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Hyperlink DOIs against preferred resolver

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This commit is contained in:
Katrin Leinweber
2018-05-30 16:49:21 +01:00
parent 8fcc933244
commit f99f8667bc
10 changed files with 18 additions and 18 deletions
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client/galaxy/scripts/components/Citations.vue
+1 -1
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@@ -143,7 +143,7 @@ export default {
}
var doiUrl = "";
if (fields.doi) {
doiUrl = `http://dx.doi.org/${fields.doi}`;
doiUrl = `https://doi.org/${fields.doi}`;
ref += `[<a href="${doiUrl}" target="_blank">doi:${fields.doi}</a>]`;
}
var url = fields.url || doiUrl;
doc/source/admin/galaxy_options.rst
+3 -3
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@@ -834,7 +834,7 @@
:Description:
Citation related caching. Tool citations information maybe
fetched from external sources such as http://dx.doi.org/ by Galaxy
fetched from external sources such as https://doi.org/ by Galaxy
- the following parameters can be used to control the caching used
to store this information.
:Default: ``file``
@@ -847,7 +847,7 @@
:Description:
Citation related caching. Tool citations information maybe
fetched from external sources such as http://dx.doi.org/ by Galaxy
fetched from external sources such as https://doi.org/ by Galaxy
- the following parameters can be used to control the caching used
to store this information.
:Default: ``database/citations/data``
@@ -860,7 +860,7 @@
:Description:
Citation related caching. Tool citations information maybe
fetched from external sources such as http://dx.doi.org/ by Galaxy
fetched from external sources such as https://doi.org/ by Galaxy
- the following parameters can be used to control the caching used
to store this information.
:Default: ``database/citations/lock``
lib/galaxy/datatypes/test/example.iqtree
+2 -2
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@@ -12,14 +12,14 @@ To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
http://dx.doi.org/10.1038/nmeth.4285
https://doi.org/10.1038/nmeth.4285
To cite IQ-TREE please use:
Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh
(2015) IQ-TREE: A fast and effective stochastic algorithm for estimating
maximum likelihood phylogenies. Mol Biol Evol, 32:268-274.
http://dx.doi.org/10.1093/molbev/msu300
https://doi.org/10.1093/molbev/msu300
SEQUENCE ALIGNMENT
------------------
lib/galaxy/managers/citations.py
+1 -1
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@@ -45,7 +45,7 @@ class DoiCache(object):
self._cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('doi')
def _raw_get_bibtex(self, doi):
dx_url = "http://dx.doi.org/" + doi
dx_url = "https://doi.org/" + doi
headers = {'Accept': 'text/bibliography; style=bibtex, application/x-bibtex'}
req = requests.get(dx_url, headers=headers)
return req.text
lib/galaxy/tools/xsd/galaxy.xsd
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@@ -5118,7 +5118,7 @@ well. Likewise, the history menu includes an option allowing users to aggregate
all such citations across an analysis in a list of citations.
BibTeX entries for citations annotated with DOIs will be fetched by Galaxy from
https://dx.doi.org/ and cached.
https://doi.org/ and cached.
```xml
<citations>
lib/galaxy/webapps/galaxy/config_schema.yml
+3 -3
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@@ -641,7 +641,7 @@ mapping:
required: false
desc: |
Citation related caching. Tool citations information maybe fetched from
external sources such as http://dx.doi.org/ by Galaxy - the following
external sources such as https://doi.org/ by Galaxy - the following
parameters can be used to control the caching used to store this information.
citation_cache_data_dir:
@@ -650,7 +650,7 @@ mapping:
required: false
desc: |
Citation related caching. Tool citations information maybe fetched from
external sources such as http://dx.doi.org/ by Galaxy - the following
external sources such as https://doi.org/ by Galaxy - the following
parameters can be used to control the caching used to store this information.
citation_cache_lock_dir:
@@ -659,7 +659,7 @@ mapping:
required: false
desc: |
Citation related caching. Tool citations information maybe fetched from
external sources such as http://dx.doi.org/ by Galaxy - the following
external sources such as https://doi.org/ by Galaxy - the following
parameters can be used to control the caching used to store this information.
collect_outputs_from:
lib/galaxy/webapps/tool_shed/config_schema.yml
+3 -3
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@@ -495,7 +495,7 @@ mapping:
required: false
desc: |
Citation related caching. Tool citations information maybe fetched from
external sources such as http://dx.doi.org/ by Galaxy - the following
external sources such as https://doi.org/ by Galaxy - the following
parameters can be used to control the caching used to store this information.
citation_cache_data_dir:
@@ -504,7 +504,7 @@ mapping:
required: false
desc: |
Citation related caching. Tool citations information maybe fetched from
external sources such as http://dx.doi.org/ by Galaxy - the following
external sources such as https://doi.org/ by Galaxy - the following
parameters can be used to control the caching used to store this information.
citation_cache_lock_dir:
@@ -513,7 +513,7 @@ mapping:
required: false
desc: |
Citation related caching. Tool citations information maybe fetched from
external sources such as http://dx.doi.org/ by Galaxy - the following
external sources such as https://doi.org/ by Galaxy - the following
parameters can be used to control the caching used to store this information.
cookie_path:
test/unit/config/1607_root_filters/config/galaxy.ini
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@@ -329,7 +329,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
#default_job_shell = /bin/bash
# Citation related caching. Tool citations information maybe fetched from
# external sources such as http://dx.doi.org/ by Galaxy - the following
# external sources such as https://doi.org/ by Galaxy - the following
# parameters can be used to control the caching used to store this information.
#citation_cache_type = file
#citation_cache_data_dir = database/citations/data
test/unit/config/1607_root_samples/config/galaxy.ini
+1 -1
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@@ -329,7 +329,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
#default_job_shell = /bin/bash
# Citation related caching. Tool citations information maybe fetched from
# external sources such as http://dx.doi.org/ by Galaxy - the following
# external sources such as https://doi.org/ by Galaxy - the following
# parameters can be used to control the caching used to store this information.
#citation_cache_type = file
#citation_cache_data_dir = database/citations/data
tools/sr_mapping/bfast_wrapper.xml
+2 -2
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@@ -196,13 +196,13 @@ Homer N, Merriman B, Nelson SF.
BFAST: An alignment tool for large scale genome resequencing.
PMID: 19907642
PLoS ONE. 2009 4(11): e7767.
http://dx.doi.org/10.1371/journal.pone.0007767
https://doi.org/10.1371/journal.pone.0007767
Homer N, Merriman B, Nelson SF.
Local alignment of two-base encoded DNA sequence.
BMC Bioinformatics. 2009 Jun 9;10(1):175.
PMID: 19508732
http://dx.doi.org/10.1186/1471-2105-10-175
https://doi.org/10.1186/1471-2105-10-175
------