diff --git a/examples/notebooks/UMLDiagram.png b/examples/notebooks/UMLDiagram.png new file mode 100644 index 0000000..0f09ead Binary files /dev/null and b/examples/notebooks/UMLDiagram.png differ diff --git a/examples/notebooks/oop_demo.ipynb b/examples/notebooks/oop_demo.ipynb new file mode 100644 index 0000000..d0d6ac8 --- /dev/null +++ b/examples/notebooks/oop_demo.ipynb @@ -0,0 +1,2389 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## PyLiPD OOP Demo" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### PyLiPD Ontologies\n", + "\n", + "The PyLiPD OOP Classes are generated from the ontologies at: https://linked.earth/ontology/\n", + "* The [Linked Earth Core Ontology](https://linked.earth/ontology/core/2.0.0/index-en.html) provides the main concepts and relationships to describe a paleoclimate dataset and its values.\n", + "* The [Archive Type Ontology](https://linked.earth/ontology/archive/2.0.0/index-en.html) describes a taxonomy of the most common types of archives.\n", + "* The [Paleo Variables Ontology](https://linked.earth/ontology/paleo_variables/2.0.0/index-en.html) describes a taxonomy of the most common types of paleo variables.\n", + "* The [Paleo Proxy Ontology](https://linked.earth/ontology/paleo_proxy/2.0.0/index-en.html) describes a taxonomy of the most common types of paleo proxies.\n", + "* The [Paleo Units Ontology](https://linked.earth/ontology/paleo_units/2.0.0/index-en.html) describes a taxonomy of the most common types of paleo units.\n", + "* The [Interpretation Ontology](https://linked.earth/ontology/interpretation/2.0.0/index-en.html) describes a taxonomy of the most common interpretations.\n", + "* The [Instrument Ontology](https://linked.earth/ontology/instrument/2.0.0/index-en.html) describes a taxonomy of the most common instrument for taking measurements.\n", + "* The [Chron Variables Ontology](https://linked.earth/ontology/chron_variables/2.0.0/index-en.html) describes a taxonomy of the most common types of chron variables.\n", + "* The [Chron Proxy Ontology](https://linked.earth/ontology/chron_proxy/2.0.0/index-en.html) describes a taxonomy of the most common types of chron proxies.\n", + "* The [Chron Units Ontology](https://linked.earth/ontology/chron_units/2.0.0/index-en.html) describes a taxonomy of the most common types of chron units.\n", + "\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### PyLiPD OOP Classes UML Diagram\n", + "![PyLiPD OOP Classes UML Diagram](UMLDiagram.png \"yLiPD OOP Classes UML Diagram\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Reading an existing LiPD file" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loading 16 LiPD files\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 16/16 [00:00<00:00, 59.56it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded..\n", + "\n", + "\n", + "Ocn-RedSea.Felis.2000\n", + "=========================\n", + "Publication: Tropical sea surface temperatures for the past four centuries reconstructed from coral archives by ['Henry C. Wu', 'Jens Zinke', 'Michael N. Evans', 'Casey P. Saenger', 'Jessica E. Tierney', 'Kevin J. Anchukaitis', 'Cyril Giry', 'K. Halimeda Kilbourne', 'Nerilie J. Abram']\n", + "Publication: A coral oxygen isotope record from the northern Red Sea documenting NAO, ENSO, and North Pacific teleconnections on Middle East climate variability since the year 1750 by ['Yossi Loya', 'Ahmed H. Nawar', 'Maoz Fine', 'Gerold Wefer', 'Jürgen Pätzold', 'Thomas Felis']\n", + "Publication: World Data Center for Paleoclimatology by ['T. Felis']\n", + "- Paleo Table: Ocn-RedSea.Felis.2000.paleo1measurement1.csv\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/html": [ + "
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Yu. Demezhko', 'I. V. Golovanova']\n", + "Publication: This study by ['D Demezhko']\n", + "- Paleo Table: Asi-SourthAndMiddleUrals.Demezhko.2007.paleo1measurement1.csv\n" + ] + }, + { + "data": { + "text/html": [ + "
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O2kLR recommends only using the Quality controlled data.', 'inCompilationBeta': {'@id': 'http://linked.earth/lipd/Pages2kTemperature.66deb385218da', 'compilationName': 'Pages2kTemperature', 'compilationVersion': '2_1_1'}, 'resolution': {'@id': 'http://linked.earth/lipd/Ocn-FeniDrift.Richter.2009.paleo2measurement1.LPDba471ae7.Mg_Ca.Resolution', 'hasMaxValue': 38.0, 'hasMeanValue': 22.9709, 'hasMedianValue': 22.0, 'hasMinValue': 11.0, 'units': 'yr AD'}, 'hasStandardVariable': 'Mg/Ca', 'TSid': 'LPDba471ae7', 'variableType': 'measured', 'dataType': 'float', 'measurementTableName': 'measurementTable1', 'proxyObservationType': 'Mg/Ca', 'paleoDataTableName': 'Dataoriginal', 'measurementTableMD5': '7c005b7c718ad460a5e2bfcb456d06f5', 'useInGlobalTemperatureAnalysis': False, 'wDSPaleoUrl': 'https://www1.ncdc.noaa.gov/pub/data/paleo/pages2k/pages2k-temperature-v2-2017/data-version-2.0.0/Ocn-FeniDrift.Richter.2009-2.txt'}\n", + "notes {'@id': 'http://linked.earth/lipd/Ocn-FeniDrift.Richter.2009.paleo2measurement1.LPD6e0eacd1.notes', 'interpretation': [{'@id': 'http://linked.earth/lipd/Ocn-FeniDrift.Richter.2009.paleo2measurement1.LPD6e0eacd1.notes.Interpretation1', 'scope': 'climate'}], 'archiveType': 'Marine sediment', 'number': 6, 'description': 'original composite dataset from Richter et al. (2009) - PLEASE USE QC DATA FOR ANALYSIS!!!!', 'variableName': 'notes', 'notes': 'These are the original, not quality controlled data. O2kLR recommends only using the Quality controlled data.', 'inCompilationBeta': {'@id': 'http://linked.earth/lipd/Pages2kTemperature.66deb38521933', 'compilationName': 'Pages2kTemperature', 'compilationVersion': '2_1_1'}, 'resolution': {'@id': 'http://linked.earth/lipd/Ocn-FeniDrift.Richter.2009.paleo2measurement1.LPD6e0eacd1.notes.Resolution', 'hasMaxValue': 38.0, 'hasMeanValue': 22.9709, 'hasMedianValue': 22.0, 'hasMinValue': 11.0, 'units': 'yr AD'}, 'hasStandardVariable': 'notes', 'TSid': 'LPD6e0eacd1', 'variableType': 'measured', 'dataType': 'str', 'measurementTableName': 'measurementTable1', 'paleoDataTableName': 'Dataoriginal', 'measurementTableMD5': '7c005b7c718ad460a5e2bfcb456d06f5', 'wDSPaleoUrl': 'https://www1.ncdc.noaa.gov/pub/data/paleo/pages2k/pages2k-temperature-v2-2017/data-version-2.0.0/Ocn-FeniDrift.Richter.2009-2.txt', 'useInGlobalTemperatureAnalysis': False}\n", + "Missing Value: NaN\n", + "- depth_top [cm]\n", + "- temperature [degC]\n", + "- depth_bottom [cm]\n", + "- year [yr AD]\n", + "- Mg_Ca\n", + "- notes\n", + "\n", + "\n", + "Eur-LakeSilvaplana.Trachsel.2010\n", + "=========================\n", + "Publication: Scanning reflectance spectroscopy (380–730 nm): a novel method for quantitative high-resolution climate reconstructions from minerogenic lake sediments by ['B. Rein', 'M. Trachsel', 'M. Grosjean', 'D. Schnyder', 'C. Kamenik']\n", + "Publication: World Data Center for Paleoclimatology by ['M. Trachsel']\n", + "- Paleo Table: Eur-LakeSilvaplana.Trachsel.2010.paleo1measurement1.csv\n" + ] + }, + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " year temperature\n", + "0 2000 14.603\n", + "1 1999 14.643\n", + "2 1998 12.074\n", + "3 1997 13.898\n", + "4 1996 13.671" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "year {'@id': 'http://linked.earth/lipd/Eur-FinnishLakelands.Helama.2014.paleo1measurement1.PYTUSB62S0A.year', 'archiveType': 'Wood', 'number': 2, 'description': 'Year AD', 'hasMaxValue': 2000.0, 'hasMeanValue': 1380.0, 'hasMedianValue': 1380.0, 'hasMinValue': 760.0, 'variableName': 'year', 'resolution': {'@id': 'http://linked.earth/lipd/Eur-FinnishLakelands.Helama.2014.paleo1measurement1.PYTUSB62S0A.year.Resolution', 'hasMaxValue': 1.0, 'hasMeanValue': 1.0, 'hasMedianValue': 1.0, 'hasMinValue': 1.0, 'units': 'yr AD'}, 'hasStandardVariable': 'year', 'units': 'yr AD', 'TSid': 'PYTUSB62S0A', 'variableType': 'inferred', 'paleoDataTableName': 'measTable', 'dataType': 'float', 'measurementTableName': 'measurementTable1', 'inferredVariableType': 'Year', 'wDSPaleoUrl': 'https://www1.ncdc.noaa.gov/pub/data/paleo/pages2k/pages2k-temperature-v2-2017/data-version-2.0.0/Eur-FinnishLakelands.Helama.2014.txt', 'measurementTableMD5': '59aaf55caeb739a42de82831c04da3d3'}\n", + "temperature {'@id': 'http://linked.earth/lipd/Eur-FinnishLakelands.Helama.2014.paleo1measurement1.Eur_005.temperature', 'calibration': [{'@id': 'http://linked.earth/lipd/Eur-FinnishLakelands.Helama.2014.paleo1measurement1.Eur_005.temperature.Calibration', 'uncertainty': 'Eur-FinnishLakelands.Helama.2014.paleo1measurement1.Eur_005.temperature.Calibration.Uncertainty'}], 'interpretation': [{'@id': 'http://linked.earth/lipd/Eur-FinnishLakelands.Helama.2014.paleo1measurement1.Eur_005.temperature.Interpretation1', 'basis': 'correlation with local meteorological correlation', 'direction': 'positive', 'scope': 'climate', 'seasonality': 'Summer', 'variable': 'temperature', 'variableDetail': 'air@surface'}], 'archiveType': 'Wood', 'number': 1, 'hasMaxValue': 15.463, 'hasMeanValue': 12.459, 'hasMedianValue': 12.47, 'hasMinValue': 9.408, 'variableName': 'temperature', 'notes': 'Calibrating and verifying the MXD chronologies against the instrumental temperature data showed a promising opportunity to reconstruct warm-season (May through September) temperature variability', 'inCompilationBeta': {'@id': 'http://linked.earth/lipd/Pages2kTemperature.66deb38546cbf', 'compilationName': 'Pages2kTemperature', 'compilationVersion': '2_1_1'}, 'proxy': 'maximum latewood density', 'resolution': {'@id': 'http://linked.earth/lipd/Eur-FinnishLakelands.Helama.2014.paleo1measurement1.Eur_005.temperature.Resolution', 'hasMaxValue': 1.0, 'hasMeanValue': 1.0, 'hasMedianValue': 1.0, 'hasMinValue': 1.0, 'units': 'yr AD'}, 'hasStandardVariable': 'temperature', 'units': 'degC', 'TSid': 'Eur_005', 'variableType': 'inferred', 'wDSPaleoUrl': 'https://www1.ncdc.noaa.gov/pub/data/paleo/pages2k/pages2k-temperature-v2-2017/data-version-2.0.0/Eur-FinnishLakelands.Helama.2014.txt', 'precededBy': 'Arc_15', 'measurementTableMD5': '59aaf55caeb739a42de82831c04da3d3', 'pages2kID': 'Eur_013', 'qCCertification': 'JPW', 'useInGlobalTemperatureAnalysis': True, 'inferredVariableType': 'Temperature', 'measurementTableName': 'measurementTable1', 'paleoDataTableName': 'measTable'}\n", + "Missing Value: NaN\n", + "- year [yr AD]\n", + "- temperature [degC]\n", + "\n", + "\n", + "Eur-NorthernScandinavia.Esper.2012\n", + "=========================\n", + "Publication: World Data Center for Paleoclimatology by ['J. Esper']\n", + "Publication: Orbital forcing of tree-ring data by ['Jürg Luterbacher', 'Rob J. S. Wilson', 'Anne Verstege', 'Mauri Timonen', 'Steffen Holzkämper', 'Sebastian Wagner', 'Jan Esper', 'Eduardo Zorita', 'Nils Fischer', 'Ulf Büntgen', 'David C. Frank', 'Daniel Nievergelt']\n", + "- Paleo Table: Eur-NorthernScandinavia.Esper.2012.paleo1measurement1.csv\n" + ] + }, + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " year temperature\n", + "0 1502 -1.7212\n", + "1 1503 -1.6382\n", + "2 1504 -0.6422\n", + "3 1505 0.1048\n", + "4 1506 -0.7252" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "year {'@id': 'http://linked.earth/lipd/Eur-Stockholm.Leijonhufvud.2009.paleo1measurement1.PYTWVH672OU.year', 'archiveType': 'Documents', 'number': 2, 'description': 'Year AD', 'hasMaxValue': 1892.0, 'hasMeanValue': 1697.0, 'hasMedianValue': 1697.0, 'hasMinValue': 1502.0, 'variableName': 'year', 'resolution': {'@id': 'http://linked.earth/lipd/Eur-Stockholm.Leijonhufvud.2009.paleo1measurement1.PYTWVH672OU.year.Resolution', 'hasMaxValue': 1.0, 'hasMeanValue': 1.0, 'hasMedianValue': 1.0, 'hasMinValue': 1.0, 'units': 'yr AD'}, 'hasStandardVariable': 'year', 'units': 'yr AD', 'TSid': 'PYTWVH672OU', 'variableType': 'inferred', 'wDSPaleoUrl': 'https://www1.ncdc.noaa.gov/pub/data/paleo/pages2k/pages2k-temperature-v2-2017/data-version-2.0.0/Eur-Stockholm.Leijonhufvud.2009.txt', 'measurementTableMD5': 'a26e3a157e304c236bf91e17f8f7751b', 'dataType': 'float', 'measurementTableName': 'measurementTable1', 'paleoDataTableName': 'measTable', 'inferredVariableType': 'Year'}\n", + "temperature {'@id': 'http://linked.earth/lipd/Eur-Stockholm.Leijonhufvud.2009.paleo1measurement1.Eur_006.temperature', 'calibration': [{'@id': 'http://linked.earth/lipd/Eur-Stockholm.Leijonhufvud.2009.paleo1measurement1.Eur_006.temperature.Calibration', 'uncertainty': 'Eur-Stockholm.Leijonhufvud.2009.paleo1measurement1.Eur_006.temperature.Calibration.Uncertainty'}], 'interpretation': [{'@id': 'http://linked.earth/lipd/Eur-Stockholm.Leijonhufvud.2009.paleo1measurement1.Eur_006.temperature.Interpretation1', 'basis': 'correlation with local meteorological correlation', 'direction': 'positive', 'scope': 'climate', 'seasonality': 'Winter', 'variable': 'temperature', 'variableDetail': 'air@surface'}], 'archiveType': 'Documents', 'number': 1, 'hasMaxValue': 4.9385, 'hasMeanValue': -0.7404, 'hasMedianValue': -0.8524, 'hasMinValue': -6.3995, 'variableName': 'temperature', 'notes': 'By refining dendroclimatological methods the time-series were composited to a mean series and calibrated (1756_1841; r2 = 66%) against Stockholm January_April temperatures.', 'inCompilationBeta': {'@id': 'http://linked.earth/lipd/Pages2kTemperature.66deb3854dc93', 'compilationName': 'Pages2kTemperature', 'compilationVersion': '2_1_1'}, 'proxy': 'historical', 'resolution': {'@id': 'http://linked.earth/lipd/Eur-Stockholm.Leijonhufvud.2009.paleo1measurement1.Eur_006.temperature.Resolution', 'hasMaxValue': 1.0, 'hasMeanValue': 1.0, 'hasMedianValue': 1.0, 'hasMinValue': 1.0, 'units': 'yr AD'}, 'hasStandardVariable': 'temperature', 'units': 'degC', 'TSid': 'Eur_006', 'variableType': 'inferred', 'wDSPaleoUrl': 'https://www1.ncdc.noaa.gov/pub/data/paleo/pages2k/pages2k-temperature-v2-2017/data-version-2.0.0/Eur-Stockholm.Leijonhufvud.2009.txt', 'qCCertification': 'JPW', 'measurementTableMD5': 'a26e3a157e304c236bf91e17f8f7751b', 'measurementTableName': 'measurementTable1', 'inferredVariableType': 'Temperature', 'useInGlobalTemperatureAnalysis': True, 'pages2kID': 'Eur_019', 'paleoDataTableName': 'measTable'}\n", + "Missing Value: NaN\n", + "- year [yr AD]\n", + "- temperature [degC]\n" + ] + } + ], + "source": [ + "# Dataset is the Main OOP Class\n", + "from pylipd.classes.dataset import Dataset\n", + "\n", + "# LiPD is the LiPD parser/writer\n", + "from pylipd.lipd import LiPD\n", + "\n", + "# Load LiPD files as usual.\n", + "# - This loads the LiPD data into the internal RDF graph\n", + "path = '../data/Pages2k'\n", + "D = LiPD()\n", + "D.load_from_dir(path)\n", + "\n", + "# Convert the LiPD datasets to the PyLiPD OOP \"Dataset\" class. \n", + "# - This allows to modify the datasets via OOP calls in memory\n", + "# - To write the LiPD back, we have to call the save function\n", + "datasets = D.get_datasets()\n", + "\n", + "for ds in datasets:\n", + " # Now we can call individual function on the dataset to get its details\n", + " print(\"\\n\")\n", + " print(ds.getName())\n", + " print(\"=========================\")\n", + " for funding in ds.getFundings():\n", + " if funding.getGrants():\n", + " print(f\"Funding: {funding.getGrants()}\")\n", + " \n", + " for pub in ds.getPublications():\n", + " print(f\"Publication: {pub.getTitle()} by {list(map(lambda x: x.getName(), pub.getAuthors()))}\")\n", + "\n", + " for pd in ds.getPaleoData():\n", + " for table in pd.getMeasurementTables():\n", + " print(f\"- Paleo Table: {table.getFileName()}\")\n", + " \n", + " # Can get the dataframe for the whole table\n", + " df = table.getDataFrame(use_standard_names=True)\n", + " display(df.head())\n", + "\n", + " # The returned dataframe also contains the attributes for the variables\n", + " for varname in df.attrs:\n", + " vardata = df.attrs[varname]\n", + " print(varname, vardata)\n", + "\n", + " # Can also get the variables one by one and make calls to their class functions\n", + " print(f\"Missing Value: {table.getMissingValue()}\")\n", + " for var in table.getVariables():\n", + " if var.getUnits():\n", + " print(f\"- {var.getName()} [{var.getUnits().getLabel()}]\")\n", + " else:\n", + " print(f\"- {var.getName()}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Editing an existing LiPD file" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loading 1 LiPD files\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 1/1 [00:00<00:00, 1.73it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded..\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " site ukprime37 age depth\n", + "0 -0.909061 -0.860013 0.500737 1.800685\n", + "1 0.236617 0.564153 -0.442693 0.713587\n", + "2 -1.355983 -0.203197 0.260957 -1.764060\n", + "3 0.465364 0.475315 -0.555199 -1.188082\n", + "4 0.182585 2.142508 -0.695586 0.322117" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Dataset is the Main OOP Class\n", + "from pylipd.classes.dataset import Dataset\n", + "\n", + "# LiPD is the LiPD parser/writer\n", + "from pylipd.classes.datatable import DataTable\n", + "from pylipd.lipd import LiPD\n", + "\n", + "# Load LiPD files as usual.\n", + "# - This loads the LiPD data into the internal RDF graph\n", + "path = '../data/ODP846.Lawrence.2006.lpd'\n", + "D = LiPD()\n", + "D.load(path)\n", + "\n", + "# Convert the LiPD datasets to the PyLiPD OOP \"Dataset\" class. \n", + "# - This allows to modify the datasets via OOP calls in memory\n", + "# - To write the LiPD back, we have to call the save function\n", + "datasets = D.get_datasets()\n", + "\n", + "ds = datasets[0]\n", + "pdata = ds.getPaleoData()[0]\n", + "\n", + "# ********************************************\n", + "# We will add a table to the paleoData here\n", + "# ********************************************\n", + "attrs = {\n", + " \"site\": {\n", + " 'number': 1, \n", + " 'variableName': 'site/hole', \n", + " 'hasStandardVariable': 'site', \n", + " 'units': 'unitless', \n", + " 'TSid': 'PYTJ3PSH0LT', \n", + " 'variableType': 'measured', \n", + " 'takenAtDepth': 'depth'\n", + " },\n", + " \"ukprime37\": {\n", + " 'number': 2,\n", + " 'interpretation': [\n", + " {\n", + " 'rank': 1.0, \n", + " 'scope': 'Climate', \n", + " 'variable': 'temperature', \n", + " 'variableDetail': 'sea surface', \n", + " 'direction': 'positive'\n", + " }\n", + " ], \n", + " 'variableName': 'ukprime37', \n", + " 'resolution': {\n", + " 'hasMaxValue': 10.856999999999971, \n", + " 'hasMeanValue': 2.3355875057418465, \n", + " 'hasMedianValue': 2.211999999999989, \n", + " 'hasMinValue': 0.06999999999993634\n", + " }, \n", + " 'units': 'unitless', \n", + " 'TSid': 'PYTM9N6HCQM', \n", + " 'variableType': 'measured', \n", + " 'takenAtDepth': 'depth', \n", + " 'proxyObservationType': 'Uk37Prime'\n", + " },\n", + " \"age\": {\n", + " 'interpretation': [\n", + " {\n", + " 'rank': 1.0, \n", + " 'scope': 'Age', \n", + " 'variableDetail': 'calendar', \n", + " 'direction': 'positive'\n", + " }\n", + " ], \n", + " 'number': 3, \n", + " 'variableName': 'age', \n", + " 'hasStandardVariable': 'age', \n", + " 'TSid': 'PYTXJB98403', \n", + " 'variableType': 'inferred', \n", + " 'takenAtDepth': 'depth', \n", + " 'inferredVariableType': 'Age'\n", + " },\n", + " \"depth\": {\n", + " 'number': 4, \n", + " 'variableName': 'depth', \n", + " 'notes': 'depth rmcd', \n", + " 'resolution': {\n", + " 'hasMaxValue': 10.856999999999971, \n", + " 'hasMeanValue': 2.3355875057418465, \n", + " 'hasMedianValue': 2.211999999999989, \n", + " 'hasMinValue': 0.06999999999993634\n", + " }, \n", + " 'hasStandardVariable': 'depth', \n", + " 'units': 'm', \n", + " 'TSid': 'PYTKRFVW61B', \n", + " 'variableType': 'measured'\n", + " }\n", + "}\n", + "\n", + "# Create a random dataframe\n", + "import pandas as pd\n", + "import numpy as np\n", + "df = pd.DataFrame(np.random.randn(100, 4), columns=attrs.keys())\n", + "df.attrs = attrs\n", + "display(df.head())\n", + "\n", + "newtable = DataTable()\n", + "newtable.setFileName(\"paleo0measurement2.csv\")\n", + "newtable.setMissingValue(\"NaN\")\n", + "newtable.setDataFrame(df)\n", + "\n", + "pdata.addMeasurementTable(newtable)\n", + "\n", + "# Create a lipd from the Dataset ds\n", + "savelipd = LiPD()\n", + "savelipd.load_datasets([ds])\n", + "savelipd.create_lipd(ds.getName(), \"./ODP846.Lawrence.2006.updated.lpd\")\n", + "pass\n" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loading 1 LiPD files\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 1/1 [00:00<00:00, 1.80it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded..\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n" + ] + } + ], + "source": [ + "# Try to load the New LiPD File, and check if everything is ok\n", + "D = LiPD()\n", + "D.load(\"./ODP846.Lawrence.2006.updated.lpd\")" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loading 1 LiPD files\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 1/1 [00:00<00:00, 1.81it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded..\n", + "\n", + "\n", + "ODP846.Lawrence.2006\n", + "=========================\n", + "- Paleo Table: paleo0measurement1.csv\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/html": [ + "
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u. peregrina d13cc. wuellerstorfi d13cc. wuellerstorfi d18ou. peregrina d18odepth compdepth crdeptheventsampleID
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'http://linked.earth/lipd/paleo0measurement1.PYTYDOYFVYD.u._peregrina_d18o.Resolution'}, 'TSid': 'PYTYDOYFVYD', 'variableType': 'measured', 'takenAtDepth': 'depth', 'sensorGenus': 'Uvigerina', 'sensorSpecies': 'peregrina', 'proxyObservationType': 'd18O'}\n", + "depth comp {'@id': 'http://linked.earth/lipd/paleo0measurement1.PYTPQ0FJO1S.depth_comp', 'number': 4, 'hasMaxValue': 196.93, 'hasMeanValue': 97.84506844281121, 'hasMedianValue': 96.359, 'hasMinValue': 0.12, 'variableName': 'depth comp', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89cee6', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement1.PYTPQ0FJO1S.depth_comp.Resolution'}, 'TSid': 'PYTPQ0FJO1S', 'variableType': 'measured', 'takenAtDepth': 'depth'}\n", + "depth cr {'@id': 'http://linked.earth/lipd/paleo0measurement1.PYT68HYMYHH.depth_cr', 'number': 5, 'hasMaxValue': 5089.802, 'hasMeanValue': 2234.3875783187873, 'hasMedianValue': 2507.177, 'hasMinValue': 0.12, 'variableName': 'depth cr', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89d077', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement1.PYT68HYMYHH.depth_cr.Resolution'}, 'TSid': 'PYT68HYMYHH', 'variableType': 'measured', 'takenAtDepth': 'depth'}\n", + "depth {'@id': 'http://linked.earth/lipd/paleo0measurement1.PYTS96EE0CB.depth', 'number': 2, 'hasMaxValue': 61.17, 'hasMeanValue': 18.667220946256318, 'hasMedianValue': 18.0, 'hasMinValue': 0.12, 'variableName': 'depth', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89cd11', 'hasStandardVariable': 'depth', 'units': 'm', 'TSid': 'PYTS96EE0CB', 'variableType': 'measured'}\n", + "event {'@id': 'http://linked.earth/lipd/paleo0measurement1.PYTE5EC1JBW.event', 'number': 1, 'hasMaxValue': 846.0, 'hasMeanValue': 606.9646302250804, 'hasMedianValue': 846.0, 'hasMinValue': 138.0, 'variableName': 'event', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89cc7a', 'hasStandardVariable': 'event', 'units': 'unitless', 'TSid': 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depthsiteageukprime37
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c37 totalsectionagetemp mullerdeleteMedepthsitetemp prahlukprime37
02.371H-15.22823.54515-160.16846B23.00.821
12.101H-18.94723.64825-260.26846B23.10.824
21.871H-111.96623.75235-360.36846B23.20.828
32.741H-114.42722.51545-460.46846B22.00.787
43.751H-116.50222.20655-560.56846B21.70.777
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" + ], + "text/plain": [ + " c37 total section age temp muller deleteMe depth site temp prahl \\\n", + "0 2.37 1H-1 5.228 23.545 15-16 0.16 846B 23.0 \n", + "1 2.10 1H-1 8.947 23.648 25-26 0.26 846B 23.1 \n", + "2 1.87 1H-1 11.966 23.752 35-36 0.36 846B 23.2 \n", + "3 2.74 1H-1 14.427 22.515 45-46 0.46 846B 22.0 \n", + "4 3.75 1H-1 16.502 22.206 55-56 0.56 846B 21.7 \n", + "\n", + " ukprime37 \n", + "0 0.821 \n", + "1 0.824 \n", + "2 0.828 \n", + "3 0.787 \n", + "4 0.777 " + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "c37 total {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT10H23U2E.c37_total', 'number': 7, 'hasMaxValue': 78.92, 'hasMeanValue': 9.900032139577593, 'hasMedianValue': 7.075, 'hasMinValue': 1.095, 'variableName': 'c37 total', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89dd80', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT10H23U2E.c37_total.Resolution', 'hasMaxValue': 10.856999999999971, 'hasMeanValue': 2.3355875057418465, 'hasMedianValue': 2.211999999999989, 'hasMinValue': 0.06999999999993634}, 'TSid': 'PYT10H23U2E', 'variableType': 'measured', 'proxyObservationType': 'Alkenone', 'takenAtDepth': 'depth'}\n", + "section {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT8BDSRW3H.section', 'number': 2, 'hasMaxValue': 19.0, 'hasMeanValue': 9.46694214876033, 'hasMedianValue': 18.0, 'hasMinValue': 1.0, 'variableName': 'section', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89d6b0', 'hasStandardVariable': 'section', 'units': 'unitless', 'TSid': 'PYT8BDSRW3H', 'variableType': 'measured', 'takenAtDepth': 'depth'}\n", + "age {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTXJB98403.age', 'interpretation': [{'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTXJB98403.age.Interpretation1', 'scope': 'Age', 'variableDetail': 'calendar', 'interpdirection': 'positive'}], 'number': 5, 'hasMaxValue': 5089.802, 'hasMeanValue': 2533.4160550964184, 'hasMedianValue': 2507.067, 'hasMinValue': 5.228, 'variableName': 'age', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTXJB98403.age.Resolution'}, 'hasStandardVariable': 'age', 'TSid': 'PYTXJB98403', 'variableType': 'inferred', 'inferredVariableType': 'Age', 'takenAtDepth': 'depth'}\n", + "temp muller {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTGO6NV72Y.temp_muller', 'interpretation': [{'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTGO6NV72Y.temp_muller.Interpretation1', 'scope': 'Climate', 'variable': 'temperature', 'variableDetail': 'sea surface', 'interpdirection': 'positive'}], 'number': 9, 'hasMaxValue': 28.388, 'hasMeanValue': 25.105362258953168, 'hasMedianValue': 25.297, 'hasMinValue': 20.558, 'variableName': 'temp muller', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTGO6NV72Y.temp_muller.Resolution', 'hasMaxValue': 10.856999999999971, 'hasMeanValue': 2.3355875057418465, 'hasMedianValue': 2.211999999999989, 'hasMinValue': 0.06999999999993634}, 'TSid': 'PYTGO6NV72Y', 'variableType': 'inferred', 'takenAtDepth': 'depth', 'inferredVariableType': 'Sea Surface Temperature'}\n", + "deleteMe {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT2ZB6MLZ9.deleteMe', 'number': 3, 'hasMaxValue': 150.0, 'hasMeanValue': 72.7043035631652, 'hasMedianValue': 3.0, 'hasMinValue': 3.0, 'variableName': 'deleteMe', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89d74e', 'hasStandardVariable': 'deleteMe', 'units': 'cm', 'TSid': 'PYT2ZB6MLZ9', 'variableType': 'measured', 'takenAtDepth': 'depth'}\n", + "depth {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTKRFVW61B.depth', 'number': 4, 'hasMaxValue': 196.93, 'hasMeanValue': 97.99932323232323, 'hasMedianValue': 96.3545, 'hasMinValue': 0.16, 'variableName': 'depth', 'notes': 'depth rmcd', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89d8e9', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTKRFVW61B.depth.Resolution', 'hasMaxValue': 10.856999999999971, 'hasMeanValue': 2.3355875057418465, 'hasMedianValue': 2.211999999999989, 'hasMinValue': 0.06999999999993634}, 'hasStandardVariable': 'depth', 'units': 'm', 'TSid': 'PYTKRFVW61B', 'variableType': 'measured'}\n", + "site {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTJ3PSH0LT.site', 'number': 1, 'hasMaxValue': 846.0, 'hasMeanValue': 846.0, 'hasMedianValue': 846.0, 'hasMinValue': 846.0, 'variableName': 'site', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89d620', 'hasStandardVariable': 'site', 'units': 'unitless', 'TSid': 'PYTJ3PSH0LT', 'variableType': 'measured', 'takenAtDepth': 'depth'}\n", + "temp prahl {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT95DVDUU3.temp_prahl', 'calibration': [{'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT95DVDUU3.temp_prahl.Calibration', 'equation': 'UK37 = 0.034T + 0.039', 'reference': 'Publication.10.1016/0016-7037(88)90132-9'}], 'interpretation': [{'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT95DVDUU3.temp_prahl.Interpretation1', 'scope': 'Climate', 'variable': 'temperature', 'variableDetail': 'sea surface', 'interpdirection': 'positive'}], 'number': 6, 'hasMaxValue': 27.7, 'hasMeanValue': 24.514049586776864, 'hasMedianValue': 24.7, 'hasMinValue': 20.1, 'variableName': 'temp prahl', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYT95DVDUU3.temp_prahl.Resolution', 'hasMaxValue': 10.856999999999971, 'hasMeanValue': 2.3355875057418465, 'hasMedianValue': 2.211999999999989, 'hasMinValue': 0.06999999999993634}, 'TSid': 'PYT95DVDUU3', 'variableType': 'inferred', 'inferredVariableType': 'Sea Surface Temperature', 'takenAtDepth': 'depth'}\n", + "ukprime37 {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTM9N6HCQM.ukprime37', 'interpretation': [{'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTM9N6HCQM.ukprime37.Interpretation1', 'scope': 'Climate', 'variable': 'temperature', 'variableDetail': 'sea surface', 'interpdirection': 'positive'}], 'number': 8, 'hasMaxValue': 0.981, 'hasMeanValue': 0.872473829201102, 'hasMedianValue': 0.879, 'hasMinValue': 0.722, 'variableName': 'ukprime37', 'physicalSample': 'http://linked.earth/lipd/Unknown.66decdd89ded8', 'resolution': {'@id': 'http://linked.earth/lipd/paleo0measurement0.PYTM9N6HCQM.ukprime37.Resolution', 'hasMaxValue': 10.856999999999971, 'hasMeanValue': 2.3355875057418465, 'hasMedianValue': 2.211999999999989, 'hasMinValue': 0.06999999999993634}, 'units': 'unitless', 'TSid': 'PYTM9N6HCQM', 'variableType': 'measured', 'takenAtDepth': 'depth', 'proxyObservationType': 'Uk37Prime'}\n", + "Missing Value: nan\n", + "- c37 total\n", + "- section [unitless]\n", + "- age\n", + "- temp muller\n", + "- deleteMe [cm]\n", + "- depth [m]\n", + "- site [unitless]\n", + "- temp prahl\n", + "- ukprime37 [unitless]\n" + ] + } + ], + "source": [ + "# Try to load the New LiPD File, and check if everything is ok\n", + "D = LiPD()\n", + "D.load(\"./ODP846.Lawrence.2006.updated.lpd\")\n", + "datasets = D.get_datasets()\n", + "\n", + "# Browse the dataset as usual\n", + "for ds in datasets:\n", + " print(\"\\n\")\n", + " print(ds.getName())\n", + " print(\"=========================\")\n", + " for pdata in ds.getPaleoData():\n", + " for table in pdata.getMeasurementTables():\n", + " print(f\"- Paleo Table: {table.getFileName()}\")\n", + " \n", + " # Can get the dataframe for the whole table\n", + " df = table.getDataFrame(use_standard_names=True)\n", + " display(df.head())\n", + "\n", + " # The returned dataframe also contains the attributes for the variables\n", + " for varname in df.attrs:\n", + " vardata = df.attrs[varname]\n", + " print(varname, vardata)\n", + "\n", + " # Can also get the variables one by one and make calls to their class functions\n", + " print(f\"Missing Value: {table.getMissingValue()}\")\n", + " for var in table.getVariables():\n", + " if var.getUnits():\n", + " print(f\"- {var.getName()} [{var.getUnits().getLabel()}]\")\n", + " else:\n", + " print(f\"- {var.getName()}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Creating a new LiPD file" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "pyleo", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.13" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/pylipd/globals/schema.py b/pylipd/globals/schema.py index 68d0269..05ba6b4 100644 --- a/pylipd/globals/schema.py +++ b/pylipd/globals/schema.py @@ -550,6 +550,7 @@ '@toJson_pre': [ '_set_units_label', '_set_seasonality_labels', + '_set_interpretation_variable_label' ], 'variable': { 'name': 'hasVariable', diff --git a/pylipd/utils/json_to_rdf.py b/pylipd/utils/json_to_rdf.py index 920a419..f0cea36 100644 --- a/pylipd/utils/json_to_rdf.py +++ b/pylipd/utils/json_to_rdf.py @@ -15,8 +15,10 @@ def _load_triple_into_graph(self, subject, prop, value): if val["@type"] == "uri": valitem = URIRef(val["@id"]) elif val["@type"] == "literal": - dtype = val["@datatype"] + dtype:str = val["@datatype"] if dtype: + if type(val["@value"]) == str: + dtype="http://www.w3.org/2001/XMLSchema#string" valitem = Literal(val["@value"], datatype=URIRef(dtype)) else: valitem = Literal(val["@value"]) diff --git a/pylipd/utils/rdf_to_lipd.py b/pylipd/utils/rdf_to_lipd.py index 1179b4f..88470f3 100644 --- a/pylipd/utils/rdf_to_lipd.py +++ b/pylipd/utils/rdf_to_lipd.py @@ -560,7 +560,17 @@ def _set_proxy_general_label(self, var, parent = None) : del var["hasProxyGeneral"] return var - + def _set_interpretation_variable_label(self, interp, parent = None) : + if "hasVariable" in interp : + if "@id" in interp["hasVariable"]: + id = interp["hasVariable"]["@id"] + if id in RSYNONYMS: + interp["variable"] = RSYNONYMS[id] + else: + interp["variable"] = interp["hasVariable"]["label"] + del interp["hasVariable"] + return interp + def _set_seasonality_labels(self, interp, parent = None) : convs = { "hasSeasonality": "seasonality",