Merge pull request #60 from ChalkLab/50-add-rruff-reader

Adds RRUFF reader to scidatalib.io.rruff

scidatalib/io/jcamp.py

@@ -555,6 +555,23 @@ def _reader(filehandle: str) -> dict:
     return jcamp_dict
 
 
+def _read_get_description(jcamp_dict: dict, keywords: List[str]) -> str:
+    """
+    Utility function to create a description string from the JCAMP
+    dictionary
+
+    :param jcamp_dict: JCAMP-DX dictionary extracted from read
+    :return: String for the description for SciData object
+    """
+    description_lines = []
+    for key in keywords:
+        if key in jcamp_dict:
+            value = jcamp_dict.get(key)
+            description_lines.append(f'{key.upper()}: {value}')
+
+    return _DESCRIPTION_KEY_SPLIT_CHAR.join(description_lines)
+
+
 def _read_get_graph_source_citation_section(jcamp_dict: dict) -> List[str]:
     """
     Extract and translate from the JCAMP-DX dictionary the SciData JSON-LD
@@ -777,7 +794,7 @@ def _read_get_datagroup_subsection(jcamp_dict: dict) -> List[dict]:
     """
     # Convert from JCAMP units -> SciData JSON-LD unitref
     xunits = jcamp_dict.get("xunits", "")
-    xunitref = _XUNIT_MAP.get(xunits)
+    xunitref = _XUNIT_MAP.get(xunits, "")
     yunitref = jcamp_dict.get("yunits", "")
 
     # Values for attributes
@@ -969,20 +986,14 @@ def _read_translate_jcamp_to_scidata(jcamp_dict: dict) -> SciData:
     scidata.starttime(f'{jcamp_date} {jcamp_time}')
 
     # Description
-    description_lines = []
     description_keywords = [
         "jcamp-dx",
         "class",
         "cas registry no",
         "sample description",
         "xydata"
     ]
-    for key in description_keywords:
-        if key in jcamp_dict:
-            value = jcamp_dict.get(key)
-            description_lines.append(f'{key.upper()}: {value}')
-
-    description = _DESCRIPTION_KEY_SPLIT_CHAR.join(description_lines)
+    description = _read_get_description(jcamp_dict, description_keywords)
     scidata.description(description)
 
     # Authors

scidatalib/io/rruff.py

@@ -0,0 +1,206 @@
+import numpy as np
+from typing import TextIO
+
+from scidatalib.scidata import SciData
+from scidatalib.io import jcamp
+
+
+_SCIDATA_UID = "scidata:rruff:jsonld"
+
+
+def read_rruff(filename: str) -> dict:
+    """
+    Reader for RRUFF database files to SciData object
+    RRUFF file format is a modified version of JCAMP, so re-use jcamp module
+
+    :param filename: Filename to read from for RRUFF files
+    :return: SciData object read in from RRUFF file
+    """
+    with open(filename, "r") as fileobj:
+        rruff_dict = _reader(fileobj)
+    scidata = _read_translate_rruff_to_scidata(rruff_dict)
+    return scidata
+
+
+def _reader(filehandle: TextIO) -> dict:
+    """
+    File reader for  RRUFF file format
+
+    :param filehandle: RRUFF file to read from
+    :return: Dictionary parsed from RRUFF file
+    """
+    rruff_dict = {}
+    y = []
+    x = []
+    for line in filehandle:
+        # Skip blank or comment lines
+        if not line.strip():
+            continue
+        if line.startswith("$$"):
+            continue
+
+        rruff_dict, _, _ = jcamp._read_parse_header_line(line, rruff_dict)
+
+        if not line.startswith("##"):
+            datavals = jcamp._read_parse_dataset_line(
+                line,
+                jcamp._DATA_FORMAT_XYXY)
+            x.extend(datavals[0::2])
+            y.extend(datavals[1::2])
+
+    x = np.array([float(xval) for xval in x])
+    y = np.array([float(yval) for yval in y])
+
+    if ("xfactor" in rruff_dict):
+        x = x * rruff_dict["xfactor"]
+    if ("yfactor" in rruff_dict):
+        y = y * rruff_dict["yfactor"]
+
+    rruff_dict['x'] = x
+    rruff_dict['y'] = y
+    return rruff_dict
+
+
+def _read_get_aspects_section(rruff_dict: dict) -> dict:
+    """
+    Extract and translate from the RRUFF dictionary the SciData JSON-LD
+    'aspects' sub-ection of the 'methodology' section
+
+    :param rruff_dict: RRUFF dictionary to extract aspects section from
+    :return: The 'aspects' section of SciData JSON-LD methodology
+    """
+    aspects = []
+
+    # Measurement
+    measurement = {
+        "@id": "measurement/1/",
+        "@type": "cao:CAO_000152",
+        "techniqueType": "obo:CHMO_0000228",
+        "technique": "obo:CHMO_0000656",
+        "instrumentType": "raman spectrometer",
+        "instrument": "Unknown",
+    }
+
+    # Settings for measurement
+    settings = []
+    if "laser_wavelength" in rruff_dict:
+        wavelength = {
+            "@id": "setting/1",
+            "@type": "sdo:setting",
+            "quantity": "wavelength",
+            "property": "Laser Wavelength",
+            "value": {
+                "@id": "setting/1/value/",
+                "number": rruff_dict.get("laser_wavelength"),
+                "unitstr": "qudt:NanoM",
+            }
+        }
+        settings.append(wavelength)
+
+    measurement.update({"settings": settings})
+
+    aspects.append(measurement)
+    return aspects
+
+
+def _read_get_facets_section(rruff_dict: dict) -> dict:
+    """
+    Extract and translate from the RRUFF dictionary the SciData JSON-LD
+    'facets' sub-section of the 'system' section
+
+    :param rruff_dict: RRUFF dictionary to extract facets section from
+    :return: The 'facets' section of SciData JSON-LD from translation
+    """
+
+    facets = []
+    material = {
+        "@id": "material",
+        "@type": ["sdo:facet", "sdo:material"],
+        "name": rruff_dict.get("names", ""),
+        "materialType": rruff_dict.get("ideal chemistry", ""),
+    }
+    facets.append(material)
+    return facets
+
+
+def _read_translate_rruff_to_scidata(rruff_dict: dict) -> dict:
+    """
+    Main translation of RRUFF to SciData object
+
+    :param rruff_dict: RRUFF dictionary extracted from read
+    :return: SciData object from translation
+    """
+    scidata = SciData(_SCIDATA_UID)
+
+    # Add champ namespace for aspect techniqueType
+    cao = {"cao": "http://champ-project.org/images/ontology/cao.owl#"}
+    scidata.namespaces(cao)
+
+    # Title
+    scidata.title(rruff_dict.get("names", ""))
+    scidata.publisher(rruff_dict.get("owner", ""))
+
+    # Description
+    description_keywords = [
+        "description",
+        "locality",
+        "status",
+    ]
+    description = jcamp._read_get_description(rruff_dict, description_keywords)
+    scidata.description(description)
+
+    # UID
+    rruff_dict.update({"rruffid": f'rruff:{rruff_dict.get("rruffid")}'})
+    scidata.graph_uid(rruff_dict.get('rruffid'))
+
+    # Authors
+    authors = []
+    author_keywords = ["source"]
+    for author_keyword in author_keywords:
+        if author_keyword in rruff_dict:
+            authors.append({
+                "@id": "author/{}".format(len(authors) + 1),
+                "@type": "dc:creator",
+                "name": rruff_dict[author_keyword]
+            })
+    scidata.author(authors)
+
+    # Sources / references
+    sources = []
+    sources.append({
+        "@id": "source/1/",
+        "@type": "dc:source",
+        "citation": "Highlights in Mineralogical Crystallography 2015 1-30",
+        "reftype": "journal article",
+        "doi": "10.1515/9783110417104-003",
+        "url": "https://doi.org/10.1515/9783110417104-003"
+    })
+
+    if "url" in rruff_dict:
+        sources.append({
+                "@id": f"source/{len(sources) + 1}",
+                "@type": "dc:source",
+                "citation": "RRUFF project database entry",
+                "url": f'https://{rruff_dict.get("url")}',
+            })
+    scidata.sources(sources)
+
+    # Discipline and sub-discipline
+    scidata.discipline("w3i:Chemistry")
+    scidata.subdiscipline("w3i:AnalyticalChemistry")
+
+    # Methodology - aspects
+    scidata.aspects(_read_get_aspects_section(rruff_dict))
+
+    # System - facets
+    scidata.facets(_read_get_facets_section(rruff_dict))
+
+    # Dataset
+    scidata.scope("material")
+    datagroup = jcamp._read_get_datagroup_subsection(rruff_dict)
+    scidata.datagroup([datagroup])
+
+    # TODO: add the dataseries
+    #   Issue: https://github.com/ChalkLab/SciDataLib/issues/43
+
+    return scidata

scidatalib/scidata.py

@@ -653,7 +653,10 @@ def tocdict(a):
             """ get the @type entry from a dictionary """
             for k, v in a.items():
                 if k == '@type':
-                    self.meta['@graph']['toc'].append(v)
+                    if isinstance(v, list):
+                        self.meta['@graph']['toc'].extend(v)
+                    else:
+                        self.meta['@graph']['toc'].append(v)
                 if isinstance(v, list):
                     toclist(v)
                 if isinstance(v, dict):