labimotion 1.4.1 → 2.0.0.rc6

data/lib/labimotion/libs/data/mapper/Chemwiki.json

@@ -0,0 +1,236 @@
+{
+  "CHMO:0000025": {
+    "index": ["A", "B", "C", "Q1", "Q2", "Q3", "G", "H", "Q4", "Q5", "K", "L", "Q6", "N", "O", "P", "Q7", "R", "S", "T", "U", "V", "W", "X", "Q8", "Q9", "Q10"],
+    "mapper": {
+      "A": {
+        "sources": ["inchikey"]
+      },
+      "B": {
+        "sources": ["molfile"]
+      },
+      "C": {
+        "sources": ["concentration"]
+      },
+      "G": {
+        "sources": ["solvent_volume"]
+      },
+      "H": {
+        "sources": ["elect_inchikey"]
+      },
+      "K": {
+        "sources": ["elect_concentration"]
+      },
+      "L": {
+        "sources": ["reference_internal"]
+      },
+      "N": {
+        "sources": ["scan_rate"]
+      },
+      "O": {
+        "sources": ["scan_number"]
+      },
+      "P": {
+        "sources": ["voltage_limit_one", "voltage_limit_two"],
+        "separator": ","
+      },
+      "R": {
+        "sources": ["atmosphere"]
+      },
+      "S": {
+        "sources": ["temperature"]
+      },
+      "T": {
+        "sources": ["condition"]
+      },
+      "U": {
+        "sources": ["we"]
+      },
+      "V": {
+        "sources": ["we_area"]
+      },
+      "W": {
+        "sources": ["ce"]
+      },
+      "X": {
+        "sources": ["re"]
+      },
+      "Q1": {
+        "sources": ["redox"],
+        "separator": ","
+      },
+      "Q2": {
+        "sources": ["solvent"]
+      },
+      "Q3": {
+        "sources": ["solvent_molfile"]
+      },
+      "Q4": {
+        "sources": ["elect_molfile"]
+      },
+      "Q5": {
+        "sources": ["elect_purity"]
+      },
+      "Q6": {
+        "sources": ["reference_internal_compound_molfile"]
+      },
+      "Q7": {
+        "sources": ["scan_direction"],
+        "separator": ","
+      },
+      "Q8": {
+        "sources": ["details"],
+        "separator": ","
+      },
+      "Q9": {
+        "sources": ["includes"],
+        "separator": ","
+      },
+      "Q10": {
+        "sources": ["base_page"],
+        "separator": ","
+      }
+    },
+    "source": {
+      "concentration": {
+        "title": "Analyte concentration [mM]",
+        "param": "sample_preparation.concentration",
+        "type": "dataset"
+      },
+      "temperature": {
+        "title": "Temperature [°C]",
+        "param": "set.temperature",
+        "type": "dataset"
+      },
+      "condition": {
+        "title": "Condition",
+        "param": "set.conditions",
+        "type": "dataset"
+      },
+      "scan_rate": {
+        "title": "Scan rate [mV/s]",
+        "param": "meas.scan_rate",
+        "type": "dataset"
+      },
+      "atmosphere": {
+        "title": "Gas",
+        "param": "set.atmosphere",
+        "type": "dataset"
+      },
+      "scan_number": {
+        "title": "Scan number",
+        "param": "meas.cycles",
+        "type": "dataset"
+      },
+      "we": {
+        "title": "Working electrode",
+        "param": "electrodes.working",
+        "type": "dataset"
+      },
+      "we_area": {
+        "title": "Working electrode surface area",
+        "param": "electrodes.working_area",
+        "type": "dataset"
+      },
+      "ce": {
+        "title": "Counter electrode",
+        "param": "electrodes.counter",
+        "type": "dataset"
+      },
+      "re": {
+        "title": "Reference electrode",
+        "param": "electrodes.reference",
+        "type": "dataset"
+      },
+      "voltage_limit_one": {
+        "title": "Potential window",
+        "param": "meas.voltage_limit_one",
+        "type": "dataset"
+      },
+      "voltage_limit_two": {
+        "title": "Potential window",
+        "param": "meas.voltage_limit_two",
+        "type": "dataset"
+      },
+      "reference_internal": {
+        "title": "Internal reference compound_inchikey",
+        "param": "meas.reference_internal",
+        "type": "dataset"
+      },
+      "elect_inchikey": {
+        "title": "Electrolyte_inchikey",
+        "param": "sample_preparation.salt",
+        "type": "dataset"
+      },
+      "elect_concentration": {
+        "title": "Electrolyte concentration [M]",
+        "param": "sample_preparation.concentration_salt",
+        "type": "dataset"
+      },
+      "solvent": {
+        "title": "Solvent A_inchikey",
+        "param": "sample_preparation.solvent",
+        "type": "dataset"
+      },
+      "solvent_volume": {
+        "title": "Solvent volume [ml]",
+        "param": "sample_preparation.amount_sol",
+        "type": "dataset"
+      },
+      "solvent_molfile": {
+        "title": "Solvent A_molfile",
+        "param": "n/a",
+        "type": "string"
+      },
+      "scan_direction": {
+        "title": "Scan direction",
+        "param": "n/a",
+        "type": "string"
+      },
+      "reference_internal_compound_molfile": {
+        "title": "Internal reference compound_molfile",
+        "param": "n/a",
+        "type": "string"
+      },
+      "elect_purity": {
+        "title": "Electrolyte purity [%]",
+        "param": "n/a",
+        "type": "string"
+      },
+      "redox": {
+        "title": "Redox-Potential",
+        "param": "n/a",
+        "type": "string"
+      },
+      "elect_molfile": {
+        "title": "Electrolyte_inchikey",
+        "param": "n/a",
+        "type": "string"
+      },
+      "inchikey": {
+        "title": "Analyte_inchikey",
+        "param": "inchikey",
+        "type": "molecule"
+      },
+      "molfile": {
+        "title": "Analyte_molfile",
+        "param": "molfile",
+        "type": "sample"
+      },
+      "details": {
+        "title": "Details",
+        "param": "n/a",
+        "type": "string"
+      },
+      "includes": {
+        "title": "Included",
+        "param": "n/a",
+        "type": "string"
+      },
+      "base_page": {
+        "title": "BasePageName",
+        "param": "n/a",
+        "type": "string"
+      }
+    }
+  }
+}

data/lib/labimotion/libs/data/mapper/Source.json

@@ -0,0 +1,78 @@
+{
+  "sourceMap": {
+    "sourceSelector": [
+      "parm",
+      "acqus",
+      "procs"
+    ],
+    "acqus": {
+      "file": "acqus",
+      "parameters": [
+        "DATE",
+        "D1",
+        "INSTRUM",
+        "NS",
+        "NUC1",
+        "NUC2",
+        "PROBHD",
+        "PULPROG",
+        "SFO1",
+        "SFO2",
+        "SOLVENT",
+        "SW",
+        "TD",
+        "TE",
+        "TITLE"
+      ]
+    },
+    "procs": {
+      "file": "pdata/1/procs",
+      "parameters": [
+        "SI",
+        "SF",
+        "WDW",
+        "LB",
+        "GB"
+      ]
+    },
+    "parm": {
+      "file": "pdata/1/parm.txt",
+      "parameters": [
+        "Date_",
+        "Time",
+        "INSTRUM",
+        "PROBHD",
+        "SOLVENT",
+        "TE",
+        "NS",
+        "PULPROG",
+        "TD",
+        "D1",
+        "SF",
+        "SFO1",
+        "SFO2",
+        "NUC1",
+        "NUC2"
+      ]
+    },
+    "parameters": {
+      "DATE": "general.date",
+      "D1": "set.done",
+      "INSTRUM": "instrument.instrument",
+      "NS": "set.ns",
+      "NUC1": "set.nucone",
+      "NUC2": "set.nuctwo",
+      "SF": "set.sf",
+      "SFO1": "set.sfoone",
+      "SFO2": "set.sfotwo",
+      "PROBHD": "equipment.probehead",
+      "PULPROG": "set.PULPROG",
+      "SOLVENT": "sample_preparation.solvent",
+      "TD": "set.td",
+      "TE": "set.temperature",
+      "TITLE": "software.Name",
+      "Version": "software.Version",
+      "Time": "general.time"
+    }
+  }
+}

data/lib/labimotion/libs/data/vocab/Standard.json

@@ -0,0 +1,385 @@
+[
+  {
+      "identifier": "std-atmosphere",
+      "name": "atmosphere",
+      "label": "Atmosphere",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C54711",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C54711",
+        "short_form": "NCIT_C54711",
+        "obo_id": "NCIT:C54711",
+        "label": "Atmosphere",
+        "description": [
+          "Non-SI unit of pressure equal to 101 325 Pa."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-calibration",
+      "name": "calibration",
+      "label": "Calibration",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C69187",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C69187",
+        "short_form": "NCIT_C69187",
+        "obo_id": "NCIT:C69187",
+        "label": "Calibration",
+        "description": [
+          "The act of checking or adjusting (by comparison with a standard) the accuracy of a measuring instrument."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-coating",
+      "name": "coating",
+      "label": "Coating",
+      "field_type": "text",
+      "ontology": {
+        "id": "afo:class:http://purl.allotrope.org/ontologies/process#AFP_0001986",
+        "iri": "http://purl.allotrope.org/ontologies/process#AFP_0001986",
+        "short_form": "AFP_0001986",
+        "obo_id": "AFP:0001986",
+        "label": "coating",
+        "description": [
+          "The application of a thin cover to a material. [CHMO]"
+        ],
+        "ontology_name": "afo",
+        "ontology_prefix": "AFO",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-coating_material",
+      "name": "coating_material",
+      "label": "Coating Material",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C172794",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C172794",
+        "short_form": "NCIT_C172794",
+        "obo_id": "NCIT:C172794",
+        "label": "Coating Material",
+        "description": [
+          "A layer of material covering the surface of a device."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-wavelength",
+      "name": "wavelength",
+      "label": "Wavelength",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C48158",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C48158",
+        "short_form": "NCIT_C48158",
+        "obo_id": "NCIT:C48158",
+        "label": "Wavelength",
+        "description": [
+          "The distance (measured in the direction of propagation) between two points in the same phase in consecutive cycles of a wave."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-sample_size",
+      "name": "sample_size",
+      "label": "Sample Size",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C53190",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C53190",
+        "short_form": "NCIT_C53190",
+        "obo_id": "NCIT:C53190",
+        "label": "Sample Size",
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-instrument",
+      "name": "instrument",
+      "label": "Instrument",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000463",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000463",
+        "short_form": "NMR:1000463",
+        "label": "instrument",
+        "description": [
+          "Description of the instrument or the mass spectrometer."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-irr_freq",
+      "name": "irr_freq",
+      "label": "Irradiation frequency",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000463",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000463",
+        "short_form": "NMR:1000463",
+        "label": "instrument",
+        "description": [
+          "Description of the instrument or the mass spectrometer."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-num_scans",
+      "name": "num_scans",
+      "label": "Number of scans",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400087",
+        "iri": "http://nmrML.org/nmrCV#NMR:1400087",
+        "short_form": "NMR:1400087",
+        "label": "number of scans",
+        "description": [
+          "def: The number of repeat scans performed and summed to create the data set for an NMR sample."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-sample_ph",
+      "name": "sample_ph",
+      "label": "Sample pH",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000019",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000019",
+        "short_form": "NMR:1000019",
+        "label": "sample pH",
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-pulse_seq",
+      "name": "pulse_seq",
+      "label": "NMR pulse sequence",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400037",
+        "iri": "http://nmrML.org/nmrCV#NMR:1400037",
+        "short_form": "NMR:1400037",
+        "label": "NMR pulse sequence",
+        "description": [
+          "def: A sequence of excitation pulses.",
+          "http://www.bmrb.wisc.edu/tools/choose_pulse_info.php"
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-sample_conc",
+      "name": "sample_conc",
+      "label": "sample concentration",
+      "field_type": "text",
+      "ontology": {
+        "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000006",
+        "iri": "http://nmrML.org/nmrCV#NMR:1000006",
+        "short_form": "NMR:1000006",
+        "label": "sample concentration",
+        "description": [
+          "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used."
+        ],
+        "ontology_name": "nmrcv",
+        "ontology_prefix": "NMRCV",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-scan_range",
+      "name": "scan_range",
+      "label": "scan range",
+      "field_type": "text",
+      "ontology": {
+        "id": "afo:class:http://purl.allotrope.org/ontologies/result#AFR_0001957",
+        "iri": "http://purl.allotrope.org/ontologies/result#AFR_0001957",
+        "short_form": "AFR_0001957",
+        "obo_id": "AFR:0001957",
+        "label": "detector scan rate setting",
+        "description": [
+          "A detector setting that sets the frequency of scans per time unit. [Allotrope]"
+        ],
+        "ontology_name": "afo",
+        "ontology_prefix": "AFO",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-software_name",
+      "name": "software_name",
+      "label": "Software Name",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C150832",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C150832",
+        "short_form": "NCIT_C150832",
+        "obo_id": "NCIT:C150832",
+        "label": "Software Name",
+        "description": [
+          "The literal identifier of the software program."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+      "identifier": "std-software_ver",
+      "name": "software_ver",
+      "label": "Software Version",
+      "field_type": "text",
+      "ontology": {
+        "id": "ncit:class:http://purl.obolibrary.org/obo/NCIT_C111093",
+        "iri": "http://purl.obolibrary.org/obo/NCIT_C111093",
+        "short_form": "NCIT_C111093",
+        "obo_id": "NCIT:C111093",
+        "label": "Software Version",
+        "description": [
+          "A form or variant of software; one of a sequence of copies of a software program, each incorporating new modifications."
+        ],
+        "ontology_name": "ncit",
+        "ontology_prefix": "NCIT",
+        "type": "class"
+      },
+      "source": "Standard"
+  },
+  {
+    "identifier": "std-solvent",
+    "name": "nmr_solvent",
+    "label": "NMR Solvent",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000330",
+      "iri": "http://nmrML.org/nmrCV#NMR:1000330",
+      "short_form": "NMR:1000330",
+      "label": "NMR solvent",
+      "description": [
+        "Use Chebi entities here."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "std-sample_volume",
+    "name": "sample_volume",
+    "label": "sample volume",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1000005",
+      "iri": "http://nmrML.org/nmrCV#NMR:1000005",
+      "short_form": "NMR:1000005",
+      "label": "sample volume",
+      "description": [
+        "Total volume of solution used."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "std-solvent_info",
+    "name": "solvent_info",
+    "label": "NMR solvent information",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1002010",
+      "iri": "http://nmrML.org/nmrCV#NMR:1002010",
+      "short_form": "NMR:1002010",
+      "label": "NMR solvent information",
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "std-sample_tube",
+    "name": "sample_tube",
+    "label": "NMR sample tube",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400132",
+      "iri": "http://nmrML.org/nmrCV#NMR:1400132",
+      "short_form": "NMR:1400132",
+      "label": "NMR sample tube",
+      "description": [
+        "http://en.wikipedia.org/wiki/NMR_tube",
+        "sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID",
+        "The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  },
+  {
+    "identifier": "temperature",
+    "name": "Temperature",
+    "label": "Temperature",
+    "field_type": "text",
+    "ontology": {
+      "id": "nmrcv:class:http://nmrML.org/nmrCV#NMR:1400025",
+      "iri": "http://nmrML.org/nmrCV#NMR:1400025",
+      "short_form": "NMR:1400025",
+      "label": "sample temperature in magnet",
+      "description": [
+        "def: The temperature of an NMR sample whilst in the magnet of an NMR instrument."
+      ],
+      "ontology_name": "nmrcv",
+      "ontology_prefix": "NMRCV",
+      "type": "class"
+    },
+    "source": "Standard"
+  }
+]