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Merge pull request #1087 from dsenalik/oboimporter20201001
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Oboimporter20201001
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@laceysanderson
laceysanderson committed Oct 15, 2020
2 parents 7b8b725 + d5d420a commit 38fecb4
Showing 1 changed file with 37 additions and 27 deletions.
64 changes: 37 additions & 27 deletions tripal_chado/includes/TripalImporter/OBOImporter.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ class OBOImporter extends TripalImporter {


/**
* An array of used cvterm objects so that we don't have to lookup them
* An array of used cvterm objects so that we don't have to look them
* up repeatedly.
*/
private $used_terms = [];
Expand Down Expand Up @@ -248,8 +248,8 @@ class OBOImporter extends TripalImporter {
$form['obo_existing']['existing_instructions'] = [
'#type' => 'item',
'#markup' => t('The vocabularies listed in the select box below have been pre-populated
upon installation of Tripal or have been previously loaded. Select one to edit
its settings or submit for loading. You may reload any vocabulary that has
upon installation of Tripal or have been previously loaded. Select one to edit
its settings or submit for loading. You may reload any vocabulary that has
already been loaded to retrieve any new updates.'),
];

Expand Down Expand Up @@ -298,16 +298,16 @@ class OBOImporter extends TripalImporter {
$form['obo_existing']['uobo_name'] = [
'#type' => 'textfield',
'#title' => t('Vocabulary Name'),
'#description' => t('Please provide a name for this vocabulary. After upload, this name will appear in the drop down
'#description' => t('Please provide a name for this vocabulary. After upload, this name will appear in the drop down
list above for use again later.'),
'#default_value' => $uobo_name,
];

$form['obo_existing']['uobo_url'] = [
'#type' => 'textfield',
'#title' => t('Remote URL'),
'#description' => t('Please enter a URL for the online OBO file. The file will be downloaded and parsed.
(e.g. http://www.obofoundry.org/ro/ro.obo)'),
'#description' => t('Please enter a URL for the online OBO file. The file will be downloaded and parsed.
(e.g. https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo)'),
'#default_value' => $uobo_url,
];

Expand All @@ -318,8 +318,8 @@ class OBOImporter extends TripalImporter {
definition file. If entering a path relative to
the Drupal installation you may use a relative path that excludes the
Drupal installation directory (e.g. sites/default/files/xyz.obo). Note
that Drupal relative paths have no preceding slash.
Otherwise, please provide the full path on the filesystem. The path
that Drupal relative paths have no preceeding slash.
Otherwise, please provide the full path on the filesystem. The path
must be accessible to the web server on which this Drupal instance is running.'),
'#default_value' => $uobo_file,
];
Expand All @@ -338,24 +338,24 @@ class OBOImporter extends TripalImporter {
];

$form['obo_new']['path_instructions'] = [
'#value' => t('Provide the name and path for the OBO file. If the vocabulary OBO file
'#value' => t('Provide the name and path for the OBO file. If the vocabulary OBO file
is stored local to the server provide a file name. If the vocabulary is stored remotely,
provide a URL. Only provide a URL or a local file, not both.'),
provide a URL. Only provide a URL or a local file, not both.'),
];

$form['obo_new']['obo_name'] = [
'#type' => 'textfield',
'#title' => t('New Vocabulary Name'),
'#description' => t('Please provide a name for this vocabulary. After upload, this name will appear in the drop down
list above for use again later. Additionally, if a default namespace is not provided in the OBO
header this name will be used as the default_namespace.'),
'#description' => t('Please provide a name for this vocabulary. After upload, this name will appear in the drop down
list above for use again later. Additionally, if a default namespace is not provided in the OBO
header this name will be used as the default_namespace.'),
];

$form['obo_new']['obo_url'] = [
'#type' => 'textfield',
'#title' => t('Remote URL'),
'#description' => t('Please enter a URL for the online OBO file. The file will be downloaded and parsed.
(e.g. http://www.obofoundry.org/ro/ro.obo)'),
(e.g. https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo)'),
];

$form['obo_new']['obo_file'] = [
Expand All @@ -365,7 +365,7 @@ class OBOImporter extends TripalImporter {
definition file. If entering a path relative to
the Drupal installation you may use a relative path that excludes the
Drupal installation directory (e.g. sites/default/files/xyz.obo). Note
that Drupal relative paths have no preceding slash.
that Drupal relative paths have no preceeding slash.
Otherwise, please provide the full path on the filesystem. The path
must be accessible to the web server on which this Drupal instance is running.'),
];
Expand Down Expand Up @@ -595,7 +595,7 @@ class OBOImporter extends TripalImporter {
tripal_populate_mview($mview_id);

// Update the cvtermpath table for each newly added CV.
$this->logMessage("Updating cvtermpath table. This may take a while...");
$this->logMessage("Updating cvtermpath table. This may take a while...");
foreach ($this->obo_namespaces as $namespace => $cv_id) {
$this->logMessage("- Loading paths for vocabulary: @vocab", ['@vocab' => $namespace]);
chado_update_cvtermpath($cv_id, $this->job);
Expand All @@ -605,7 +605,7 @@ class OBOImporter extends TripalImporter {
/**
* A wrapper function for importing the user specified OBO file into Chado by
* specifying the obo_id of the OBO. It requires that the file be in OBO v1.2
* compatible format. This function is typically executed via the Tripal
* compatible format. This function is typically executed via the Tripal
* jobs
* management after a user submits a job via the Load Ontologies form.
*
Expand Down Expand Up @@ -653,7 +653,7 @@ class OBOImporter extends TripalImporter {
/**
* A wrapper function for importing the user specified OBO file into Chado by
* specifying the filename and path of the OBO. It requires that the file be
* in OBO v1.2 compatible format. This function is typically executed via
* in OBO v1.2 compatible format. This function is typically executed via
* the Tripal jobs management after a user submits a job via the Load
* Ontologies form.
*
Expand All @@ -664,7 +664,7 @@ class OBOImporter extends TripalImporter {
* The path on the file system where the ontology can be found
* @param $is_new
* Set to TRUE if this is a new ontology that does not yet exist in the
* tripal_cv_obo table. If TRUE the OBO will be added to the table.
* tripal_cv_obo table. If TRUE the OBO will be added to the table.
*
* @ingroup tripal_obo_loader
*/
Expand Down Expand Up @@ -888,6 +888,17 @@ class OBOImporter extends TripalImporter {
}
}

// If we still don't have a namespace defined, use the one from the form
// in the "New Vocabulary Name" field
if (!$namespace and array_key_exists('run_args', $this->arguments)
and array_key_exists('obo_name', $this->arguments['run_args'])) {
$namespace = $this->arguments['run_args']['obo_name'];
}
if (!$namespace and array_key_exists('run_args', $this->arguments)
and array_key_exists('uobo_name', $this->arguments['run_args'])) {
$namespace = $this->arguments['run_args']['uobo_name'];
}

// If we can't find the namespace or the short_name then bust.
if (!$namespace and !$short_name) {
throw new ErrorException('Cannot determine the namespace or ontology prefix from this OBO file. It is missing both the "default-namespace" and "ontology" headers.');
Expand All @@ -900,7 +911,6 @@ class OBOImporter extends TripalImporter {
$cv = $this->addCV($this->default_namespace);
$this->obo_namespaces[$namespace] = $cv->cv_id;


}

/**
Expand All @@ -916,13 +926,13 @@ class OBOImporter extends TripalImporter {
// Check if the EBI ontology search has this ontology:
try {
$results = $this->oboEbiLookup($ontology, 'ontology');
if (array_key_exists('default-namespace', $results['config']['annotations'])) {
if ($results and array_key_exists('config', $results) and array_key_exists('default-namespace', $results['config']['annotations'])) {
$namespace = $results['config']['annotations']['default-namespace'];
if (is_array($namespace)) {
$namespace = $namespace[0];
}
}
elseif (array_key_exists('namespace', $results['config'])) {
elseif ($results and array_key_exists('config', $results) and array_key_exists('namespace', $results['config'])) {
$namespace = $results['config']['namespace'];
}
// If we can't find the namespace at EBI, then just default to using the
Expand Down Expand Up @@ -983,7 +993,7 @@ class OBOImporter extends TripalImporter {
"Lookup Service to retrieve the information for this term. " .
"Please note, that vocabularies with many non-local terms " .
"require remote lookups and these lookups can dramatically " .
"decrease loading time. ",
"increase loading time. ",
['!vocab' => $this->default_namespace], TRIPAL_WARNING);
$this->ebi_warned = TRUE;

Expand Down Expand Up @@ -1016,15 +1026,15 @@ class OBOImporter extends TripalImporter {
$ontology_results = drupal_json_decode($response->data);
if ($ontology_results['error']) {

$this->logMessage(t('Cannot find the ontology via an EBI OLS lookup: !short_name. \n' .
$this->logMessage('Cannot find the ontology via an EBI OLS lookup: !short_name. \n' .
'We tried to access: !url' .
'EBI Reported: !message. ' .
'Consider finding the OBO file for this ontology and manually loading it first.',
[
'!message' => $ontology_results['message'],
'!short_name' => $short_name,
'!url' => $full_url,
]), TRIPAL_WARNING);
], TRIPAL_WARNING);
}
//What should happen with this stuff?
$base_iri = $ontology_results['config']['baseUris'][0];
Expand Down Expand Up @@ -1053,7 +1063,7 @@ class OBOImporter extends TripalImporter {
// If EBI sent an error message then throw an error.
if ($results['error']) {
$this->logMessage('Cannot find the term via an EBI OLS lookup: !term. ' .
'We tried to access: !url' .
'We tried to access: "!url" ' .
'EBI Reported: !message. Consider finding the OBO file for this ontology and manually loading it first.',
[
'!message' => $results['message'],
Expand Down Expand Up @@ -2079,7 +2089,7 @@ class OBOImporter extends TripalImporter {
// add the ID to the name to ensure it doesn't.
if (array_key_exists($stanza['name'][0], $this->term_names)) {
$new_name = $stanza['name'][0] . '(' . $stanza['id'][0] . ')';
$stanza['name'][0] = $stanza['name'][0];
$stanza['name'][0] = $new_name;
}

$this->cacheTermStanza($stanza, $type);
Expand Down

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