inm_rspace.core module

Examples

Get all documents in an RSpace Folder or Notebook:

import inm_rspace as rs
docs = rs.get_docs_in_notebook(7074)
print([doc['name'] for doc in docs])

Output:

Create a new RSpace Form from a JSON metadata file:

json_content = json.load(open('metadata.json'))
form_fields = rs.form_fields_from_json(json_content, default=True)
rs_form = rs.ELN.create_form('inm-rspace_json', fields=form_fields)
print(f"Created form {rs_form['globalId']}")

For more examples on managing JSON schemas and RSpace Forms, refer to this script.

API documentation

class inm_rspace.core.ELNClass

Bases: ELNClient

ELN class enhancing the rspace_client.eln.ELNClient class

connect(url, key)

class inm_rspace.core.InventoryClass

Bases: InventoryClient

Inventory class enhancing the rspace_client.inv.InventoryClient class

connect(url, key)

inm_rspace.core.compare_forms(form1, form2)

Deprecated version of forms_are_compatible.

inm_rspace.core.document_fields_from_json(json_dict: dict)

Convert a JSON-style dict with key,value pairs into a list of RSpace document fields of format [{‘name’: <key>, ‘content’: <value>}, …]

Parameters:

json_dict (dict) – JSON-style dict

Returns:

list<dict> – RSpace document-style list of {‘name’: …, ‘content’: …} dicts.

inm_rspace.core.field_index(document, field_name)

get index of the (first) field from an Rspace document dict with a given name.

Parameters:

• document (dict) – input document

• field_name (str) – name of the field to be accessed

Returns:

idx (int) – the index of the field with the given name

inm_rspace.core.fields_are_compatible(fields1, fields2, subset=False)

determine whether two field lists are identical (or one is a subset of the other).

Parameters:

• fields1 (dict) – a list of RSpace field dicts containing at least the keys ‘name’ and ‘type’.

• fields2 (dict) – a list of RSpace field dicts containing at least the keys ‘name’ and ‘type’.

• subset (bool) – if True, the function only checks whether the fields of <form1> are a subset of the fields in <form2>.

Returns:

match (bool) – True if both forms are compatible, False otherwise.

inm_rspace.core.fill_form_fields(meta: dict, form_fields: list, term_map={}, strict=False)

Create RSpace Document (list of document fields) from a JSON-style metadata dict and an RSpace Form (list of form fields).

Parameters:

• meta (dict) – JSON-style metadata dict

• form_fields (list<dict>) – list of Form field dicts of format {‘name’: …, ‘type’: …, (…)}

• term_map (dict) – map between terms in the form and in the metadata

• strict (bool) – If True, an error will be raised if the metadata dict contains any terms that are present in neither the form_fields nor the term_map. If False, only a warning is printed.

Returns:

list<dict> – List of RSpace Document fields.

inm_rspace.core.form_fields_from_json(json_dict: dict, default: bool = False)

Convert a JSON-style dict with key,value pairs into a list of RSpace Form fields of format [{‘name’: <key>, ‘type’: type(<value>)}, …]

Parameters:

• json_dict (dict) – JSON-style dict

• default (bool) – if True, supplied values in the JSON-style dict are considered to be the default in the RSpace Form.

Returns:

list<dict> – RSpace Form field list of {‘name’: …, ‘type’: …, (…)} dicts.

inm_rspace.core.forms_are_compatible(form1, form2, subset=False)

determine whether two forms are identical (or one is a subset of the other).

Parameters:

• form1 (dict) – an RSpace Form-style dict containing at least the keys ‘name’ and ‘fields’.

• form2 (dict) – an RSpace Form-style dict containing at least the keys ‘name’ and ‘fields’.

• subset (bool) – if True, the function only checks whether the fields of <form1> are a subset of the fields in <form2>.

Returns:

match (bool) – True if both forms are compatible, False otherwise.

inm_rspace.core.get_docs_in_folder(folder_id, form_pattern=None, verbose=False)

scan for Rspace documents in a given folder whose form name matches a pattern

Parameters:

• folder_id (str) – folderID of the Rspace folder to search for matches

• form_pattern (str) – glob-style pattern that the form name must match

Returns:

results (list<dict>) – list of documents matching the form name

inm_rspace.core.get_docs_in_notebook(notebook_id, form_pattern=None, verbose=False)

scan for Rspace documents in a given folder whose form name matches a pattern

Parameters:

• notebook_id (str) – notebookID of the Rspace notebook to search for matches

• form_pattern (str) – glob-style pattern that the form name must match

Returns:

results (list<dict>) – list of documents matching the form name

inm_rspace.core.get_field(document, field_name)

get (the first) field from an Rspace document dict with a given name.

Parameters:

• document (dict) – input document

• field_name (str) – name of the field to be accessed

Returns:

field (dict) – field with the given name

inm_rspace.core.get_files(document, field_key=None)

list files attached to (a field in) an Rspace document

Parameters:

• document (RspaceDocument) – input document

• field_key (int or str, optional) – name of the field, from which files are extracted. If None, files from all fields are listed.

Returns:

files (list<tuple<str,str>>) – files found as globalId,filename-pairs.

inm_rspace.core.get_form_by_dict(new_form, subset=False)

If it exists, return the (first) Rspace Form matching a given RSpace Form definition dict. Otherwise, create this Form and return it.

Parameters:

• new_form (dict) – a dict corresponding to an RSpace Form definition containing at least the keys ‘name’ and ‘fields’.

• subset (bool) – if True, the function only checks whether the fields of <new_form> are a subset of the fields in an existing RSpace Form.

Returns:

rs_form (dict) – the found/newly created RSpace form.

inm_rspace.core.get_line(string, index)

inm_rspace.core.get_requests(shared_folder_id, verbose=False)

get all shared documents requesting a workflow to be performed

Parameters:

shared_folder_id (str) – folderId of the “Shared” Folder in Rspace

Returns:

results (list<dict>) – list of shared Rspace documents using a Request:* form

inm_rspace.core.html_ref(rspace_obj)

html string to reference an Rspace object

Parameters:

rspace_obj (file or document) – Rspace object

Returns:

string (str) – string that can be inserted in an html string to reference the given object.

Raises:

ValueError – raised if the rspace object type is not recognized

inm_rspace.core.tables_from_xml(xml_string, file, delimiter=',', replace={' ': '_', ',': '.', '</p>': '', '<p>': ''})

extract all tabular data from an xml string and save it as a csv file.

Parameters:

• xml_string (str) – input xml string

• file (str) – file path to use, although an appendix is going to be inserted to enumerate multiple tables in the xml string.

• delimiter (str, optional) – field delimiter to be used in the csv file

• replace (dict, optional) – key,value pairs indicating strings (keys) to be replaced with their corresponding value.

Returns:

files (list<str>) – List of files exported.