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gubi/_parser.php

Last active November 1, 2018 10:58
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PHP script that extract data from the `resultAgrovoc_filled_20181029.xlsx` file
Raw
_parser.php
<?php
header("Content-type: text/plain");
require 'vendor/autoload.php';
use PhpOffice\PhpSpreadsheet\Spreadsheet;
use PhpOffice\PhpSpreadsheet\IOFactory;
use Monolog\Logger;
use Monolog\Handler\StreamHandler;
define("FILENAME", "resultAgrovoc_filled_20181029.xlsx");
$spreadsheet = new Spreadsheet();
$reader = new \PhpOffice\PhpSpreadsheet\Reader\Xlsx();
$spreadsheet = $reader->load(FILENAME);
$worksheet = $spreadsheet->getActiveSheet();
$json = [];
$json[FILENAME] = [];
function url_open($url) {
$logger = new Logger("agrovoc-indexing");
$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, $url);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
$output = curl_exec($ch);
if(curl_getinfo($ch, CURLINFO_HTTP_CODE) !== 200) {
$logger->pushHandler(new StreamHandler(getcwd() . "/curl.log", Logger::ERROR));
$logger->error($output);
return json_decode($output);
}
// $logger->pushHandler(new StreamHandler(getcwd() . "/curl.log", Logger::INFO));
// $logger->info($output->data);
return json_decode($output)->data;
curl_close($ch);
}
function parse_xml($json, $row, $worksheet, $visible) {
$visible_label = ($visible) ? "visible" : "not visible";
$rownr = 0;
$highestRow = $worksheet->getHighestRow(); // e.g. 10
$highestColumn = $worksheet->getHighestColumn(); // e.g 'F'
$highestColumnIndex = \PhpOffice\PhpSpreadsheet\Cell\Coordinate::columnIndexFromString($highestColumn); // e.g. 5
for($col = 1; $col <= $highestColumnIndex; $col++) {
// $lastCellAddress = $worksheet->getCellByColumnAndRow($$col, 1)->getCoordinate();
// The first row is used for labels
$title = $worksheet->getCellByColumnAndRow($col, 1)->getValue();
$value = $worksheet->getCellByColumnAndRow($col, $row->getRowIndex())->getValue();
if($row->getRowIndex() == 1) { // ---------------------------------> "_labels" section
$column_name = $worksheet->getCellByColumnAndRow($col, 1)->getCoordinate();
// Split keywords in sub-labels
if(strpos($title, "__") !== false) {
$keywords = explode("__", $title);
$json[$visible_label]["_labels"]["row " . $row->getRowIndex()]["_keywords"][$column_name] = $keywords[1];
} else {
$json[$visible_label]["_labels"]["row " . $row->getRowIndex()][$column_name] = $value;
}
} elseif($row->getRowIndex() > 1) { // ----------------------------> "contents" section
// $visible_rows = [];
// Split keywords in sub-labels
if(strpos($title, "__") !== false) {
$keywords = explode("__", $title);
$json[$visible_label]["contents"]["row " . $row->getRowIndex()]["_keywords"][$keywords[1]] = $value;
} else {
$json[$visible_label]["contents"]["row " . $row->getRowIndex()][$title] = $value;
}
if($title == "id") {
$doi = substr(parse_url($value)["path"], 1);
$dataset_api_url = "https://dataverse.harvard.edu/api/datasets/:persistentId?persistentId=doi:" . $doi;
$json[$visible_label]["contents"]["row " . $row->getRowIndex()]["dataset"] = parse_url($value);
if($visible) {
$json[$visible_label]["contents"]["row " . $rownr]["dataset"]["doi"] = $doi;
$json[$visible_label]["contents"]["row " . $rownr]["dataset"]["dataset_api_url"] = $dataset_api_url;
// $json[$visible_label]["contents"]["row " . $rownr]["dataset"]["data"] = json_decode(url_open($dataset_api_url), 1)["data"];
// LOG
// $logger->warning(escapeshellcmd(url_open($dataset_api_url)));
// print $dataset_api_url ."\n";
$json[$visible_label]["contents"]["row " . $rownr]["dataset"]["data"] = url_open($dataset_api_url);
}
}
}
}
$rownr++;
// print_r($json);
return $json;
}
foreach($spreadsheet->getActiveSheet()->getRowIterator() as $row) {
// print $spreadsheet->getActiveSheet()->getRowDimension($row->getRowIndex())->getVisible();
if($spreadsheet->getActiveSheet()->getRowDimension($row->getRowIndex())->getVisible()) {
// print $row->getRowIndex() . "\n";
// exit();
$json[FILENAME] = parse_xml($json[FILENAME], $row, $worksheet, true);
} else {
$json[FILENAME] = parse_xml($json[FILENAME], $row, $worksheet, false);
}
}
print_r($json);
file_put_contents(getcwd() . "/output.txt", print_r($json, true));
file_put_contents(getcwd() . "/output.json", json_encode($json));
// header("Content-type: application/json");
// print_r(json_encode($json));
?>
Raw
output.json
{
"resultAgrovoc_filled_20181029.xlsx": {
"visible": {
"_labels": {
"row 1": {
"A1": null,
"B1": "id",
"C1": "name",
"_keywords": {
"D1": "value",
"E1": "agrovoc label",
"G1": "uri",
"H1": "score"
},
"F1": "Vocabulary"
}
},
"contents": {
"row 24": {
"": 32,
"id": "http://dx.doi.org/10.7910/DVN/27480",
"dataset": {
"scheme": "http",
"host": "dx.doi.org",
"path": "/10.7910/DVN/27480"
},
"name": "GPS inventory of timber trees from which local communities gather food resources in Cameroon, Gabon and the DRC.",
"_keywords": {
"value": "baillonella toxisperma",
"agrovoc label": "BAILLONELLA TOXISPERMA",
"uri": "http://purl.obolibrary.org/obo/NCBITaxon_568231",
"score": 0.5
},
"Vocabulary": "NCBI"
},
"row 0": {
"dataset": {
"doi": "10.7910/DVN/UHULV3",
"dataset_api_url": "https://dataverse.harvard.edu/api/datasets/:persistentId?persistentId=doi:10.7910/DVN/UHULV3",
"data": {
"id": 3092844,
"identifier": "DVN/UHULV3",
"persistentUrl": "https://doi.org/10.7910/DVN/UHULV3",
"protocol": "doi",
"authority": "10.7910",
"publisher": "Harvard Dataverse",
"publicationDate": "2018-01-17",
"storageIdentifier": "file",
"latestVersion": {
"id": 131598,
"storageIdentifier": "file",
"versionNumber": 1,
"versionMinorNumber": 0,
"versionState": "RELEASED",
"productionDate": "Production Date",
"UNF": "UNF:6:dv7tWHrPFs1CfcXjTkGxcg==",
"lastUpdateTime": "2018-01-17T12:54:00Z",
"releaseTime": "2018-01-17T12:54:00Z",
"createTime": "2017-12-22T14:01:04Z",
"license": "NONE",
"termsOfUse": "<a rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"><img alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by/4.0/88x31.png\" /></a><br />This work is licensed under a <a rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\">Creative Commons Attribution 4.0 International License</a>.",
"citationRequirements": "Kidane, Y.G.; Mancini, C. ; Mengistu, D.K; Frascaroli, E.; Fadda, C.; Pè, M.E.; Dell’Acqua, M. ; Hailemariam, B.N., 2018, \"Genome wide association study to identify the genetic base of smallholder farmer preferences of durum wheat traits\", doi:10.7910/DVN/UHULV3 ",
"disclaimer": "Bioversity International adheres to the principle of unrestricted public access to its own final research outputs and will make such outputs freely available. These datasets are provided \"as is\" and in no event shall Bioversity International be liable for any damages resulting from use of the data. While great effort was taken to obtain high quality data, the accuracy or reliability of the data is not guaranteed or warranted in any way. Bioversity International encourages the use of these datasets, but emphasizes that many of them contain \"raw data\" files. When applicable, all information which would allow individuals to be identified has been deleted from the files. For some of the datasets, the user will need to take care in handling missing observations, outlier values and violations of logical consistency. ",
"metadataBlocks": {
"citation": {
"displayName": "Citation Metadata",
"fields": [
{
"typeName": "title",
"multiple": false,
"typeClass": "primitive",
"value": "Genome wide association study to identify the genetic base of smallholder farmer preferences of durum wheat traits"
},
{
"typeName": "author",
"multiple": true,
"typeClass": "compound",
"value": [
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Kidane, Y.G."
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Bioversity International"
}
},
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Mancini, C. "
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Scuola Superiore Sant'Anna, Pisa (Italy)"
}
},
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Mengistu, D.K"
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Mekelle University"
}
},
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Frascaroli, E."
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Univeristy of Bologna"
}
},
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Fadda, C."
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Bioversity International"
}
},
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Pè, M.E."
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Scuola Superiore Sant'Anna, Pisa (Italy)"
}
},
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Dell’Acqua, M. "
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Scuola Superiore Sant'Anna, Pisa (Italy)"
}
},
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Hailemariam, B.N."
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Scuola Superiore Sant'Anna, Pisa (Italy)"
}
}
]
},
{
"typeName": "datasetContact",
"multiple": true,
"typeClass": "compound",
"value": [
{
"datasetContactName": {
"typeName": "datasetContactName",
"multiple": false,
"typeClass": "primitive",
"value": "Yosef G. Kidane"
},
"datasetContactAffiliation": {
"typeName": "datasetContactAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Bioversity International"
},
"datasetContactEmail": {
"typeName": "datasetContactEmail",
"multiple": false,
"typeClass": "primitive",
"value": "[email protected]"
}
}
]
},
{
"typeName": "dsDescription",
"multiple": true,
"typeClass": "compound",
"value": [
{
"dsDescriptionValue": {
"typeName": "dsDescriptionValue",
"multiple": false,
"typeClass": "primitive",
"value": "The study was conducted during the 2012 wheat growing season in two locations in the Ethiopian highlands. The first location was in the Geregera area, in the village of Workaye, Meket district (Amhara region, 11◦40′N/38◦52′E, WGS84). The second location was in the Hagreselam district, in the village of Melfa (Tigray region, 13◦39′N/39◦10′E, WGS84). In each location, 30 smallholder farmers growing wheat were selected on a voluntary basis, but keeping a 50:50 gender representation Farmers were asked to list the traits they used to evaluate wheat varieties, hereafter termed farmer traits (FT), and these were ranked by importance. Technicians collected 10 metrics traits on these sites and farmers provided a score for their overall plot evaluation. The genetic material here analyzed is a diversity panel comprising 400 Ethiopian wheat accessions conserved ex situ at the Ethiopian Biodiversity Institute. DNA extraction for genotyping was conducted in Ethiopia, at the Mekelle University Molecular and Biotechnology Laboratory (Mekelle,Tigray). "
}
}
]
},
{
"typeName": "subject",
"multiple": true,
"typeClass": "controlledVocabulary",
"value": [
"Agricultural Sciences"
]
},
{
"typeName": "keyword",
"multiple": true,
"typeClass": "compound",
"value": [
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "HARD WHEAT"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "AGROVOC"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://aims.fao.org/aos/agrovoc/c_11456"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "COMMUNITY INVOLVMENT"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "AGROVOC"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": " http://aims.fao.org/aos/agrovoc/c_37559"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "CULTIVAR SELECTION"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "AGROVOC"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://aims.fao.org/aos/agrovoc/c_330719"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "GENOMES"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "AGROVOC"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": " http://aims.fao.org/aos/agrovoc/c_3224"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "PHENOTYPES"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "AGROVOC"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://aims.fao.org/aos/agrovoc/c_5776"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "EVALUATION"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "AGROVOC"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://aims.fao.org/aos/agrovoc/c_2736"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "QUANTITATIVE TRAIT LOCI"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "AGROVOC"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://aims.fao.org/aos/agrovoc/c_37974"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "BOOTING TIME"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000191"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "ANTHESIS TIME"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000121)"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "MATURITY TIME"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000022"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "GRAIN YIELD"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000013"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "PLANT HEIGHT"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000020"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "SPIKE LENGTH"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000056"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "GRAIN NUMBER PER SPIKE"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000038"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "ABOVE GROUND BIOMASS BY MATURITY"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000005"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "GRAIN WEIGHT"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0001213"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "TILLERING CAPACITY"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000189"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "AGRONOMIC SCORE"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "CROP ONTOLOGY"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "http://www.cropontology.org/rdf/CO_321:0000025"
}
},
{
"keywordValue": {
"typeName": "keywordValue",
"multiple": false,
"typeClass": "primitive",
"value": "TRITICUM TURGIDUM SUBSP. DURUM"
},
"keywordVocabulary": {
"typeName": "keywordVocabulary",
"multiple": false,
"typeClass": "primitive",
"value": "NCBI Taxonomy"
},
"keywordVocabularyURI": {
"typeName": "keywordVocabularyURI",
"multiple": false,
"typeClass": "primitive",
"value": "https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCBITaxon_4567"
}
}
]
},
{
"typeName": "publication",
"multiple": true,
"typeClass": "compound",
"value": [
{
"publicationCitation": {
"typeName": "publicationCitation",
"multiple": false,
"typeClass": "primitive",
"value": "Kidane, Y.G.; Mancini, C.; Mengistu, D.K.; Frascaroli, E.; Fadda, C.; Pe, M.E.; Dell'Acqua, M. (2017) Genome wide association study to identify the genetic base of smallholder farmer preferences of Durum wheat traits. Frontiers in Plant Science. Online first paper (17JUL17). ISSN: 1664-462X"
},
"publicationIDType": {
"typeName": "publicationIDType",
"multiple": false,
"typeClass": "controlledVocabulary",
"value": "handle"
},
"publicationIDNumber": {
"typeName": "publicationIDNumber",
"multiple": false,
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