# HG changeset patch
# User siwaa
# Date 1709020735 0
# Node ID 5edb952b394ead6507a10ae8c20b5269bc03a008

planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_text commit c9272a57d834895bf21c987be7d7416532cfa23f-dirty

diff -r 000000000000 -r 5edb952b394e erecord_text.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/erecord_text.xml	Tue Feb 27 07:58:55 2024 +0000
@@ -0,0 +1,101 @@
+<tool id="erecord_text" name="erecord_text" version="1.0.0">
+
+  <description>erecord returning .json</description>
+
+  <requirements>
+
+    <!-- singularity -->
+    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/erecord-deploy/rep_recordb:9d6ea1defd50dd63fe036a7545a9ea527572192e</container>
+
+    <!-- image locale -->
+    <!-- container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/erecord-deploy/containers/_fab_SIMG/rep_recordb.simg</container-->
+
+  </requirements>
+
+  <command detect_errors="aggressive">
+    <![CDATA[
+    . /PYVENV/bin/activate;
+    /bin/bash -c "python3 $__tool_directory__/main_text.py -data '${input_text}' -datafolder ${datafolder}";
+    cp WS/OUT/output.json ${output_json};
+    ]]>
+  </command>
+
+  <inputs>
+
+    <param name="input_text" optional="true" type="text" area="true"
+           label="Input json as text"/>
+
+    <param name="datafolder" optional="true" type="data" format="zip"
+           label="Add a datafolder zip file (available and used only in 'post_vpz_output' or 'post_vpz_inout' cases)"
+           help="Precisions sur forme du dossier..."/>
+
+  </inputs>
+
+  <outputs>
+    <data format="json" name="output_json" label="jsonoutput"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help><![CDATA[
+
+erecord_text.xml
+
+================
+
+Actions:
+
+-------
+
+- Available :
+
+  - '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'
+
+- Unavailable (actions with 2 output files) :
+
+  - 'get_vpz_experiment' 'post_vpz_experiment'
+  - 'get_vpz_report_conditions' 'post_vpz_report_conditions'
+  - 'get_vpz_report' 'post_vpz_report'
+
+Code:
+
+----
+
+- main_text.py
+
+Inputs:
+
+-------
+
+- data json as text (optional) (text, param type="text") 
+
+  - This data contains the action value
+  - 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"}
+
+- datafolder (optional) (only in 'post_vpz_output', 'post_vpz_inout' cases)
+
+Outputs:
+
+--------
+
+- data json file (no other file returned)
+
+Credits:
+
+--------
+
+-  Author: Nathalie Rousse nathalie.rousse@inrae.fr
+-  Copyright: INRAE
+
+  ]]>
+  </help>
+
+</tool>
diff -r 000000000000 -r 5edb952b394e main_text.py
--- /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 --")
+