdb_interface_pip/atdb_interface.egg-info/SOURCES.txt
delete mode 100644 atdb_interface_pip/atdb_interface.egg-info/dependency_links.txt
delete mode 100644 atdb_interface_pip/atdb_interface.egg-info/entry_points.txt
delete mode 100644 atdb_interface_pip/atdb_interface.egg-info/requires.txt
delete mode 100644 atdb_interface_pip/atdb_interface.egg-info/top_level.txt
delete mode 100644 atdb_interface_pip/atdb_interface/__init__.py
delete mode 100644 atdb_interface_pip/atdb_interface/atdb_interface.py
delete mode 100644 atdb_interface_pip/atdb_interface/examples/arg00_post_new_dataproducts
delete mode 100644 atdb_interface_pip/build.sh
delete mode 100644 atdb_interface_pip/dist/atdb_interface-1.2.8.tar.gz
delete mode 100644 atdb_interface_pip/dist/atdb_interface-1.2.9.tar.gz
delete mode 100644 atdb_interface_pip/setup.py
delete mode 100644 atdb_interface_pip/upload_to_nexus.sh
diff --git a/README.md b/README.md
index faeee5c1..66f4d98e 100644
--- a/README.md
+++ b/README.md
@@ -41,6 +41,8 @@ Deployment Diagram:
> export DOCKER_BUILD_DIR=$HOME/my_docker/atdb-ldv/atdb-ldv/atdb
> export DOCKER_COMPOSE_DIR=$DOCKER_BUILD_DIR/docker
+ > cd $DOCKER_BUILD_DIR
+ > git pull
> cd $DOCKER_COMPOSE_DIR
> docker-compose -p atdb up -d
diff --git a/atdb/taskdatabase/models.py b/atdb/taskdatabase/models.py
index c69d4727..66d48412 100644
--- a/atdb/taskdatabase/models.py
+++ b/atdb/taskdatabase/models.py
@@ -111,7 +111,6 @@ class Observation(TaskObject):
end_band = models.IntegerField(null=True)
# ARTS SC4
- process_triggers = models.BooleanField(default=False)
beams = models.CharField(max_length=255, default="0..39")
quality = models.CharField(max_length=30, default="unknown")
diff --git a/atdb/taskdatabase/serializers.py b/atdb/taskdatabase/serializers.py
index df64b011..0b0a4c74 100644
--- a/atdb/taskdatabase/serializers.py
+++ b/atdb/taskdatabase/serializers.py
@@ -57,7 +57,7 @@ class ObservationSerializer(serializers.ModelSerializer):
'generated_dataproducts','telescopes',
'data_location', 'irods_collection','node','control_parameters',
'skip_auto_ingest','observing_mode','science_mode','parset_location',
- 'par_file_name','number_of_bins','start_band','end_band','process_triggers','beams', 'delay_center_offset',
+ 'par_file_name','number_of_bins','start_band','end_band','beams', 'delay_center_offset',
'locality_policy','max_lifetime_on_disk','quality','science_observation','filler','ingest_progress',
'timestamp_starting','timestamp_running','timestamp_completing',
'timestamp_ingesting','timestamp_archived','timestamp_aborted','timestamp_ingest_error')
diff --git a/atdb/taskdatabase/templates/taskdatabase/index.html b/atdb/taskdatabase/templates/taskdatabase/index.html
index da4c482f..fa35e9ae 100644
--- a/atdb/taskdatabase/templates/taskdatabase/index.html
+++ b/atdb/taskdatabase/templates/taskdatabase/index.html
@@ -46,7 +46,7 @@
</div>
{% include 'taskdatabase/pagination.html' %}
</div>
- <p class="footer"> Version 2.0.0 (11 dec 2020)</p>
+ <p class="footer"> Version 2.0.0 (15 dec 2020 - 08:00)</p>
<script type="text/javascript">
(function(seconds) {
diff --git a/atdb/taskdatabase/views.py b/atdb/taskdatabase/views.py
index 7ab9e6d3..4f216d30 100644
--- a/atdb/taskdatabase/views.py
+++ b/atdb/taskdatabase/views.py
@@ -48,7 +48,6 @@ class ObservationFilter(filters.FilterSet):
'irods_collection': ['exact', 'icontains'],
'node': ['exact', 'in'],
'skip_auto_ingest': ['exact'],
- 'process_triggers': ['exact'],
'beams': ['exact', 'icontains'],
'delay_center_offset': ['exact', 'icontains'],
'quality': ['exact', 'icontains'],
diff --git a/atdb_interface_pip/README.rst b/atdb_interface_pip/README.rst
deleted file mode 100644
index ee327091..00000000
--- a/atdb_interface_pip/README.rst
+++ /dev/null
@@ -1,34 +0,0 @@
-atdb_interface
-==============
-This module contains a service that run standalone and interact with the Apertif Task Database REST API.
-
-See 'atdb_interface -h' for help and 'atdb_interface -e' for examples.
-
-This package is required when using atdb_services
-
-Installing
-^^^^^^^^^^
-To install a version from Nexus repository use::
-
- > pip install <<nexus url>> --upgrade
- or download and install the tarball,
- > pip install atdb_interface.tar.gz --upgrade
-
-Within the development environment such as with PyCharm one can install the package within the virtualenv with which
-PyCharm is configured. To avoid uninstall and install after each code change pip can install packages within development
-mode::
-
- (.env) > pip install -e ..project../atdb_interface_pip --upgrade
-
-This will install the package with soft links to the original code, such that one gets immediate refresh within PyCharm,
-which is used for refactoring, code completion, imports etc.
-
-Uninstalling
-^^^^^^^^^^^^
-Uninstall is trivial using the command (watch out for the '-')::
-
- > pip uninstall atdb-interface
-
-or without confirmation::
-
- > pip uninstall --yes atdb-interface
\ No newline at end of file
diff --git a/atdb_interface_pip/atdb_interface.egg-info/PKG-INFO b/atdb_interface_pip/atdb_interface.egg-info/PKG-INFO
deleted file mode 100644
index b7592a3f..00000000
--- a/atdb_interface_pip/atdb_interface.egg-info/PKG-INFO
+++ /dev/null
@@ -1,10 +0,0 @@
-Metadata-Version: 1.0
-Name: atdb-interface
-Version: 1.2.9
-Summary: ATDB interface
-Home-page: https://www.astron.nl/wsrt/wiki/doku.php?id=atdb:atdb_interface
-Author: Nico Vermaas - Astron
-Author-email: vermaas@astron.nl
-License: BSD
-Description: UNKNOWN
-Platform: UNKNOWN
diff --git a/atdb_interface_pip/atdb_interface.egg-info/SOURCES.txt b/atdb_interface_pip/atdb_interface.egg-info/SOURCES.txt
deleted file mode 100644
index e4282e34..00000000
--- a/atdb_interface_pip/atdb_interface.egg-info/SOURCES.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-README.rst
-setup.py
-atdb_interface/__init__.py
-atdb_interface/atdb_interface.py
-atdb_interface.egg-info/PKG-INFO
-atdb_interface.egg-info/SOURCES.txt
-atdb_interface.egg-info/dependency_links.txt
-atdb_interface.egg-info/entry_points.txt
-atdb_interface.egg-info/requires.txt
-atdb_interface.egg-info/top_level.txt
\ No newline at end of file
diff --git a/atdb_interface_pip/atdb_interface.egg-info/dependency_links.txt b/atdb_interface_pip/atdb_interface.egg-info/dependency_links.txt
deleted file mode 100644
index 8b137891..00000000
--- a/atdb_interface_pip/atdb_interface.egg-info/dependency_links.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/atdb_interface_pip/atdb_interface.egg-info/entry_points.txt b/atdb_interface_pip/atdb_interface.egg-info/entry_points.txt
deleted file mode 100644
index a5448a6f..00000000
--- a/atdb_interface_pip/atdb_interface.egg-info/entry_points.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-[console_scripts]
-atdb_interface = atdb_interface.atdb_interface:main
-
diff --git a/atdb_interface_pip/atdb_interface.egg-info/requires.txt b/atdb_interface_pip/atdb_interface.egg-info/requires.txt
deleted file mode 100644
index f2293605..00000000
--- a/atdb_interface_pip/atdb_interface.egg-info/requires.txt
+++ /dev/null
@@ -1 +0,0 @@
-requests
diff --git a/atdb_interface_pip/atdb_interface.egg-info/top_level.txt b/atdb_interface_pip/atdb_interface.egg-info/top_level.txt
deleted file mode 100644
index 643d97a1..00000000
--- a/atdb_interface_pip/atdb_interface.egg-info/top_level.txt
+++ /dev/null
@@ -1 +0,0 @@
-atdb_interface
diff --git a/atdb_interface_pip/atdb_interface/__init__.py b/atdb_interface_pip/atdb_interface/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/atdb_interface_pip/atdb_interface/atdb_interface.py b/atdb_interface_pip/atdb_interface/atdb_interface.py
deleted file mode 100644
index 44cb7b02..00000000
--- a/atdb_interface_pip/atdb_interface/atdb_interface.py
+++ /dev/null
@@ -1,825 +0,0 @@
-#!/usr/bin/python3
-import sys
-import os
-import requests
-import json
-import argparse
-import datetime
-
-from pkg_resources import get_distribution
-pkg_version = get_distribution('atdb_interface').version
-"""
-atdb_interface.py : a commandline tool to interface with the ATDB REST API.
-:author Nico Vermaas - Astron
-"""
-LAST_UPDATE = "31 oct 2019"
-
-# ====================================================================
-
-# The request header
-ATDB_HEADER = {
- 'content-type': "application/json",
- 'cache-control': "no-cache",
- 'authorization': "Basic YWRtaW46YWRtaW4="
-}
-
-DEFAULT_BACKEND_HOST = "http://atdb-test.astron.nl/atdb"
-ATDB_HOST_DEV = "http://localhost:8000/atdb/" # your local development environment with Django webserver
-ATDB_HOST_VM = "http://192.168.22.25/atdb" # your local Ansible/Vagrant setup for testing
-ATDB_HOST_ACC = "http://192.168.22.25/atdb" # your local Ansible/Vagrant acceptance setup
-ATDB_HOST_TEST = "http://atdb-test.astron.nl/atdb" # the atdb test environment
-ATDB_HOST_PROD = "http://atdb.astron.nl/atdb" # the atdb production environment.
-
-TIME_FORMAT = "%Y-%m-%dT%H:%M:%SZ"
-
-
-class ATDB:
- """
- Calibrators class, use to parse SIP and update the backend database
- through REST API calls.
- """
- def __init__(self, host, verbose=False):
- """
- Constructor.
- :param host: the host name of the backend.
- :param username: The username known in Django Admin.
- :param verbose: more information runtime.
- :param header: Request header for Atdb REST requests with token authentication.
- """
- # accept some presets to set host to dev, test, acc or prod
- self.host = host
- if self.host=='dev':
- self.host = DEFAULT_BACKEND_HOST
- elif self.host=='vm':
- self.host = ATDB_HOST_VM
- elif self.host=='test':
- self.host = ATDB_HOST_TEST
- elif self.host=='acc':
- self.host = ATDB_HOST_ACC
- elif self.host=='prod':
- self.host = ATDB_HOST_PROD
- if not self.host.endswith('/'):
- self.host += '/'
-
- self.verbose = verbose
- self.header = ATDB_HEADER
-
- def verbose_print(self, info_str):
- """
- Print info string if verbose is enabled (default False)
- :param info_str: String to print
- """
- if self.verbose:
- timestamp = datetime.datetime.now().strftime(TIME_FORMAT)
- print(str(timestamp)+ ' - '+info_str)
-
- # === Backend requests ================================================================================
- @staticmethod
- def reconstruct_beams_obsolete(payload_string):
- """
- Normally, to translate the specification string to a json payload that the http requests understand,
- all substrings like 'a,b,c' are replaced with "a","b","c". But this should not be done for the beams list,
- which is given as something like beams=1..10,11,12 or beams=[1..10,11,12] in the specification.
- So this function reconstructs that stting. (a bit ugly, but as usual time constraints force me to cut a corner).
- :param payload_string:
- :return:
- """
-
- # find the part where the 'beams' are already converted to a messy string: "beams": ""beams" : "1..10" , "11" , "12" , "new_status"", "new_status"
- start = payload_string.find('"beams"') + 10
-
- if (start>=10):
- # if no beams were found, then ignore this step
- end = payload_string.find('"new_status"') -3
-
- # save the before and after parts of the string
- before = payload_string[0:start]
- after = payload_string[end:]
-
- # extract the middle part that needs to be changed: 1..10" , "11" , "12
- middle = payload_string[start:end]
-
- # remove all " and spaces, and surround it with "" again.
- middle = middle.replace("\"","")
- middle = middle.replace(" ","")
- middle = '"' + middle + '"'
-
- # reconstruct the payload string
- payload_string = before + middle + after
-
- return payload_string
-
-
- def jsonifyPayload_obsolete(self, payload):
- """
- {name=WSRTA180223003_B003.MS,filename=WSRTA180223003_B003.MS} =>
- {"name" : "WSRTA180223003_B003.MS" , "filename" : "WSRTA180223003_B003.MS"}
- :param payload:
- :return: payload_string
- """
-
- payload_string = str(payload).replace("{","{\"")
- payload_string = payload_string.replace("}", "\"}")
- payload_string = payload_string.replace("=", "\" : \"")
- payload_string = payload_string.replace(",", "\" , \"")
-
- # reconstruct the lists by moving the brackets outside the double quotes
- payload_string = payload_string.replace("\"[", "[\"")
- payload_string = payload_string.replace("]\"", "\"]")
- payload_string = payload_string.replace("/,", "/\",\"")
- payload_string = payload_string.replace("u\"", "\"")
-
- #payload_string = json.dumps(payload)
- # ugly: reconstruct beams string
- payload_string = self.reconstruct_beams_obsolete(payload_string)
-
- self.verbose_print("payload_string: [" + payload_string+"]")
- return payload_string
-
- def encodePayload(self, payload):
- """
-
- The POST body does not simply accept a payload dict, it needs to be translated to a string with some
- peculiarities
- :param payload:
- :return: payload_string
- """
-
- payload_string = str(payload).replace("'","\"")
- #payload_string = payload_string.replace(",", ",\n")
-
- # reconstruct the lists by moving the brackets outside the double quotes
- payload_string = payload_string.replace("\"[", "[\"")
- payload_string = payload_string.replace("]\"", "\"]")
- payload_string = payload_string.replace("/,", "/\",\"")
- payload_string = payload_string.replace("u\"", "\"")
-
- self.verbose_print("The payload_string: [" + payload_string+"]")
- return payload_string
-
-
- def GET_TaskObjectByTaskId(self, resource, taskid):
- """
- Do a http GET request to the alta backend to find the Observation with the given runId
- :runId runId:
- """
-
- url = self.host + resource
- # create the querystring, external_ref is the mapping of this element to the alta datamodel lookup field
- querystring = {"taskID": taskid}
-
- response = requests.request("GET", url, headers=self.header, params=querystring)
- self.verbose_print("[GET " + response.url + "]")
-
- try:
- json_response = json.loads(response.text)
- results = json_response["results"]
- taskobject = results[0]
- return taskobject
- except:
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
- # ------------------------------------------------------------------------------#
- # Main User functions #
- # ------------------------------------------------------------------------------#
-
-
- def do_GET_ID(self, key, value):
- """
- Get the id based on a field value of a resource. This is a generic way to retrieve the id.
- :param resource: contains the resource, for example 'observations', 'dataproducts'
- :param field: the field to search on, this will probably be 'name' or 'filename'
- :param value: the value of the 'field' to search on.
- :return id
- """
-
- # split key in resource and field
- params = key.split(":")
- resource = params[0]
- field = params[1]
-
- url = self.host + resource + "?" + field + "=" + value
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
-
- try:
- json_response = json.loads(response.text)
- results = json_response["results"]
- result = results[0]
- id = result['id']
- return id
- except:
- return '-1'
- #raise (Exception("ERROR: " + response.url + " not found."))
-
-
- def do_GET(self, key, id, taskid):
- """
- Do a http GET request to the ATDB backend to find the value of one field of an object
- :param key: contains the name of the resource and the name of the field separated by a colon.
- :param id: the database id of the object.
- :param taskid (optional): when the taskid (of an activity) is known it can be used instead of id.
- """
-
- # split key in resource and field
- params = key.split(":")
- resource = params[0]
- field = params[1]
-
- if taskid!=None:
- taskObject = self.GET_TaskObjectByTaskId(resource, taskid)
- id = taskObject['id']
-
- if id==None:
- # give up and throw an exception.
- raise (Exception("ERROR: no valid 'id' or 'taskid' provided"))
-
- url = self.host + resource + "/" + str(id) + "/"
- self.verbose_print(('url: ' + url))
-
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
-
- try:
- json_response = json.loads(response.text)
- value = json_response[field]
- return value
- except Exception as err:
- self.verbose_print("Exception : " + str(err))
- raise (
- Exception("ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- def do_GET_LIST_page(self, key, query, page):
- """
- get a list of objects that match the query. (oiginal do_GET_LIST function was left intact for
- backward compatibility reasons).
- The backend is paginated, so you may want to indicate which page you want to retrieve.
- The function returns a list of values of the field indicated in 'key'.
- The function also returns the total count, so you can calculate the number of pages to retrieve
- :param key:
- :param query:
- :param page:
- :return:
- """
-
- self.verbose_print("do_GET_LIST(" + key + "," + query + ")")
- # split key in resource and field
- params = key.split(":")
- resource = params[0]
- field = params[1]
-
- url = self.host + resource + "?" + str(query)
- if (page != None):
- url = url + "&page=" + str(page)
-
- # self.verbose_print("url = " + url)
-
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
-
- try:
- json_response = json.loads(response.text)
- results = json_response["results"]
- # results = json.loads(response.text)
- # loop through the list of results and extract the requested field (probably taskID),
- # and add it to the return list.
- list = []
- for result in results:
- value = result[field]
- list.append(value)
-
- count = json_response["count"]
-
- try:
- # return the next page number, if available
- next = json_response["next"]
- pos_start = next.find("page")
- pos_end = next.find("&",pos_start)
- page_number = next[pos_start+5:pos_end]
-
- except:
- page_number = 0
-
- return list, count, page_number
-
- except Exception as err:
- self.verbose_print("Exception : " + str(err))
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- # python atdb_interface.py -o GET_LIST --key observations:taskID --query status=valid
- def do_GET_LIST(self, key, query):
-
- self.verbose_print("do_GET_LIST(" + key + "," + query + ")")
- # split key in resource and field
- params = key.split(":")
- resource = params[0]
- field = params[1]
-
- url = self.host + resource + "?" + str(query)
-
- # self.verbose_print("url = " + url)
-
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
-
- try:
- json_response = json.loads(response.text)
- results = json_response["results"]
- #results = json.loads(response.text)
- # loop through the list of results and extract the requested field (probably taskID),
- # and add it to the return list.
- list = []
- for result in results:
- value = result[field]
- list.append(value)
-
- return list
-
- except Exception as err:
- self.verbose_print("Exception : " + str(err))
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- def do_GET_NextTaskID(self, timestamp, taskid_postfix=""):
- """
- :param timestamp: timestamp on which the taskid is based
- :param taskid_postfix: optional addition to the taskid,
- like when taskid_postfix="_IMG" the taskid will become "190405001_IMG"
- :return: taskid
- """
-
- self.verbose_print("do_GET_NextTaskID(" + str(timestamp) + ")")
-
- # construct the url
- url = self.host + "get_next_taskid?timestamp=" + str(timestamp)+"&taskid_postfix="+taskid_postfix
-
- # do the request to the ATDB backend
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
-
- # parse the response
- try:
- json_response = json.loads(response.text)
- taskID = json_response["taskID"]
- return taskID
- except Exception as err:
- self.verbose_print("Exception : " + str(err))
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- def do_GET_Observation(self, taskid):
- """
- Do a http request to the ATDB backend get all the observation parameters in the response
- :param taskid
- """
- self.verbose_print("do_GET_Observation(" + taskid + ")")
-
- # construct the url
- url = self.host + "observations?taskID=" + str(taskid)
-
- # do the request to the ATDB backend
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
-
- # parse the response
- try:
- json_response = json.loads(response.text)
- results = json_response["results"]
- observation = results[0]
- return observation
- except Exception as err:
- self.verbose_print("Exception : " + str(err))
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
-
- def do_GET_NextObservation(self, my_status, observing_mode, datawriter):
- """
- Do a http request to the ATDB backend get the next observation of a given status and observing_mode
- :param my_status: status to search for (probably 'scheduled')
- :param observing_mode: imaging or arts
- :param taskid (optional): when the taskid (of an activity) is known it can be used instead of id.
- """
- self.verbose_print("do_GET_NextObservation(" + my_status + "," + observing_mode + "," + datawriter + ")")
-
- # construct the url
- url = self.host + "get_next_observation?my_status=" + str(my_status) + "&observing_mode=" + str(observing_mode) + "&datawriter=" + str(datawriter)
-
- # do the request to the ATDB backend
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
-
- # parse the response
- try:
- json_response = json.loads(response.text)
- taskID = json_response["taskID"]
- minutes_left = json_response["minutes_left"]
- return taskID, minutes_left
- except Exception as err:
- self.verbose_print("Exception : " + str(err))
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- def do_PUT(self, key='observations', id=None, value=None, taskid=None):
- """
- PUT a value to an existing field of a resource (table).
- :param key: contains the name of the resource and the name of the field separated by a dot. observations.description
- :param id: the database id of the object.
- :param value: the value that has to be PUT in the key. If omitted, an empty put will be done to trigger the signals.
- :param taskid (optional): when the taskid of an observation is known it can be used instead of id.
- """
-
- # split key in resource and field
- if key.find(':')>0:
- params = key.split(":")
- resource = params[0]
- field = params[1]
- else:
- resource = key
- field = None
-
- if taskid!=None:
- taskObject = self.GET_TaskObjectByTaskId(resource, taskid)
- id = taskObject['id']
-
- url = self.host + resource + "/" + str(id) + "/"
- if id==None:
- raise (Exception("ERROR: no valid 'id' or 'taskid' provided"))
-
- payload = {}
- if field!=None:
- payload[field]=value
- payload = self.encodePayload(payload)
- try:
- response = requests.request("PUT", url, data=payload, headers=self.header)
- self.verbose_print("[PUT " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
- except:
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- # do_PUT_LIST(key = observations:new_status, taskid = 180223003, value = valid)
- def do_PUT_LIST(self, key='dataproducts', taskid=None, value=None):
- """
- PUT a value to an existing field of resource (table).
- :param key: contains the name of the resource and the name of the field separated by a colon. observations:new_status
- :param value: the value that has to be PUT in the key. If omitted, an empty put will be done to trigger the signals.
- :param taskid: the value is PUT to all objects with the provided taskid
- """
-
- # split key in resource and field
- if key.find(':')>0:
- params = key.split(":")
- resource = params[0]
- field = params[1]
- else:
- resource = key
- field = None
-
- get_key = resource+':id'
- get_query= 'taskID='+taskid
- ids = self.do_GET_LIST(get_key,get_query)
-
- for id in ids:
- url = self.host + resource + "/" + str(id) + "/"
- self.verbose_print(('url: ' + url))
-
- payload = {}
- if field!=None:
- payload[field]=value
- payload = self.encodePayload(payload)
- try:
- response = requests.request("PUT", url, data=payload, headers=self.header)
- self.verbose_print("[PUT " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
- except:
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- def do_POST_obsolete(self, resource, payload):
- """
- POST a payload to a resource (table). This creates a new object (observation or dataproduct)
- This is the old function, left for backward compatibility. Use 'do_POST_json()' now.
- :param resource: contains the resource, for example 'observations', 'dataproducts'
- :param payload: the contents of the object to create in json format
- """
-
- url = self.host + resource + '/'
- self.verbose_print(('payload: ' + payload))
-
- payload = self.jsonifyPayload_obsolete(payload)
- try:
- response = requests.request("POST", url, data=payload, headers=self.header)
- self.verbose_print("[POST " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
- if not (response.status_code==200 or response.status_code==201):
- raise Exception()
- except Exception:
- raise (Exception("ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- def do_POST_json(self, resource, payload):
- """
- POST a payload to a resource (table). This creates a new object (observation or dataproduct)
- This function replaces the old do_POST function that still needed to convert the json content in a very ugly
- :param resource: contains the resource, for example 'observations', 'dataproducts'
- :param payload: the contents of the object to create in json format
- """
-
- url = self.host + resource + '/'
- self.verbose_print(('payload: ' + payload))
-
- try:
- response = requests.request("POST", url, data=payload, headers=self.header)
- self.verbose_print("[POST " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
- if not (response.status_code==200 or response.status_code==201):
- raise Exception()
- except Exception:
- raise (Exception("ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- def do_POST_dataproducts(self, taskid, dataproducts):
- """
- POST (create) a batch of dataproducts for the (observation) with the given taskid.
- This is done with a custom made http request to the ATDB backend
- :param taskid: taskid of the observation
- :param dataproducts: json list of dataproducts to be added to the provided taskid
- """
-
- # is 'dataproducts' a valid list of dataproducts?
- try:
- number_of_dataproducts = len(dataproducts)
- self.verbose_print("do_POST_dataproducts(" + taskid + "," + str(number_of_dataproducts) + ")")
- except Exception as err:
- raise (Exception(
- "ERROR: " + str(err)))
-
- # construct the url
- url = self.host + "post_dataproducts?taskID=" + str(taskid)
-
- # encode the dictonary as proper json
- payload = self.encodePayload(dataproducts)
- try:
- # do a POST request to the 'post_dataproducts' resource of the ATDB backend
- response = requests.request("POST", url, data=payload, headers=self.header)
- self.verbose_print("[POST " + response.url + "]")
-
- # if anything went wrong, throw an exception.
- if not (response.status_code==200 or response.status_code==201):
- raise Exception(str(response.status_code) + " - " + str(response.reason))
- except Exception as err:
- raise (Exception("ERROR: " + str(err)))
-
- # if it has all succeeded, give back the taskid as an indication of success
- return taskid
-
-
- def do_DELETE(self, resource, id):
- """
- Do a http DELETE request to the ATDB backend
- """
- if id == None:
- raise (Exception("ERROR: no valid 'id' provided"))
-
- # if a range of ID's is given then do multiple deletes
- if (str(id).find('..')>0):
- self.verbose_print("Deleting " + str(id) + "...")
- s = id.split('..')
- start = int(s[0])
- end = int(s[1]) + 1
- else:
- # just a single delete
- start = int(id)
- end = int(id) + 1
-
- for i in range(start,end):
- url = self.host + resource + "/" + str(i) + "/"
-
- try:
- response = requests.request("DELETE", url, headers=self.header)
- self.verbose_print("[DELETE " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
- except:
- raise (Exception("ERROR: deleting " + url + "failed." + response.url))
-
-
- def do_setquality(self, key='observations', id=None, value=None, taskid=None):
- """
- PUT a value to the quality field and call the setquality functionality to transmit the value to ALTA.
- The interface of this function is as close as possible to the regular do_PUT function to avoid confusion.
- :param key: contains the name of the resource and the name of the field separated by a dot. observations.description
- :param id: the database id of the object.
- :param value: the value that has to be PUT in the key. If omitted, an empty put will be done to trigger the signals.
- :param taskid (optional): when the taskid of an observation is known it can be used instead of id.
- """
-
- # split key in resource and field
- if key.find(':') > 0:
- params = key.split(":")
- resource = params[0]
- field = params[1]
- else:
- resource = key
- field = "quality"
-
- if taskid != None:
- taskObject = self.GET_TaskObjectByTaskId(resource, taskid)
- id = taskObject['id']
-
- # this operation requires to http requests...
-
- # the first request is a PUT to ATDB to set the Quality field
- url = self.host + resource + "/" + str(id) + "/"
- if id==None:
- raise (Exception("ERROR: no valid 'id' or 'taskid' provided"))
-
- payload = {}
- if field!=None:
- payload[field]=value
- payload = self.encodePayload(payload)
- try:
- response = requests.request("PUT", url, data=payload, headers=self.header)
- self.verbose_print("[PUT " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
- except:
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(response.content)))
-
-
- # the second request is a GET to ATDB's 'setquality' resource, which will trigger a call to ALTA
- url = self.host + resource + "/" + str(id) + "/setquality/" + value + "/1"
-
- try:
- response = requests.request("GET", url, headers=self.header)
- self.verbose_print("[GET " + response.url + "]")
- self.verbose_print("Response: " + str(response.status_code) + ", " + str(response.reason))
- except:
- raise (Exception(
- "ERROR: " + str(response.status_code) + ", " + str(response.reason) + ', ' + str(
- response.content)))
-
-
-
-# ------------------------------------------------------------------------------#
-# Module level functions #
-# ------------------------------------------------------------------------------#
-def exit_with_error(message):
- """
- Exit the code for an error.
- :param message: the message to print.
- """
- print(message)
- sys.exit(-1)
-
-
-def get_arguments(parser):
- """
- Gets the arguments with which this application is called and returns
- the parsed arguments.
- If a parfile is give as argument, the arguments will be overrided
- The args.parfile need to be an absolute path!
- :param parser: the argument parser.
- :return: Returns the arguments.
- """
- args = parser.parse_args()
- if args.parfile:
- args_file = args.parfile
- if os.path.exists(args_file):
- parse_args_params = ['@' + args_file]
- # First add argument file
- # Now add command-line arguments to allow override of settings from file.
- for arg in sys.argv[1:]: # Ignore first argument, since it is the path to the python script itself
- parse_args_params.append(arg)
- print(parse_args_params)
- args = parser.parse_args(parse_args_params)
- else:
- raise (Exception("Can not find parameter file " + args_file))
- return args
-# ------------------------------------------------------------------------------#
-# Main #
-# ------------------------------------------------------------------------------#
-
-
-def main():
- """
- The main module.
- """
- parser = argparse.ArgumentParser(fromfile_prefix_chars='@')
- parser.add_argument("-v","--verbose", default=False, help="More information at run time.",action="store_true")
- parser.add_argument("--host", nargs="?", default='test', help="Presets are 'dev', 'vm', 'test', 'acc', 'prod'. Otherwise give a full url like https://atdb.astron.nl/atdb")
- parser.add_argument("--version", default=False, help="Show current version of this program", action="store_true")
- parser.add_argument("--operation","-o", default="GET", help="GET, GET_ID, GET_LIST, POST, PUT, DELETE. Note that these operations will only work if you have the proper rights in the ALTA user database.")
- parser.add_argument("--id", default=None, help="id of the object to PUT to.")
- parser.add_argument("-t", "--taskid", nargs="?", default=None, help="Optional taskID which can be used instead of '--id' to lookup Observations or Dataproducts.")
- parser.add_argument("--key", default="observations.title", help="resource.field to PUT a value to. Example: observations.title")
- parser.add_argument("--query", "-q", default="taskID=180223003", help="Query to the REST API")
- parser.add_argument("--value", default="", help="value to PUT in the resource.field. If omitted it will PUT the object without changing values, but the built-in 'signals' will be triggered.")
- parser.add_argument("--payload", "-p", default="{}", help="Payload in json for the POST operation. To create new Observations or Dataproducts. (see examples)")
- parser.add_argument("--show_examples", "-e", default=False, help="Show some examples",action="store_true")
- parser.add_argument('--parfile', nargs='?', type=str, help='Parameter file')
-
- args = get_arguments(parser)
- try:
- atdb = ATDB(args.host, args.verbose)
-
- if (args.show_examples):
-
- print('atdb_interface.py version = '+ pkg_version + " (last updated " + LAST_UPDATE + ")")
- print('---------------------------------------------------------------------------------------------')
- print()
- print('--- basic examples --- ')
- print()
- print("Show the 'status' for Observation with taskID 180720003")
- print("> atdb_interface -o GET --key observations:my_status --taskid 180223003")
- print()
- print("GET the ID of Observation with taskID 180223003")
- print("> atdb_interface -o GET_ID --key observations:taskID --value 180223003")
- print()
- print("GET the ID of Dataproduct with name WSRTA180223003_ALL_IMAGE.jpg")
- print("> atdb_interface -o GET_ID --key dataproducts:name --value WSRTA180223003_ALL_IMAGE.jpg")
- print()
- print("GET the 'status' for Dataproduct with ID = 45")
- print("> atdb_interface -o GET --key dataproducts:my_status --id 45")
- print()
- print("PUT the 'status' of dataproduct with ID = 45 on 'copied'")
- print("> atdb_interface -o PUT --key dataproducts:new_status --id 45 --value copied")
- print()
- print("PUT the 'status' of observation with taskID 180720003 on 'valid'")
- print("> atdb_interface -o PUT --key observations:new_status --value valid --taskid 180223003")
- print()
- print("DELETE dataproduct with ID = 46 from the database (no files will be deleted).")
- print("> atdb_interface -o DELETE --key dataproducts --id 46")
- print()
- print("DELETE dataproducts with ID's ranging from 11..15 from the database (no files will be deleted).")
- print("> atdb_interface -o DELETE --key dataproducts --id 11..15 -v")
- print()
- print('--- advanced examples --- ')
- print()
- print("GET_LIST of taskIDs for observations with status = 'valid'")
- print("> atdb_interface -o GET_LIST --key observations:taskID --query status=valid")
- print()
- print("GET_LIST of IDs for dataproducts with status = 'invalid'")
- print("> atdb_interface -o GET_LIST --key dataproducts:id --query status=invalid")
- print()
- print("PUT the field 'new_status' on 'valid' for all dataproducts with taskId = '180816001'")
- print("> atdb_interface -o PUT_LIST --key dataproducts:new_status --taskid 180816001 --value valid")
- print('---------------------------------------------------------------------------------------------')
- return
-
- if (args.version):
- print('--- atdb_interface.py version = '+ pkg_version + " (last updated " + LAST_UPDATE + ") ---")
- return
-
- if (args.operation=='GET'):
- result = atdb.do_GET(key=args.key, id=args.id, taskid=args.taskid)
- print(result)
-
- if (args.operation == 'GET_ID'):
- result = atdb.do_GET_ID(key=args.key, value=args.value)
- print(result)
-
- if (args.operation == 'GET_LIST'):
- result = atdb.do_GET_LIST(key=args.key, query=args.query)
- print(result)
-
- if (args.operation=='PUT_LIST'):
- atdb.do_PUT_LIST(key=args.key, taskid=args.taskid, value=args.value)
-
- if (args.operation=='PUT'):
- atdb.do_PUT(key=args.key, id=args.id, value=args.value, taskid=args.taskid)
-
- if (args.operation=='SET_QUALITY'):
- atdb.do_setquality(key=args.key, id=args.id, value=args.value, taskid=args.taskid)
-
- if (args.operation=='POST'):
- atdb.do_POST_json(resource=args.key, payload=args.payload)
-
- if (args.operation=='DELETE'):
- atdb.do_DELETE(resource=args.key, id=args.id)
-
- except Exception as exp:
- exit_with_error(str(exp))
-
- sys.exit(0)
-
-
-if __name__ == "__main__":
- main()
-
diff --git a/atdb_interface_pip/atdb_interface/examples/arg00_post_new_dataproducts b/atdb_interface_pip/atdb_interface/examples/arg00_post_new_dataproducts
deleted file mode 100644
index 3f481592..00000000
--- a/atdb_interface_pip/atdb_interface/examples/arg00_post_new_dataproducts
+++ /dev/null
@@ -1,3 +0,0 @@
---operation=POST
---key=dataproducts
---payload={name=WSRTA180223003_B003.MS,filename=WSRTA180223003_B003.MS,description=WSRTA180223003_B003.MS,dataproduct_type=visibility,taskID=180223003,size=54321,quality=raw,new_status=defined,new_location=datawriter}
diff --git a/atdb_interface_pip/build.sh b/atdb_interface_pip/build.sh
deleted file mode 100644
index ac4426a8..00000000
--- a/atdb_interface_pip/build.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-# This script make a source distribution for the pip installable package in the current folder
-echo "Build a source distribution for ATDB interface"
-python --version
-# Explicit give format otherwise a zip is created (Windows?)
-python setup.py sdist --formats=gztar
-
-# Next command will not close the window, can be handy if something goes wrong
-#exec $SHELL
\ No newline at end of file
diff --git a/atdb_interface_pip/dist/atdb_interface-1.2.8.tar.gz b/atdb_interface_pip/dist/atdb_interface-1.2.8.tar.gz
deleted file mode 100644
index a431d44d98b0b9097fe70af666c42518a3342e01..0000000000000000000000000000000000000000
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diff --git a/atdb_interface_pip/setup.py b/atdb_interface_pip/setup.py
deleted file mode 100644
index 6fdd44c1..00000000
--- a/atdb_interface_pip/setup.py
+++ /dev/null
@@ -1,21 +0,0 @@
-from setuptools import setup, find_packages
-
-def readme():
- with open('README.rst') as f:
- return f.read()
-
-setup(name='atdb_interface',
- version='1.2.9',
- description='ATDB interface',
- url='https://www.astron.nl/wsrt/wiki/doku.php?id=atdb:atdb_interface',
- author='Nico Vermaas - Astron',
- author_email='vermaas@astron.nl',
- license='BSD',
- install_requires=['requests'],
- packages=find_packages(),
- entry_points={
- 'console_scripts': [
- 'atdb_interface=atdb_interface.atdb_interface:main',
- ],
- },
- )
\ No newline at end of file
diff --git a/atdb_interface_pip/upload_to_nexus.sh b/atdb_interface_pip/upload_to_nexus.sh
deleted file mode 100644
index a5b6f8f0..00000000
--- a/atdb_interface_pip/upload_to_nexus.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/bash
-
-##---------------------------------------------------------------------------------------------------------------------#
-##! \brief Description: This script uploads the created atdb_interface artifact to the Nexus repository
-##! In: $1 [Optional] Additional Artifact version tag which can be anything
-##! Out: None
-##! Returns: None
-##! Preconditions:
-##! - build should be done /dist/atdb_interface-[version].tar.gz is available
-##! Postconditions:
-##! - artifact uploaded to https://support.astron.nl/nexus/content/repositories/snapshots/nl/astron/atdb/ATDB_interface-[version][additional version tag].tar.gz
-##! Examples: .\upload_to_nexus
-##! .\upload_to_nexus 20180913
-##! .\upload_to_nexus test
-##---------------------------------------------------------------------------------------------------------------------#
-
-VERSION=$(python setup.py --version)
-ARTIFACT_NAME="ATDB_interface"
-ARTIFACT_BUILD="/dist/atdb_interface-${VERSION}.tar.gz"
-
-ARTIFACT_UPLOAD_BASE_PATH="https://support.astron.nl/nexus/content/repositories/snapshots/nl/astron/atdb/"
-if [[ $# -eq 1 ]]; then
- ARTIFACT_VERSION="-${VERSION}-${1}"
-else
- ARTIFACT_VERSION="-${VERSION}"
-fi
-
-ARTIFACT_UPLOAD_PATH="${ARTIFACT_UPLOAD_BASE_PATH}${ARTIFACT_NAME}${ARTIFACT_VERSION}.tar.gz"
-ARTIFACT_BUILD_PATH="$(pwd)${ARTIFACT_BUILD}"
-
-echo "Upload ${ARTIFACT_BUILD_PATH} to $ARTIFACT_UPLOAD_PATH"
-curl --insecure --upload-file ${ARTIFACT_BUILD_PATH} -u upload:upload ${ARTIFACT_UPLOAD_PATH}
-
-# Next command will not close the window, can be handy if something goes wrong
-exec $SHELL
\ No newline at end of file
--
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