Re-org some constant strings

mzspeclib/backends/base.py

@@ -16,10 +16,21 @@
 from mzspeclib.cluster import SpectrumCluster
 
 from mzspeclib.index import MemoryIndex, SQLIndex, IndexBase
-from mzspeclib.spectrum import LIBRARY_SPECTRUM_INDEX, LIBRARY_SPECTRUM_KEY, Spectrum
-from mzspeclib.analyte import Analyte, Interpretation, InterpretationMember, ANALYTE_MIXTURE_TERM
+from mzspeclib.spectrum import Spectrum
+from mzspeclib.analyte import Analyte, Interpretation, InterpretationMember
 from mzspeclib.attributes import Attributed, AttributedEntity, AttributeSet, AttributeManagedProperty
 from mzspeclib.ontology import _VocabularyResolverMixin
+from mzspeclib.const import (
+    FORMAT_VERSION_TERM,
+    LIBRARY_NAME_TERM,
+    LIBRARY_IDENTIFIER_TERM,
+    LIBRARY_VERSION_TERM,
+    LIBRARY_URI_TERM,
+    LIBRARY_DESCRIPTION_TERM,
+    ANALYTE_MIXTURE_TERM,
+    LIBRARY_SPECTRUM_INDEX,
+    LIBRARY_SPECTRUM_KEY
+)
 
 from .utils import open_stream, _LineBuffer
 
@@ -31,14 +42,6 @@
 
 ANALYTE_MIXTURE_CURIE = ANALYTE_MIXTURE_TERM.split("|")[0]
 
-FORMAT_VERSION_TERM = 'MS:1003186|library format version'
-LIBRARY_NAME_TERM = "MS:1003188|library name"
-LIBRARY_VERSION_TERM = "MS:1003190|library version"
-LIBRARY_IDENTIFIER_TERM = "MS:1003187|library identifier"
-LIBRARY_DESCRIPTION_TERM = "MS:1003189|library description"
-LIBRARY_URI_TERM = "MS:1003191|library URI"
-
-
 DEFAULT_VERSION = '1.0'
 
 

mzspeclib/const.py

@@ -23,4 +23,9 @@
 SPECTRUM_NAME = "MS:1003061|library spectrum name"
 LIBRARY_SPECTRUM_KEY = "MS:1003237|library spectrum key"
 LIBRARY_SPECTRUM_INDEX = "MS:1003062|library spectrum index"
-PRECURSOR_MZ = "MS:1003208|experimental precursor monoisotopic m/z"
+PRECURSOR_MZ = "MS:1003208|experimental precursor monoisotopic m/z"
+THEORETICAL_MZ = "MS:1003053|theoretical monoisotopic m/z"
+
+SPECTRUM_AGGREGATION_TYPE = "MS:1003065|spectrum aggregation type"
+NUMBER_OF_REPLICATE_SPECTRA_USED = "MS:1003070|number of replicate spectra used"
+NUMBER_OF_REPLICATE_SPECTRA_AVAILABLE = "MS:1003069|number of replicate spectra available"

mzspeclib/spectrum.py

@@ -9,7 +9,9 @@
     AttributeProxy as _AttributeProxy, AttributeFacet
 )
 from mzspeclib.analyte import Analyte, InterpretationCollection, Interpretation
-from .const import (SPECTRUM_NAME, LIBRARY_SPECTRUM_INDEX, LIBRARY_SPECTRUM_KEY, PRECURSOR_MZ, CHARGE_STATE)
+from .const import (SPECTRUM_NAME, LIBRARY_SPECTRUM_INDEX, LIBRARY_SPECTRUM_KEY, PRECURSOR_MZ, CHARGE_STATE,
+                    SPECTRUM_AGGREGATION_TYPE, NUMBER_OF_REPLICATE_SPECTRA_USED, NUMBER_OF_REPLICATE_SPECTRA_AVAILABLE,
+                    THEORETICAL_MZ, PEAK_ATTRIBUTE)
 
 if TYPE_CHECKING:
     from mzspeclib.spectrum_library import SpectrumLibrary
@@ -18,9 +20,9 @@
 
 
 class SpectrumAggregation(_AttributeProxy):
-    aggregation_type = AttributeManagedProperty("MS:1003065|spectrum aggregation type")
-    replicates_used = AttributeManagedProperty[int]("MS:1003070|number of replicate spectra used")
-    replicates_available = AttributeManagedProperty[int]("MS:1003069|number of replicate spectra available")
+    aggregation_type = AttributeManagedProperty(SPECTRUM_AGGREGATION_TYPE)
+    replicates_used = AttributeManagedProperty[int](NUMBER_OF_REPLICATE_SPECTRA_USED)
+    replicates_available = AttributeManagedProperty[int](NUMBER_OF_REPLICATE_SPECTRA_AVAILABLE)
 
 
 class Spectrum(AttributeManager):
@@ -82,12 +84,12 @@ def __init__(self, attributes=None, peak_list=None, analytes=None,
 
     precursor_mz = AttributeListManagedProperty[float](
         [PRECURSOR_MZ,
-         "MS:1003053|theoretical monoisotopic m/z"])
+         THEORETICAL_MZ])
 
     _precursor_charge = AttributeManagedProperty[int](CHARGE_STATE)
 
     spectrum_aggregation = AttributeFacet[SpectrumAggregation](SpectrumAggregation)
-    peak_aggregations = AttributeManagedProperty("MS:1003254|peak attribute", multiple=True)
+    peak_aggregations = AttributeManagedProperty(PEAK_ATTRIBUTE, multiple=True)
 
     @property
     def precursor_charge(self) -> int: