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JonathanNokyJonathanNoky
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Some changes after meeting with lauri (#3)
* Changed identifying keys to include $ sign * Changed mapper key to be in results.eln.lab_ids * Changing example to ELNMeasurements * Changed example upload to use basesections, removed own example classes * Fixing test * Fix regex pattern in mainfile_contents_dict * added pagination to query * Changed example from Measurement to Process * Fix escape character in mainfile_contents_dict
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‎docs/reference/references.md‎

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- ```main_key```: Mandatory for all schemas except the one with ```"is_main": "True"```. Gives the key in the main NOMAD schema, where this section is attached. Can be nested with ".". Format: string.
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- ```repeats```: Optional, indicates that the ```main_key``` point is a repeatable subsection, where this schema is just appended to. Default value: False. Format: boolean.
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- ```is_archive```: Optional, indicates that this schema is a separate archive and only the reference is linked in the main entry. Default value: False. Format: boolean.
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- ```rules```: Mandatory, contains mapping rules for the data. Simple mappings (also nested with ".") from source to target can be given just by ```"source": "target"```, more complex mapping rules are possible as described in the [Transformer]().
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- ```rules```: Mandatory, contains mapping rules for the data. Simple mappings (also nested with ".") from source to target can be given just by ```"source": "target"```, more complex mapping rules are possible as described in the [Transformer](https://nomad-lab.eu/prod/v1/docs/howto/manage/program/json_transformer.html).
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## The data file
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‎pyproject.toml‎

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json_mapper_schema_package = "nomad_json_parser.schema_packages:json_mapper_schema_package"
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json_mapper_parser = "nomad_json_parser.parsers:json_mapper_parser"
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mapped_json_parser = "nomad_json_parser.parsers:mapped_json_parser"
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example_schema_package = "nomad_json_parser.schema_packages:example_schema_package"
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example_upload_entry_point = "nomad_json_parser.example_uploads:example_upload_entry_point"
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[tool.cruft]

‎src/nomad_json_parser/example_uploads/json_mapper/README.MD‎

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@@ -7,9 +7,9 @@ This is an example of a mapping from a JSON file to a NOMAD schema. Firstly, a m
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Below, you find an overview of your uploaded data.
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Click on the `> /` button to get a list of your data or select **FILES** from the top menu of this upload.
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The `example_mapper.json` contains the `json_mapper_class_key` against which the data files are tested later on. Additionally, it defines the classes used in the NOMAD schema and contains the rules how to map between the data JSON and the schema. The mapping rules follow the ones of the [NOMAD Transformer](https://nomad-lab.eu/prod/v1/docs/howto/programmatic/json_transformer.html).
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The `example_mapper.json` contains the `$json_mapper_class_key` against which the data files are tested later on. Additionally, it defines the classes used in the NOMAD schema and contains the rules how to map between the data JSON and the schema. The mapping rules follow the ones of the [NOMAD Transformer](https://nomad-lab.eu/prod/v1/docs/howto/programmatic/json_transformer.html).
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The `example_data.json` contains the `mapped_json_class_key` to identify the suitable mapper and all data that should be mapped into the NOMAD schema.
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The `example_data.json` contains the `$mapped_json_class_key` to identify the suitable mapper and all data that should be mapped into the NOMAD schema.
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You can create your own mapper and data files and try them out here or in separate uploads.
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‎src/nomad_json_parser/example_uploads/json_mapper/example_data.json‎

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{
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"mapped_json_class_key": "examplemapper",
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"Mainname": "This is the main name",
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"Sublevels": {"SublevelOne": "This is sublevel 1 name", "Sublevel2name": "This is sublevel 2 name", "Further": {"Sublevel3name": "This is sublevel 3 name"}},
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"Repeating": {"R1": "First section", "R2": "Second section"},
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"value": 1,
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"unit": "cm",
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"value_list": [1,3.4,1.5,2.6],
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"value_unit": "g",
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"reference_name": "This is the reference name"
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"$mapped_json_class_key": "basesectionexamplemapper",
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"title": "Create NaCl solution",
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"What_did_I_do": "Solution by stirring",
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"Details": {
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"Step_1": {
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"step_name": "NaCl into H2O",
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"step_description": "Put NaCl into H2O"
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},
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"Step_2": {
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"step_name": "Stirring",
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"step_description": "Stir clockwise",
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"How_long_did_it_take": 300.0,
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"time_unit": "seconds"
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}
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},
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"Chemicals": {
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"name": "Rocksalt",
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"labid": "JN123_NaCl",
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"substance_formula": "NaCl"
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}
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}

‎src/nomad_json_parser/example_uploads/json_mapper/example_mapper.json‎

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{
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"json_mapper_class_key": "examplemapper",
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"$json_mapper_class_key": "basesectionexamplemapper",
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"main_schema": {
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"is_main": "True",
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"schema": "nomad_json_parser.schema_packages.example.MainLevel",
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"rules": {
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"ID":{
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"source": "Mainname",
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"target": "string"
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},
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"name": {
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"source": "Main_name_real",
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"target": "name",
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"default_value": "default_name"
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}
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}
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},
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"Sublevel1": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevel1",
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"main_key": "nesting",
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"rules": {
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"ID":{
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"source": "Sublevels.SublevelOne",
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"target": "string"
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}
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}
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},
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"Sublevel2": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevel2",
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"main_key": "nesting.nesting",
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"rules": {
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"ID":{
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"source": "Sublevels.Sublevel2name",
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"target": "string"
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},
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"IDfd":{
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"source": "Sublevels.Sublevel2name",
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"target": "name"
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"schema": "nomad.datamodel.metainfo.basesections.v1.Process",
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"rules": {
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"title": "name",
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"What_did_I_do": "method",
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"location": {
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"source": "location",
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"target": "location",
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"default_value": "MPI CPfS Dresden"
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}
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}
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},
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"Sublevel3": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevel3",
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"main_key": "nesting.nesting.nesting",
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"rules": {
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"ID":{
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"source": "Sublevels.Further.Sublevel3name",
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"target": "string"
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}
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}
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},
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"Repeating1": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevelRepeating",
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"main_key": "repeating",
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"Activity_Step1": {
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"schema": "nomad.datamodel.metainfo.basesections.v1.ProcessStep",
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"main_key": "steps",
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"repeats": "True",
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"rules": {
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"Repeating.R1": "string"
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"Details.Step_1.step_name": "name",
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"Details.Step_1.step_description": "description"
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}
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},
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"Repeating2": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevelRepeating",
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"main_key": "repeating",
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"ProcessStep2": {
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"schema": "nomad.datamodel.metainfo.basesections.v1.ProcessStep",
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"main_key": "steps",
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"repeats": "True",
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"rules": {
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"Repeating.R2": "string"
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"Details.Step_2.step_name": "name",
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"Details.Step_2.step_description": "description",
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"Details.Step_2.How_long_did_it_take": "duration",
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"Details.Step_2.time_unit": "tempunits.duration"
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}
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},
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"Unit": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevelUnit",
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"main_key": "unit",
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"rules": {
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"value": "unit",
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"unit": "tempunits.unit"
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}
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},
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"List": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevelList",
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"main_key": "list",
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"Sample": {
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"schema": "nomad.datamodel.metainfo.basesections.v1.CompositeSystemReference",
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"main_key": "samples",
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"repeats": "True",
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"rules": {
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"value_list": "unit",
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"value_unit": "tempunits.unit"
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"Chemicals.name": "name"
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}
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},
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"Reference": {
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"schema": "nomad_json_parser.schema_packages.example.SubLevelReference",
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"main_key": "reference",
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"System": {
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"schema": "nomad.datamodel.metainfo.basesections.v1.CompositeSystem",
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"main_key": "samples.reference",
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"is_archive": "True",
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"rules": {
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"reference_name": "name"
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"Chemicals.labid": "lab_id",
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"Chemicals.substance_formula": "name"
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}
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}
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}

‎src/nomad_json_parser/parsers/__init__.py‎

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name='MapperParser for Json Mapper files',
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description="""Parser for Json Mapping files.""",
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mainfile_name_re=r'.+\.json',
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mainfile_mime_re='application/json',
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mainfile_contents_re=r'.+json_mapper_class_key',
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# mainfile_mime_re='application/json',
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mainfile_contents_dict={'__has_key': r'\$json_mapper_class_key'},
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)
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name='JsonParser for Json Mapped files',
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description="""Parser for Json Mapped files.""",
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mainfile_name_re=r'.+\.json',
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mainfile_mime_re='application/json',
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mainfile_contents_re=r'.+mapped_json_class_key',
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# mainfile_mime_re='application/json',
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mainfile_contents_dict={'__has_key': r'\$mapped_json_class_key'},
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)

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