diff main_text.py @ 0:5edb952b394e draft default tip

planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_text commit c9272a57d834895bf21c987be7d7416532cfa23f-dirty
author siwaa
date Tue, 27 Feb 2024 07:58:55 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/main_text.py	Tue Feb 27 07:58:55 2024 +0000
@@ -0,0 +1,131 @@
+# -*- coding: UTF-8 -*-
+""" 
+    main_text
+
+    Requests having only 1 json data as OUTput
+
+    Accepts actions :
+    'get_vpz_input' 'post_vpz_input'
+    'get_vpz_output' 'post_vpz_output'
+    'get_vpz_inout' 'post_vpz_inout'
+    'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
+    'help'
+
+    Refused actions :
+    'get_vpz_experiment' 'post_vpz_experiment'
+    'get_vpz_report_conditions' 'post_vpz_report_conditions'
+    'get_vpz_report' 'post_vpz_report'
+
+    Parameters (Inputs) :
+    - '-data' parameter : data (string format) (optional)
+      A required action value must be included into data.
+    - '-datafolder' parameter : datafolder file path (optional,
+      available only in some cases)
+
+   Outputs :
+   - output.json data file (jsonoutput_filepath)
+"""
+
+MAIN_DEBUG=False # True for more information returned
+
+import argparse
+import json
+import erecord.api.erecord as erecord_api
+
+import os
+
+PM = "[main_text.py]"
+
+UNACCEPTED_ACTIONS_LIST = ['get_vpz_experiment', 'post_vpz_experiment',
+                   'get_vpz_report_conditions', 'post_vpz_report_conditions',
+                   'get_vpz_report', 'post_vpz_report']
+
+r = dict()
+
+import sys
+if MAIN_DEBUG: r["sys.path"] = sys.path # debug
+if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
+
+data = dict()
+json_response = dict()
+
+# default configuration + maybe some modifications
+config = erecord_api.conf() # default (vle-2.0.0 version)
+config.DB_add_vpz(vpz_id=1312, vpzname="wwdm.vpz", pkgname="wwdm")
+
+try :
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-data", type=str, help="data in string format")
+    parser.add_argument("-datafolder", type=str, help="datafolder file path")
+
+    args = parser.parse_args()
+
+    if (args.data is None) or (args.data == 'None') :
+        warn = "NO data (string format) given => action enforced to 'help'"
+        r["warning"] = warn
+        data = {'action':'help'} # enforced (default)
+    else:
+        #jsoninput_filename = args.data
+        #inputfile = open(jsoninput_filename, 'r')
+        #data = json.load(inputfile) # get data
+
+        # examples
+        # {"action":"pkg_list"}
+        # {"action": "post_vpz_output", "pkgname": "wwdm", "vpzname": "wwdm.vpz", "style": "compactlist", "plan":"linear", "restype" : "matrix", "cond_wwdm.A": [0.0063, 0.0065, 0.0067], "cond_wwdm.B": 0.00201, "duration":6.0, "outselect": "view"}
+
+        jsoninput_text = args.data
+        try :
+
+            # restore sanitized text
+            MAPPING = {'>': '__gt__', '<': '__lt__', "'": '__sq__', '"': '__dq__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__', '@': '__at__', '\n': '__cn__', '\r': '__cr__', '\t': '__tc__', '#': '__pd__'}
+            for key, value in MAPPING.items():
+                jsoninput_text = jsoninput_text.replace(value, key)
+
+            data = json.loads(jsoninput_text) # get data
+        except:
+            warn = "Failed to get json data from string '" +jsoninput_text+ "'"
+            warn = warn + " => action enforced to 'help'"
+            r["warning"] = warn
+            data = {'action':'help'} # enforced (default)
+
+        if (args.datafolder is None) or (args.datafolder == 'None') :
+            pass # NO datafolder given
+        else :
+            data['datafolder'] = args.datafolder
+
+    # Pre-filtering : Unaccepted actions => enforced to 'help' action
+    if "action" in data.keys() :
+        a = data["action"]
+        if a in UNACCEPTED_ACTIONS_LIST :
+            warn = "Unaccepted action '"+a+"' => action enforced to 'help'"
+            r["warning"] = warn
+            data["action"] = 'help'
+
+    r["data"] = data
+
+    # configuration
+    if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug
+
+    r_init = erecord_api.init(config)
+    if MAIN_DEBUG: r["init"] = r_init # debug
+
+    response = erecord_api.action(config, data)
+    json_response = json.loads(response)
+
+except Exception as e :
+
+    response = erecord_api.error_case(data=data, msg=PM, e=e)
+    json_response = json.loads(response)
+
+r["response"] = json_response
+
+try :
+    # Restitution : json file
+    jsonoutput_filepath = os.path.join(config.out_path,
+                                       config.jsonoutput_filename)
+    with open(jsonoutput_filepath, "w") as outfile:
+        json.dump(r, outfile)
+
+except :
+    print(PM, " -- error when trying to open output json file --")
+