2.1.4

progenetix · Jan 31, 2025 · f6ef6dd · f6ef6dd
1 parent c7ea2c0
commit f6ef6dd
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Showing 92 changed files with 618 additions and 1,246 deletions.
diff --git a/beaconplusWeb/env/staging b/beaconplusWeb/env/staging
@@ -1,5 +1,3 @@
-SERVER=https://staging.beaconplus.org/
 NEXT_PUBLIC_API_PATH=/
-NEXT_PUBLIC_PREFETCH_API_PATH=$SERVER
 NEXT_PUBLIC_USE_PROXY=false
-NEXT_PUBLIC_SITE_URL=$SERVER
+NEXT_PUBLIC_SITE_URL=https://beaconplus.progenetix.org/
diff --git a/beaconplusWeb/package-lock.json b/beaconplusWeb/package-lock.json
diff --git a/beaconplusWeb/package.json b/beaconplusWeb/package.json
@@ -30,7 +30,7 @@
     "lodash": "^4.17.21",
     "match-sorter": "^6.2.0",
     "materialize-css": "^1.0.0-rc.2",
-    "next": "^12.1.0",
+    "next": "^12.3.4",
     "prop-types": "^15.7.2",
     "react": "^17.0.2",
     "react-chartjs-2": "^5.2.0",

diff --git a/bycon/byconServiceLibs/bycon_bundler.py b/bycon/byconServiceLibs/bycon_bundler.py
@@ -90,7 +90,7 @@ def read_pgx_file(self, filepath):
                 if line.startswith("#"):
                     h_lines.append(line)
 
-        d_lines, fieldnames = read_tsv_to_dictlist(self.filepath, max_count=0)
+        d_lines, fieldnames = ByconTSVreader().file_to_dictlist(self.filepath, max_count=0)
         self.header = h_lines
         self.data = d_lines
         self.fieldnames = fieldnames
@@ -104,7 +104,7 @@ def read_probedata_file(self, filepath):
         self.filepath = filepath
         self.probedata = []
 
-        p_lines, fieldnames = read_tsv_to_dictlist(self.filepath, max_count=0)
+        p_lines, fieldnames = ByconTSVreader().file_to_dictlist(self.filepath, max_count=0)
 
         p_o = {
             "probe_id": False,
@@ -404,7 +404,6 @@ def __flatten_keyed_bundle(self):
     #--------------------------------------------------------------------------#
 
     def __analysisBundleCreateIsets(self, label=""):
-
         # self.dataset_ids = list(set([cs.get("dataset_id", "NA") for cs in self.bundle["analyses"]]))
         GB = GenomeBins()
         for ds_id in self.datasets_results.keys():

diff --git a/bycon/byconServiceLibs/datatable_utils.py b/bycon/byconServiceLibs/datatable_utils.py
@@ -1,52 +1,111 @@
-import csv, re, requests
-# from attrdictionary import AttrDict
+import csv, re, requests, sys
+from os import path
 
 # bycon
-from bycon import RefactoredValues, prdbug, prdlhead, prjsonnice, BYC, BYC_PARS, ENV
+from bycon import (
+    BYC,
+    BYC_PARS,
+    RefactoredValues,
+    prdbug,
+    prdlhead,
+    prjsonnice
+)
+
+services_lib_path = path.join(path.dirname(path.abspath(__file__)))
+sys.path.append(services_lib_path)
+from file_utils import ExportFile
+
 
 ################################################################################
 
-def export_datatable_download(flattened_data):
-    dt_m = BYC["datatable_mappings"]
-    r_t = BYC.get("response_entity_id", "___none___")
-    if not r_t in dt_m["$defs"]:
-        return
-    sel_pars = BYC_PARS.get("delivery_keys", [])
-    io_params = dt_m["$defs"][ r_t ]["parameters"]
-    if len(sel_pars) > 0:
-        io_params = { k: v for k, v in io_params.items() if k in sel_pars }
-    prdlhead(f'{r_t}.tsv')
-    header = create_table_header(io_params)
-    print("\t".join( header ))
-
-    for pgxdoc in flattened_data:
-        line = [ ]
-        for par, par_defs in io_params.items():
+class ByconDatatableExporter:
+    def __init__(self, file_type=None):
+        self.datatable_mappings = BYC.get("datatable_mappings", {"$defs": {}})
+        self.entity = BYC.get("response_entity_id", "___none___")
+        if not self.entity in self.datatable_mappings["$defs"]:
+            # TODO: proper error handling
+            return
+
+        self.file_name = f'{self.entity}.tsv'
+
+        sel_pars = BYC_PARS.get("delivery_keys", [])      
+        io_params = self.datatable_mappings["$defs"][self.entity]["parameters"]
+        if len(sel_pars) > 0:
+            io_params = { k: v for k, v in io_params.items() if k in sel_pars }
+
+        self.io_params = io_params
+
+
+    # -------------------------------------------------------------------------#
+    # ----------------------------- public ------------------------------------#
+    # -------------------------------------------------------------------------#
+
+    def stream_datatable(self, flattened_data):
+        prdlhead(self.file_name)
+        print(f'{self.__create_table_header()}\n')
+        for pgxdoc in flattened_data:
+            print(f'{self.__table_line_from_pgxdoc(pgxdoc)}\n')
+        exit()
+
+
+    # -------------------------------------------------------------------------#
+
+    def export_datatable(self, flattened_data):
+        if not (table_file := ExportFile().check_outputfile_path()):
+            return
+
+        t_f = open(table_file, "w")
+        t_f.write(f'{self.__create_table_header()}\n')
+        for pgxdoc in flattened_data:
+            t_f.write(f'{self.__table_line_from_pgxdoc(pgxdoc)}\n')
+        t_f.close()
+        exit()
+
+
+    # -------------------------------------------------------------------------#
+    # ---------------------------- private ------------------------------------#
+    # -------------------------------------------------------------------------#
+
+    def __table_line_from_pgxdoc(self, pgxdoc):
+        line = []
+        for par, par_defs in self.io_params.items():
             parameter_type = par_defs.get("type", "string")
             db_key = par_defs.get("db_key", "___undefined___")
             v = get_nested_value(pgxdoc, db_key)
-            # TODO !!! This does not handle the object exports properly !!!
-            if isinstance(v, list):
-                line.append("&&".join(map(str, (v))))
-            else:
-                line.append(str(v))
-        print("\t".join( line ))
+            line.append(RefactoredValues(par_defs).strVal(v))
+        return "\t".join( line )
 
-    exit()
+    # -------------------------------------------------------------------------#
 
+    def __create_table_header(self):
+        """
+        """
+        header_labs = [ ]
+        for par, par_defs in self.io_params.items():
+            pres = par_defs.get("prefix_split", {})
+            if len(pres.keys()) < 1:
+                header_labs.append( par )
+                continue
+            for pre in pres.keys():
+                header_labs.append( par+"_id"+"___"+pre )
+                header_labs.append( par+"_label"+"___"+pre )
 
+        return "\t".join(header_labs)
+
+
+################################################################################
+################################################################################
 ################################################################################
 
 def import_datatable_dict_line(parent, fieldnames, lineobj, primary_scope="biosample"):
     dt_m = BYC["datatable_mappings"]
     if not primary_scope in dt_m["$defs"]:
         return
     io_params = dt_m["$defs"][ primary_scope ]["parameters"]
-    def_params = create_table_header(io_params)
     for f_n in fieldnames:
         if "#"in f_n:
             continue
-        if f_n not in def_params:
+        if f_n not in io_params.keys():
             continue
         if not (par_defs := io_params.get(f_n, {})):
             continue
@@ -81,23 +140,6 @@ def import_datatable_dict_line(parent, fieldnames, lineobj, primary_scope="biosa
 
     return parent
 
-################################################################################
-
-def create_table_header(io_params):
-    """
-    """
-    header_labs = [ ]
-    for par, par_defs in io_params.items():
-        pres = par_defs.get("prefix_split", {})
-        if len(pres.keys()) < 1:
-            header_labs.append( par )
-            continue
-        for pre in pres.keys():
-            header_labs.append( par+"_id"+"___"+pre )
-            header_labs.append( par+"_label"+"___"+pre )
-
-    return header_labs
-
 
 ################################################################################
 

diff --git a/bycon/byconServiceLibs/export_file_generation.py b/bycon/byconServiceLibs/export_file_generation.py
@@ -6,8 +6,9 @@
 from bycon import (
     BYC,
     BYC_PARS,
-    DB_MONGOHOST,
     ByconVariant,
+    DB_MONGOHOST,
+    ENV,
     prdbug,
     return_paginated_list,
     select_this_server,
@@ -17,8 +18,7 @@
 services_lib_path = path.join( path.dirname( path.abspath(__file__) ) )
 sys.path.append( services_lib_path )
 from interval_utils import GenomeBins
-from service_helpers import open_text_streaming, close_text_streaming
-from datatable_utils import assign_nested_value, get_nested_value
+from datatable_utils import get_nested_value
 
 ################################################################################
 
@@ -491,3 +491,21 @@ def export_vcf_download(datasets_results, ds_id):
 
     close_text_streaming()
 
+
+################################################################################
+
+def open_text_streaming(filename="data.pgxseg"):
+    if not "___shell___" in ENV:
+        print('Content-Type: text/plain')
+        if not "browser" in filename:
+            print('Content-Disposition: attachment; filename="{}"'.format(filename))
+        print('status: 200')
+        print()
+
+
+################################################################################
+
+def close_text_streaming():
+    print()
+    prdbug(f'... closing text streaming at {datetime.datetime.now().strftime("%H:%M:%S")}')
+    exit()