From 66a5cc9dcbde4d4a3ae2135f7a624fd070fb7b83 Mon Sep 17 00:00:00 2001 From: frehburg <43171336+frehburg@users.noreply.github.com> Date: Wed, 25 Sep 2024 09:00:15 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20BIH-CEI/?= =?UTF-8?q?phenopacket=5Fmapper@321dbfa3351a5ecccb7e973c5cdb1c92a7471a8c?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../data_standards/data_model.html | 3 +++ .../data_standards/date.html | 22 +++++++++++++++++- .../phenopacket_mapper/mapping/mapper.html | 7 +++++- .../mapping/phenopacket_element.html | 7 +++++- ...henopacket_mapper.data_standards.date.html | 12 ++++++++++ .../phenopacket_mapper.data_standards.html | 12 ++++++++++ latest/genindex.html | 10 ++++++-- latest/objects.inv | Bin 2866 -> 2889 bytes latest/searchindex.js | 2 +- 9 files changed, 69 insertions(+), 6 deletions(-) diff --git a/latest/_modules/phenopacket_mapper/data_standards/data_model.html b/latest/_modules/phenopacket_mapper/data_standards/data_model.html index 7b8636a9..79b99c68 100644 --- a/latest/_modules/phenopacket_mapper/data_standards/data_model.html +++ b/latest/_modules/phenopacket_mapper/data_standards/data_model.html @@ -546,6 +546,9 @@

Source code for phenopacket_mapper.data_standards.data_model

:param fields: Data fields to be preprocessed, will be passed onto `mapping` :param mapping: A dictionary or method to use for preprocessing """ + if not isinstance(fields, list): + fields = [fields] + field_ids = list() for f in fields: if isinstance(field, str): diff --git a/latest/_modules/phenopacket_mapper/data_standards/date.html b/latest/_modules/phenopacket_mapper/data_standards/date.html index 8deb1a3c..2e9c80a1 100644 --- a/latest/_modules/phenopacket_mapper/data_standards/date.html +++ b/latest/_modules/phenopacket_mapper/data_standards/date.html @@ -71,7 +71,9 @@

Source code for phenopacket_mapper.data_standards.date

-from dataclasses import dataclass, field
+from google.protobuf.timestamp_pb2 import Timestamp
+
+from dataclasses import dataclass, field
 from datetime import datetime
 from typing import Tuple, Union, Literal
 
@@ -163,6 +165,24 @@ 
Source code for phenopacket_mapper.data_standards.date
+ self.hour_str + ":" + self.minute_str + ":" + self.second_str + "Z")

 
 
+

+[docs]
+    def protobuf_timestamp(self) -> Timestamp:
+        """
+        Returns the date in a Google Protobuf Timestamp object
+
+        :return: the date in a Google Protobuf Timestamp object
+        """
+        return Timestamp().fromDatetime(datetime(
+            year=self.year,
+            month=self.month,
+            day=self.day,
+            hour=self.hour,
+            minute=self.minute,
+            second=self.second
+        ))

+
+
 

 [docs]
     def formatted_string(self, fmt: str) -> str:
diff --git a/latest/_modules/phenopacket_mapper/mapping/mapper.html b/latest/_modules/phenopacket_mapper/mapping/mapper.html
index 9bf50eaa..9aefa49a 100644
--- a/latest/_modules/phenopacket_mapper/mapping/mapper.html
+++ b/latest/_modules/phenopacket_mapper/mapping/mapper.html
@@ -145,7 +145,12 @@ 
Source code for phenopacket_mapper.mapping.mapper
data_field = e
                     try:
                         value: DataFieldValue = getattr(instance, data_field.id).value
-                        kwargs[key] = value
+                        from phenopacket_mapper.data_standards import Date
+                        if isinstance(value, Date):
+                            date = value
+                            kwargs[key] = date.protobuf_timestamp()
+                        else:
+                            kwargs[key] = value
                     except AttributeError:
                         continue
                 elif isinstance(e, PhenopacketElement):
diff --git a/latest/_modules/phenopacket_mapper/mapping/phenopacket_element.html b/latest/_modules/phenopacket_mapper/mapping/phenopacket_element.html
index 15a1f4bf..ae49cb90 100644
--- a/latest/_modules/phenopacket_mapper/mapping/phenopacket_element.html
+++ b/latest/_modules/phenopacket_mapper/mapping/phenopacket_element.html
@@ -117,7 +117,12 @@ 
Source code for phenopacket_mapper.mapping.phenopacket_element
df = e
                 try:
                     value: DataFieldValue = getattr(instance, df.id).value
-                    kwargs[key] = value
+                    from phenopacket_mapper.data_standards import Date
+                    if isinstance(value, Date):
+                        date = value
+                        kwargs[key] = date.protobuf_timestamp()
+                    else:
+                        kwargs[key] = value
                 except AttributeError:
                     continue
             elif isinstance(e, PhenopacketElement):
diff --git a/latest/apidocs/phenopacket_mapper.data_standards.date.html b/latest/apidocs/phenopacket_mapper.data_standards.date.html
index 0f849d81..d84164b5 100644
--- a/latest/apidocs/phenopacket_mapper.data_standards.date.html
+++ b/latest/apidocs/phenopacket_mapper.data_standards.date.html
@@ -62,6 +62,7 @@
 
  • Date.minute_str
    • 
 
  • Date.second_str
    • 
 
  • Date.iso_8601_datestring()
    • 
+
  • Date.protobuf_timestamp()
    • 
 
  • Date.formatted_string()
    • 
 
  • Date.from_datetime()
    • 
 
  • Date.from_iso_8601()
    • 
@@ -191,6 +192,17 @@
 
    
 
 
+
    
+
    
+protobuf_timestamp() → Timestamp[source]
    
+
    Returns the date in a Google Protobuf Timestamp object
    
+
    
+
    Returns:
    
+
    the date in a Google Protobuf Timestamp object
    
+
    
+
    
+
    
+
 
    
 
    
 formatted_string(fmt: str) → str[source]
    
diff --git a/latest/apidocs/phenopacket_mapper.data_standards.html b/latest/apidocs/phenopacket_mapper.data_standards.html
index 83e673e5..01918494 100644
--- a/latest/apidocs/phenopacket_mapper.data_standards.html
+++ b/latest/apidocs/phenopacket_mapper.data_standards.html
@@ -122,6 +122,7 @@
 
  • Date.minute_str
    • 
 
  • Date.second_str
    • 
 
  • Date.iso_8601_datestring()
    • 
+
  • Date.protobuf_timestamp()
    • 
 
  • Date.formatted_string()
    • 
 
  • Date.from_datetime()
    • 
 
  • Date.from_iso_8601()
    • 
@@ -728,6 +729,17 @@
 
    
 
 
+
    
+
    
+protobuf_timestamp() → Timestamp[source]
    
+
    Returns the date in a Google Protobuf Timestamp object
    
+
    
+
    Returns:
    
+
    the date in a Google Protobuf Timestamp object
    
+
    
+
    
+
    
+
 
    
 
    
 formatted_string(fmt: str) → str[source]
    
diff --git a/latest/genindex.html b/latest/genindex.html
index 525a2108..347ce8c3 100644
--- a/latest/genindex.html
+++ b/latest/genindex.html
@@ -828,8 +828,6 @@ 
    P
    
         
  • module
 
    • 
       
-  
-  
      
       
    • 
     phenopacket_mapper.mapping.map_field
 
@@ -837,6 +835,8 @@ 
      P
      
         
    • module
 
      • 
       
    
+  
+  
diff --git a/latest/objects.inv b/latest/objects.inv
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diff --git a/latest/searchindex.js b/latest/searchindex.js
index fae7a709..61e608d2 100644
--- a/latest/searchindex.js
+++ b/latest/searchindex.js
@@ -1 +1 @@
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42], "value_str": [34, 40, 41], "valueerror": [7, 9, 12, 34, 36, 37], "valueset": [1, 7, 11, 16, 21, 22, 34, 42], "variabl": [1, 7, 9, 10, 11, 15, 16, 17, 19, 21, 44], "variat": [7, 15, 34, 38], "version": [7, 9, 10, 34, 36], "viabl": [7, 16], "warn": [7, 9, 11, 12, 21, 22, 34, 36, 37], "we": [4, 7, 16], "when": [7, 11, 12, 21, 22, 34, 37], "where": [7, 15, 30, 31, 34, 39], "whether": [7, 9, 11, 15, 21, 22, 34, 36, 38], "which": [4, 5, 7, 11, 15, 17, 20, 34, 38, 39], "while": [4, 7, 15], "width": 11, "within": [7, 11], "work": [7, 11, 34, 41], "wrapper": [34, 41], "write": [1, 4, 5, 21, 24, 26, 29, 30, 31], "write_to_fil": [30, 31], "wrong": [30, 33], "year": [7, 15], "year_str": [7, 15], "z": [7, 11, 15], "zero": [7, 15]}, "titles": ["API reference", "phenopacket_mapper package", "phenopacket_mapper.cli package", "phenopacket_mapper.cli.main module", "phenopacket_mapper.cli.mapping_command module", "phenopacket_mapper.cli.quickstart_command module", "phenopacket_mapper.cli.validate_command module", "phenopacket_mapper.data_standards package", "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module", "phenopacket_mapper.data_standards.code module", "phenopacket_mapper.data_standards.code_system module", "phenopacket_mapper.data_standards.data_model module", "phenopacket_mapper.data_standards.data_models package", "phenopacket_mapper.data_standards.data_models.erdri_cds module", "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module", "phenopacket_mapper.data_standards.date module", "phenopacket_mapper.data_standards.value_set module", "phenopacket_mapper.mapping package", "phenopacket_mapper.mapping.map_field module", "phenopacket_mapper.mapping.mapper module", "phenopacket_mapper.mapping.phenopacket_element module", "phenopacket_mapper.pipeline package", "phenopacket_mapper.pipeline.input module", "phenopacket_mapper.pipeline.mapper module", "phenopacket_mapper.pipeline.output module", 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"while": [4, 7, 15], "width": 11, "within": [7, 11], "work": [7, 11, 34, 41], "wrapper": [34, 41], "write": [1, 4, 5, 21, 24, 26, 29, 30, 31], "write_to_fil": [30, 31], "wrong": [30, 33], "year": [7, 15], "year_str": [7, 15], "z": [7, 11, 15], "zero": [7, 15]}, "titles": ["API reference", "phenopacket_mapper package", "phenopacket_mapper.cli package", "phenopacket_mapper.cli.main module", "phenopacket_mapper.cli.mapping_command module", "phenopacket_mapper.cli.quickstart_command module", "phenopacket_mapper.cli.validate_command module", "phenopacket_mapper.data_standards package", "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module", "phenopacket_mapper.data_standards.code module", "phenopacket_mapper.data_standards.code_system module", "phenopacket_mapper.data_standards.data_model module", "phenopacket_mapper.data_standards.data_models package", "phenopacket_mapper.data_standards.data_models.erdri_cds module", "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module", "phenopacket_mapper.data_standards.date module", "phenopacket_mapper.data_standards.value_set module", "phenopacket_mapper.mapping package", "phenopacket_mapper.mapping.map_field module", "phenopacket_mapper.mapping.mapper module", "phenopacket_mapper.mapping.phenopacket_element module", "phenopacket_mapper.pipeline package", "phenopacket_mapper.pipeline.input module", "phenopacket_mapper.pipeline.mapper module", "phenopacket_mapper.pipeline.output module", "phenopacket_mapper.pipeline.validate module", "phenopacket_mapper.preprocessing package", "phenopacket_mapper.preprocessing.preprocess module", "phenopacket_mapper.preprocessing.preprocess_dict module", "phenopacket_mapper.preprocessing.preprocess_method module", "phenopacket_mapper.utils package", "phenopacket_mapper.utils.create_ipynb_in_code module", "phenopacket_mapper.utils.get_field_name module", "phenopacket_mapper.utils.pandas_utils module", "phenopacket_mapper.utils.parsing package", "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module", "phenopacket_mapper.utils.parsing.parse_coding module", "phenopacket_mapper.utils.parsing.parse_data_type module", "phenopacket_mapper.utils.parsing.parse_date module", "phenopacket_mapper.utils.parsing.parse_ordinal module", "phenopacket_mapper.utils.parsing.parse_primitive_data_value module", "phenopacket_mapper.utils.parsing.parse_value module", "phenopacket_mapper.utils.parsing.parse_value_set module", "phenopacket_mapper.utils.str_to_valid_id module", "Phenopacket Mapper"], "titleterms": {"api": 0, "cli": [2, 3, 4, 5, 6], "code": 9, "code_system": 10, "create_ipynb_in_cod": 31, "data_model": [11, 12, 13, 14], "data_standard": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16], "datamodel2phenopacketschema": 8, "date": 15, "erdri_cd": 13, "get_codesystem_by_namespace_prefix": 35, "get_field_nam": 32, "indic": 44, "input": 22, "main": 3, "map": [17, 18, 19, 20], "map_field": 18, "mapper": [19, 23, 44], "mapping_command": 4, "modul": [3, 4, 5, 6, 8, 9, 10, 11, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43], "output": 24, "packag": [1, 2, 7, 12, 17, 21, 26, 30, 34], "pandas_util": 33, "pars": [34, 35, 36, 37, 38, 39, 40, 41, 42], "parse_cod": 36, "parse_d": 38, "parse_data_typ": 37, "parse_ordin": 39, "parse_primitive_data_valu": 40, "parse_valu": 41, "parse_value_set": 42, "phenopacket": 44, "phenopacket_el": 20, "phenopacket_mapp": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43], "pipelin": [21, 22, 23, 24, 25], "preprocess": [26, 27, 28, 29], "preprocess_dict": 28, "preprocess_method": 29, "quickstart_command": 5, "rarelink_datamodel": 14, "refer": 0, "str_to_valid_id": 43, "submodul": [2, 7, 12, 17, 21, 26, 30, 34], "subpackag": [1, 7, 30], "tabl": 44, "util": [30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43], "valid": 25, "validate_command": 6, "value_set": 16}})
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