inst/stuff/search.md
In ropensci/solrium: General Purpose R Interface to 'Solr'
Solr search
A general purpose R interface to Apache Solr
Solr info
- Solr home page
- Highlighting help
- Faceting help
- Install and Setup SOLR in OSX, including running Solr
Installation
Stable version from CRAN
install.packages("solrium")
Or the development version from GitHub
install.packages("devtools")
devtools::install_github("ropensci/solrium")
Load
library("solrium")
Setup connection
You can setup for a remote Solr instance or on your local machine.
(conn <- SolrClient$new(host = "api.plos.org", path = "search", port = NULL))
#> <Solr Client>
#> host: api.plos.org
#> path: search
#> port:
#> scheme: http
#> errors: simple
#> proxy:
Rundown
solr_search() only returns the docs element of a Solr response body. If docs is
all you need, then this function will do the job. If you need facet data only, or mlt
data only, see the appropriate functions for each of those below. Another function,
solr_all() has a similar interface in terms of parameter as solr_search(), but
returns all parts of the response body, including, facets, mlt, groups, stats, etc.
as long as you request those.
Search docs
solr_search() returns only docs. A basic search:
conn$search(params = list(q = '*:*', rows = 2, fl = 'id'))
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0058099/materials_and_methods
#> 2 10.1371/journal.pone.0030394/introduction
Search in specific fields with :
Search for word ecology in title and cell in the body
conn$search(params = list(q = 'title:"ecology" AND body:"cell"', fl = 'title', rows = 5))
#> # A tibble: 5 x 1
#> title
#> <chr>
#> 1 The Ecology of Collective Behavior
#> 2 Ecology's Big, Hot Idea
#> 3 Chasing Ecological Interactions
#> 4 Spatial Ecology of Bacteria at the Microscale in Soil
#> 5 Biofilm Formation As a Response to Ecological Competition
Wildcards
Search for word that starts with "cell" in the title field
conn$search(params = list(q = 'title:"cell*"', fl = 'title', rows = 5))
#> # A tibble: 5 x 1
#> title
#> <chr>
#> 1 Cancer Stem Cell-Like Side Population Cells in Clear Cell Renal Cell Car…
#> 2 Tumor Cell Recognition Efficiency by T Cells
#> 3 Enhancement of Chemotactic Cell Aggregation by Haptotactic Cell-To-Cell …
#> 4 Cell-Cell Adhesions and Cell Contractility Are Upregulated upon Desmosom…
#> 5 Dcas Supports Cell Polarization and Cell-Cell Adhesion Complexes in Deve…
Proximity search
Search for words "sports" and "alcohol" within four words of each other
conn$search(params = list(q = 'everything:"stem cell"~7', fl = 'title', rows = 3))
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell…
#> 2 A Mathematical Model of Cancer Stem Cell Driven Tumor Initiation: Implic…
#> 3 Phenotypic Evolutionary Models in Stem Cell Biology: Replacement, Quiesc…
Range searches
Search for articles with Twitter count between 5 and 10
conn$search(params = list(q = '*:*', fl = c('alm_twitterCount', 'id'), fq = 'alm_twitterCount:[5 TO 50]', rows = 10))
#> # A tibble: 10 x 2
#> id alm_twitterCount
#> <chr> <int>
#> 1 10.1371/journal.pbio.0030378/title 8
#> 2 10.1371/journal.pbio.0030378/abstract 8
#> 3 10.1371/journal.pbio.0030378/references 8
#> 4 10.1371/journal.pone.0184491 10
#> 5 10.1371/journal.pone.0184491/title 10
#> 6 10.1371/journal.pone.0184491/abstract 10
#> 7 10.1371/journal.pone.0184491/references 10
#> 8 10.1371/journal.pone.0184491/body 10
#> 9 10.1371/journal.pone.0184491/introduction 10
#> 10 10.1371/journal.pone.0184491/results_and_discussion 10
Boosts
Assign higher boost to title matches than to body matches (compare the two calls)
conn$search(params = list(q = 'title:"cell" abstract:"science"', fl = 'title', rows = 3))
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 I Want More and Better Cells! – An Outreach Project about Stem Cells and…
#> 2 Globalization of Stem Cell Science: An Examination of Current and Past C…
#> 3 Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as …
conn$search(params = list(q = 'title:"cell"^1.5 AND abstract:"science"', fl = 'title', rows = 3))
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 I Want More and Better Cells! – An Outreach Project about Stem Cells and…
#> 2 Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as …
#> 3 Globalization of Stem Cell Science: An Examination of Current and Past C…
Search all
solr_all() differs from solr_search() in that it allows specifying facets, mlt, groups,
stats, etc, and returns all of those. It defaults to parsetype = "list" and wt="json",
whereas solr_search() defaults to parsetype = "df" and wt="csv". solr_all() returns
by default a list, whereas solr_search() by default returns a data.frame.
A basic search, just docs output
conn$all(params = list(q = '*:*', rows = 2, fl = 'id'))
#> $search
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0058099/materials_and_methods
#> 2 10.1371/journal.pone.0030394/introduction
#>
#> $facet
#> list()
#>
#> $high
#> # A tibble: 0 x 0
#>
#> $mlt
#> $mlt$docs
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0058099/materials_and_methods
#> 2 10.1371/journal.pone.0030394/introduction
#>
#> $mlt$mlt
#> list()
#>
#>
#> $group
#> numFound start id
#> 1 2263584 0 10.1371/journal.pone.0058099/materials_and_methods
#> 2 2263584 0 10.1371/journal.pone.0030394/introduction
#>
#> $stats
#> NULL
Get docs, mlt, and stats output
conn$all(params = list(q = 'ecology', rows = 2, fl = 'id', mlt = 'true', mlt.count = 2, mlt.fl = 'abstract', stats = 'true', stats.field = 'counter_total_all'))
#> $search
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0001248
#> 2 10.1371/journal.pone.0059813
#>
#> $facet
#> list()
#>
#> $high
#> # A tibble: 0 x 0
#>
#> $mlt
#> $mlt$docs
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0001248
#> 2 10.1371/journal.pone.0059813
#>
#> $mlt$mlt
#> $mlt$mlt$`10.1371/journal.pone.0001248`
#> # A tibble: 2 x 3
#> numFound start id
#> <int> <int> <chr>
#> 1 236603 0 10.1371/journal.pbio.1002448
#> 2 236603 0 10.1371/journal.pone.0155843
#>
#> $mlt$mlt$`10.1371/journal.pone.0059813`
#> # A tibble: 2 x 3
#> numFound start id
#> <int> <int> <chr>
#> 1 228703 0 10.1371/journal.pone.0204749
#> 2 228703 0 10.1371/journal.pone.0175014
#>
#>
#>
#> $group
#> numFound start id
#> 1 49638 0 10.1371/journal.pone.0001248
#> 2 49638 0 10.1371/journal.pone.0059813
#>
#> $stats
#> $stats$data
#> min max count missing sum sumOfSquares mean
#> counter_total_all 0 1322780 49638 0 264206214 1.119659e+13 5322.66
#> stddev
#> counter_total_all 14044.15
#>
#> $stats$facet
#> NULL
Facet
conn$facet(params = list(q = '*:*', facet.field = 'journal', facet.query = c('cell', 'bird')))
#> $facet_queries
#> # A tibble: 2 x 2
#> term value
#> <chr> <int>
#> 1 cell 181404
#> 2 bird 19370
#>
#> $facet_fields
#> $facet_fields$journal
#> # A tibble: 9 x 2
#> term value
#> <fct> <fct>
#> 1 plos one 1878564
#> 2 plos genetics 69743
#> 3 plos pathogens 62807
#> 4 plos neglected tropical diseases 61216
#> 5 plos computational biology 56361
#> 6 plos biology 39732
#> 7 plos medicine 27839
#> 8 plos clinical trials 521
#> 9 plos medicin 9
#>
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL
Highlight
conn$highlight(params = list(q = 'alcohol', hl.fl = 'abstract', rows = 2))
#> # A tibble: 2 x 2
#> names abstract
#> <chr> <chr>
#> 1 10.1371/journal.pone… "\nAcute <em>alcohol</em> administration can lead …
#> 2 10.1371/journal.pone… Objectives: <em>Alcohol</em>-related morbidity and…
Stats
out <- conn$stats(params = list(q = 'ecology', stats.field = c('counter_total_all', 'alm_twitterCount'), stats.facet = c('journal', 'volume')))
out$data
#> min max count missing sum sumOfSquares
#> counter_total_all 0 1322780 49638 0 264206214 1.119659e+13
#> alm_twitterCount 0 3438 49638 0 304236 8.148536e+07
#> mean stddev
#> counter_total_all 5322.660341 14044.1498
#> alm_twitterCount 6.129095 40.0507
out$facet
#> $counter_total_all
#> $counter_total_all$volume
#> # A tibble: 17 x 9
#> volume min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 11 0 287793 5264 0 18895052 343471377354 3589. 7237.
#> 2 12 0 516798 5076 0 14049766 457686530584 2768. 9084.
#> 3 13 0 153970 4715 0 5936439 86585551129 1259. 4097.
#> 4 14 0 141744 3293 0 2631930 53269058704 799. 3942.
#> 5 15 0 50449 380 0 1602416 24738162692 4217. 6888.
#> 6 16 0 36261 154 0 829924 8698444092 5389. 5255.
#> 7 17 0 42811 108 0 228662 2794636940 2117. 4647.
#> 8 1 2127 331494 81 0 1989864 220314081736 24566. 46291.
#> 9 2 2141 155085 482 0 7419080 277345781732 15392. 18417.
#> 10 3 1621 138038 741 0 9765264 305018983590 13178. 15436.
#> 11 4 866 404016 1010 0 12543775 550954124849 12420. 19790.
#> 12 5 125 248082 1539 0 16437056 451150556196 10680. 13386.
#> 13 6 95 396324 2948 0 25087216 729164435884 8510. 13228.
#> 14 7 62 270034 4825 0 36102767 872710683283 7482. 11176.
#> 15 8 34 611601 6360 0 42214728 1329098761134 6638. 12843.
#> 16 9 57 1322780 6620 0 40933803 3662802686107 6183. 22697.
#> 17 10 428 887162 6042 0 27538472 1820785780330 4558. 16752.
#>
#> $counter_total_all$journal
#> # A tibble: 9 x 9
#> journal min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 1 0 391184 1272 0 22099069 1251395524029 17373. 26125.
#> 2 2 0 270034 335 0 6608325 400062632503 19726. 28417.
#> 3 3 1354 221758 1249 0 9088713 227814882055 7277. 11382.
#> 4 4 9348 18512 2 0 27860 430079248 13930 6480.
#> 5 5 0 887162 41465 0 187628028 6833430419632 4525. 12014.
#> 6 6 0 138374 906 0 7870667 145153611759 8687. 9211.
#> 7 7 0 153848 1101 0 10283498 199515141164 9340. 9698.
#> 8 8 0 323752 2290 0 12009181 244148093179 5244. 8897.
#> 9 9 0 1322780 1018 0 8590873 1894639252767 8439. 42328.
#>
#>
#> $alm_twitterCount
#> $alm_twitterCount$volume
#> # A tibble: 17 x 9
#> volume min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 11 0 2142 5264 0 52248 11395704 9.93 45.5
#> 2 12 0 1877 5076 0 38615 10903883 7.61 45.7
#> 3 13 0 578 4715 0 15920 2404482 3.38 22.3
#> 4 14 0 984 3293 0 14247 3956965 4.33 34.4
#> 5 15 0 453 380 0 5640 906810 14.8 46.6
#> 6 16 0 456 154 0 2830 414458 18.4 48.7
#> 7 17 0 44 108 0 170 4882 1.57 6.57
#> 8 1 0 47 81 0 208 6306 2.57 8.49
#> 9 2 0 125 482 0 1116 63658 2.32 11.3
#> 10 3 0 504 741 0 1407 271861 1.90 19.1
#> 11 4 0 313 1010 0 1655 155545 1.64 12.3
#> 12 5 0 165 1539 0 2694 142070 1.75 9.45
#> 13 6 0 968 2948 0 5709 1631337 1.94 23.4
#> 14 7 0 860 4825 0 21860 2578512 4.53 22.7
#> 15 8 0 2029 6360 0 40719 10854695 6.40 40.8
#> 16 9 0 1880 6620 0 55292 17030904 8.35 50.0
#> 17 10 0 3438 6042 0 43906 18763286 7.27 55.3
#>
#> $alm_twitterCount$journal
#> # A tibble: 9 x 9
#> journal min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 1 0 2142 1272 0 39045 15091795 30.7 105.
#> 2 2 0 831 335 0 5826 1217690 17.4 57.8
#> 3 3 0 455 1249 0 7368 576290 5.90 20.7
#> 4 4 0 3 2 0 3 9 1.5 2.12
#> 5 5 0 3438 41465 0 211665 60964301 5.10 38.0
#> 6 6 0 250 906 0 8476 414748 9.36 19.3
#> 7 7 0 230 1101 0 9237 461117 8.39 18.7
#> 8 8 0 968 2290 0 11804 1555638 5.15 25.6
#> 9 9 0 578 1018 0 10812 1203770 10.6 32.7
More like this
solr_mlt is a function to return similar documents to the one
out <- conn$mlt(params = list(q = 'title:"ecology" AND body:"cell"', mlt.fl = 'title', mlt.mindf = 1, mlt.mintf = 1, fl = 'counter_total_all', rows = 5))
out$docs
#> # A tibble: 5 x 2
#> id counter_total_all
#> <chr> <int>
#> 1 10.1371/journal.pbio.1001805 23958
#> 2 10.1371/journal.pbio.0020440 26090
#> 3 10.1371/journal.pbio.1002559 11628
#> 4 10.1371/journal.pone.0087217 16196
#> 5 10.1371/journal.pbio.1002191 27371
out$mlt
#> $`10.1371/journal.pbio.1001805`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 4678 0 10.1371/journal.pone.0098876 4047
#> 2 4678 0 10.1371/journal.pone.0082578 3244
#> 3 4678 0 10.1371/journal.pone.0102159 2434
#> 4 4678 0 10.1371/journal.pone.0193049 1274
#> 5 4678 0 10.1371/journal.pcbi.1003408 11685
#>
#> $`10.1371/journal.pbio.0020440`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 1375 0 10.1371/journal.pone.0162651 3463
#> 2 1375 0 10.1371/journal.pone.0003259 3417
#> 3 1375 0 10.1371/journal.pntd.0003377 4613
#> 4 1375 0 10.1371/journal.pone.0068814 9701
#> 5 1375 0 10.1371/journal.pone.0101568 6017
#>
#> $`10.1371/journal.pbio.1002559`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 6288 0 10.1371/journal.pone.0155028 2881
#> 2 6288 0 10.1371/journal.pone.0023086 9361
#> 3 6288 0 10.1371/journal.pone.0041684 26571
#> 4 6288 0 10.1371/journal.pone.0155989 2519
#> 5 6288 0 10.1371/journal.pone.0129394 2111
#>
#> $`10.1371/journal.pone.0087217`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 5565 0 10.1371/journal.pone.0204743 103
#> 2 5565 0 10.1371/journal.pone.0175497 1088
#> 3 5565 0 10.1371/journal.pone.0159131 4937
#> 4 5565 0 10.1371/journal.pcbi.0020092 26453
#> 5 5565 0 10.1371/journal.pone.0133941 1336
#>
#> $`10.1371/journal.pbio.1002191`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 14595 0 10.1371/journal.pbio.1002232 3055
#> 2 14595 0 10.1371/journal.pone.0191705 1040
#> 3 14595 0 10.1371/journal.pone.0070448 2497
#> 4 14595 0 10.1371/journal.pone.0131700 3353
#> 5 14595 0 10.1371/journal.pone.0121680 4980
Groups
solr_groups() is a function to return similar documents to the one
conn$group(params = list(q = 'ecology', group.field = 'journal', group.limit = 1, fl = c('id', 'alm_twitterCount')))
#> groupValue numFound start
#> 1 plos one 41465 0
#> 2 plos computational biology 1018 0
#> 3 plos biology 1272 0
#> 4 plos neglected tropical diseases 2290 0
#> 5 plos pathogens 906 0
#> 6 plos genetics 1101 0
#> 7 none 1249 0
#> 8 plos medicine 335 0
#> 9 plos clinical trials 2 0
#> id alm_twitterCount
#> 1 10.1371/journal.pone.0001248 0
#> 2 10.1371/journal.pcbi.1003594 21
#> 3 10.1371/journal.pbio.0060300 0
#> 4 10.1371/journal.pntd.0004689 13
#> 5 10.1371/journal.ppat.1005780 19
#> 6 10.1371/journal.pgen.1005860 135
#> 7 10.1371/journal.pone.0043894 0
#> 8 10.1371/journal.pmed.1000303 1
#> 9 10.1371/journal.pctr.0020010 0
Parsing
solr_parse() is a general purpose parser function with extension methods for parsing outputs from functions in solr. solr_parse() is used internally within functions to do parsing after retrieving data from the server. You can optionally get back raw json, xml, or csv with the raw=TRUE, and then parse afterwards with solr_parse().
For example:
(out <- conn$highlight(params = list(q = 'alcohol', hl.fl = 'abstract', rows = 2), raw = TRUE))
#> [1] "{\n \"response\":{\"numFound\":31528,\"start\":0,\"maxScore\":4.6573215,\"docs\":[\n {\n \"id\":\"10.1371/journal.pone.0201042\",\n \"journal\":\"PLOS ONE\",\n \"eissn\":\"1932-6203\",\n \"publication_date\":\"2018-07-26T00:00:00Z\",\n \"article_type\":\"Research Article\",\n \"author_display\":[\"Graeme Knibb\",\n \"Carl. A. Roberts\",\n \"Eric Robinson\",\n \"Abi Rose\",\n \"Paul Christiansen\"],\n \"abstract\":[\"\\nAcute alcohol administration can lead to a loss of control over drinking. Several models argue that this ‘alcohol priming effect’ is mediated by the effect of alcohol on inhibitory control. Alternatively, beliefs about how alcohol affects behavioural regulation may also underlie alcohol priming and alcohol-induced inhibitory impairments. Here two studies examine the extent to which the alcohol priming effect and inhibitory impairments are moderated by beliefs regarding the effects of alcohol on the ability to control behaviour. In study 1, following a priming drink (placebo or .5g/kg of alcohol), participants were provided with bogus feedback regarding their performance on a measure of inhibitory control (stop-signal task; SST) suggesting that they had high or average self-control. However, the bogus feedback manipulation was not successful. In study 2, before a SST, participants were exposed to a neutral or experimental message suggesting acute doses of alcohol reduce the urge to drink and consumed a priming drink and this manipulation was successful. In both studies craving was assessed throughout and a bogus taste test which measured ad libitum drinking was completed. Results suggest no effect of beliefs on craving or ad lib consumption within either study. However, within study 2, participants exposed to the experimental message displayed evidence of alcohol-induced impairments of inhibitory control, while those exposed to the neutral message did not. These findings do not suggest beliefs about the effects of alcohol moderate the alcohol priming effect but do suggest beliefs may, in part, underlie the effect of alcohol on inhibitory control.\\n\"],\n \"title_display\":\"The effect of beliefs about alcohol’s acute effects on alcohol priming and alcohol-induced impairments of inhibitory control\",\n \"score\":4.6573215},\n {\n \"id\":\"10.1371/journal.pone.0185457\",\n \"journal\":\"PLOS ONE\",\n \"eissn\":\"1932-6203\",\n \"publication_date\":\"2017-09-28T00:00:00Z\",\n \"article_type\":\"Research Article\",\n \"author_display\":[\"Jacqueline Willmore\",\n \"Terry-Lynne Marko\",\n \"Darcie Taing\",\n \"Hugues Sampasa-Kanyinga\"],\n \"abstract\":[\"Objectives: Alcohol-related morbidity and mortality are significant public health issues. The purpose of this study was to describe the prevalence and trends over time of alcohol consumption and alcohol-related morbidity and mortality; and public attitudes of alcohol use impacts on families and the community in Ottawa, Canada. Methods: Prevalence (2013–2014) and trends (2000–2001 to 2013–2014) of alcohol use were obtained from the Canadian Community Health Survey. Data on paramedic responses (2015), emergency department (ED) visits (2013–2015), hospitalizations (2013–2015) and deaths (2007–2011) were used to quantify the acute and chronic health effects of alcohol in Ottawa. Qualitative data were obtained from the “Have Your Say” alcohol survey, an online survey of public attitudes on alcohol conducted in 2016. Results: In 2013–2014, an estimated 595,300 (83%) Ottawa adults 19 years and older drank alcohol, 42% reported binge drinking in the past year. Heavy drinking increased from 15% in 2000–2001 to 20% in 2013–2014. In 2015, the Ottawa Paramedic Service responded to 2,060 calls directly attributable to alcohol. Between 2013 and 2015, there were an average of 6,100 ED visits and 1,270 hospitalizations per year due to alcohol. Annually, alcohol use results in at least 140 deaths in Ottawa. Men have higher rates of alcohol-attributable paramedic responses, ED visits, hospitalizations and deaths than women, and young adults have higher rates of alcohol-attributable paramedic responses. Qualitative data of public attitudes indicate that alcohol misuse has greater repercussions not only on those who drink, but also on the family and community. Conclusions: Results highlight the need for healthy public policy intended to encourage a culture of drinking in moderation in Ottawa to support lower risk alcohol use, particularly among men and young adults. \"],\n \"title_display\":\"The burden of alcohol-related morbidity and mortality in Ottawa, Canada\",\n \"score\":4.65702}]\n },\n \"highlighting\":{\n \"10.1371/journal.pone.0201042\":{\n \"abstract\":[\"\\nAcute <em>alcohol</em> administration can lead to a loss of control over drinking. Several models argue\"]},\n \"10.1371/journal.pone.0185457\":{\n \"abstract\":[\"Objectives: <em>Alcohol</em>-related morbidity and mortality are significant public health issues\"]}}}\n"
#> attr(,"class")
#> [1] "sr_high"
#> attr(,"wt")
#> [1] "json"
Then parse
solr_parse(out, 'df')
#> # A tibble: 2 x 2
#> names abstract
#> <chr> <chr>
#> 1 10.1371/journal.pone… "\nAcute <em>alcohol</em> administration can lead …
#> 2 10.1371/journal.pone… Objectives: <em>Alcohol</em>-related morbidity and…
Please report any issues or bugs.
ropensci/solrium documentation built on Sept. 12, 2022, 3:01 p.m.
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Solr search
A general purpose R interface to Apache Solr
Solr info
- Solr home page
- Highlighting help
- Faceting help
- Install and Setup SOLR in OSX, including running Solr
Installation
Stable version from CRAN
install.packages("solrium")
Or the development version from GitHub
install.packages("devtools")
devtools::install_github("ropensci/solrium")
Load
library("solrium")
Setup connection
You can setup for a remote Solr instance or on your local machine.
(conn <- SolrClient$new(host = "api.plos.org", path = "search", port = NULL))
#> <Solr Client>
#> host: api.plos.org
#> path: search
#> port:
#> scheme: http
#> errors: simple
#> proxy:
Rundown
solr_search() only returns the docs element of a Solr response body. If docs is
all you need, then this function will do the job. If you need facet data only, or mlt
data only, see the appropriate functions for each of those below. Another function,
solr_all() has a similar interface in terms of parameter as solr_search(), but
returns all parts of the response body, including, facets, mlt, groups, stats, etc.
as long as you request those.
Search docs
solr_search() returns only docs. A basic search:
conn$search(params = list(q = '*:*', rows = 2, fl = 'id'))
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0058099/materials_and_methods
#> 2 10.1371/journal.pone.0030394/introduction
Search in specific fields with :
Search for word ecology in title and cell in the body
conn$search(params = list(q = 'title:"ecology" AND body:"cell"', fl = 'title', rows = 5))
#> # A tibble: 5 x 1
#> title
#> <chr>
#> 1 The Ecology of Collective Behavior
#> 2 Ecology's Big, Hot Idea
#> 3 Chasing Ecological Interactions
#> 4 Spatial Ecology of Bacteria at the Microscale in Soil
#> 5 Biofilm Formation As a Response to Ecological Competition
Wildcards
Search for word that starts with "cell" in the title field
conn$search(params = list(q = 'title:"cell*"', fl = 'title', rows = 5))
#> # A tibble: 5 x 1
#> title
#> <chr>
#> 1 Cancer Stem Cell-Like Side Population Cells in Clear Cell Renal Cell Car…
#> 2 Tumor Cell Recognition Efficiency by T Cells
#> 3 Enhancement of Chemotactic Cell Aggregation by Haptotactic Cell-To-Cell …
#> 4 Cell-Cell Adhesions and Cell Contractility Are Upregulated upon Desmosom…
#> 5 Dcas Supports Cell Polarization and Cell-Cell Adhesion Complexes in Deve…
Proximity search
Search for words "sports" and "alcohol" within four words of each other
conn$search(params = list(q = 'everything:"stem cell"~7', fl = 'title', rows = 3))
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell…
#> 2 A Mathematical Model of Cancer Stem Cell Driven Tumor Initiation: Implic…
#> 3 Phenotypic Evolutionary Models in Stem Cell Biology: Replacement, Quiesc…
Range searches
Search for articles with Twitter count between 5 and 10
conn$search(params = list(q = '*:*', fl = c('alm_twitterCount', 'id'), fq = 'alm_twitterCount:[5 TO 50]', rows = 10))
#> # A tibble: 10 x 2
#> id alm_twitterCount
#> <chr> <int>
#> 1 10.1371/journal.pbio.0030378/title 8
#> 2 10.1371/journal.pbio.0030378/abstract 8
#> 3 10.1371/journal.pbio.0030378/references 8
#> 4 10.1371/journal.pone.0184491 10
#> 5 10.1371/journal.pone.0184491/title 10
#> 6 10.1371/journal.pone.0184491/abstract 10
#> 7 10.1371/journal.pone.0184491/references 10
#> 8 10.1371/journal.pone.0184491/body 10
#> 9 10.1371/journal.pone.0184491/introduction 10
#> 10 10.1371/journal.pone.0184491/results_and_discussion 10
Boosts
Assign higher boost to title matches than to body matches (compare the two calls)
conn$search(params = list(q = 'title:"cell" abstract:"science"', fl = 'title', rows = 3))
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 I Want More and Better Cells! – An Outreach Project about Stem Cells and…
#> 2 Globalization of Stem Cell Science: An Examination of Current and Past C…
#> 3 Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as …
conn$search(params = list(q = 'title:"cell"^1.5 AND abstract:"science"', fl = 'title', rows = 3))
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 I Want More and Better Cells! – An Outreach Project about Stem Cells and…
#> 2 Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as …
#> 3 Globalization of Stem Cell Science: An Examination of Current and Past C…
Search all
solr_all() differs from solr_search() in that it allows specifying facets, mlt, groups,
stats, etc, and returns all of those. It defaults to parsetype = "list" and wt="json",
whereas solr_search() defaults to parsetype = "df" and wt="csv". solr_all() returns
by default a list, whereas solr_search() by default returns a data.frame.
A basic search, just docs output
conn$all(params = list(q = '*:*', rows = 2, fl = 'id'))
#> $search
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0058099/materials_and_methods
#> 2 10.1371/journal.pone.0030394/introduction
#>
#> $facet
#> list()
#>
#> $high
#> # A tibble: 0 x 0
#>
#> $mlt
#> $mlt$docs
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0058099/materials_and_methods
#> 2 10.1371/journal.pone.0030394/introduction
#>
#> $mlt$mlt
#> list()
#>
#>
#> $group
#> numFound start id
#> 1 2263584 0 10.1371/journal.pone.0058099/materials_and_methods
#> 2 2263584 0 10.1371/journal.pone.0030394/introduction
#>
#> $stats
#> NULL
Get docs, mlt, and stats output
conn$all(params = list(q = 'ecology', rows = 2, fl = 'id', mlt = 'true', mlt.count = 2, mlt.fl = 'abstract', stats = 'true', stats.field = 'counter_total_all'))
#> $search
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0001248
#> 2 10.1371/journal.pone.0059813
#>
#> $facet
#> list()
#>
#> $high
#> # A tibble: 0 x 0
#>
#> $mlt
#> $mlt$docs
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0001248
#> 2 10.1371/journal.pone.0059813
#>
#> $mlt$mlt
#> $mlt$mlt$`10.1371/journal.pone.0001248`
#> # A tibble: 2 x 3
#> numFound start id
#> <int> <int> <chr>
#> 1 236603 0 10.1371/journal.pbio.1002448
#> 2 236603 0 10.1371/journal.pone.0155843
#>
#> $mlt$mlt$`10.1371/journal.pone.0059813`
#> # A tibble: 2 x 3
#> numFound start id
#> <int> <int> <chr>
#> 1 228703 0 10.1371/journal.pone.0204749
#> 2 228703 0 10.1371/journal.pone.0175014
#>
#>
#>
#> $group
#> numFound start id
#> 1 49638 0 10.1371/journal.pone.0001248
#> 2 49638 0 10.1371/journal.pone.0059813
#>
#> $stats
#> $stats$data
#> min max count missing sum sumOfSquares mean
#> counter_total_all 0 1322780 49638 0 264206214 1.119659e+13 5322.66
#> stddev
#> counter_total_all 14044.15
#>
#> $stats$facet
#> NULL
Facet
conn$facet(params = list(q = '*:*', facet.field = 'journal', facet.query = c('cell', 'bird')))
#> $facet_queries
#> # A tibble: 2 x 2
#> term value
#> <chr> <int>
#> 1 cell 181404
#> 2 bird 19370
#>
#> $facet_fields
#> $facet_fields$journal
#> # A tibble: 9 x 2
#> term value
#> <fct> <fct>
#> 1 plos one 1878564
#> 2 plos genetics 69743
#> 3 plos pathogens 62807
#> 4 plos neglected tropical diseases 61216
#> 5 plos computational biology 56361
#> 6 plos biology 39732
#> 7 plos medicine 27839
#> 8 plos clinical trials 521
#> 9 plos medicin 9
#>
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL
Highlight
conn$highlight(params = list(q = 'alcohol', hl.fl = 'abstract', rows = 2))
#> # A tibble: 2 x 2
#> names abstract
#> <chr> <chr>
#> 1 10.1371/journal.pone… "\nAcute <em>alcohol</em> administration can lead …
#> 2 10.1371/journal.pone… Objectives: <em>Alcohol</em>-related morbidity and…
Stats
out <- conn$stats(params = list(q = 'ecology', stats.field = c('counter_total_all', 'alm_twitterCount'), stats.facet = c('journal', 'volume')))
out$data
#> min max count missing sum sumOfSquares
#> counter_total_all 0 1322780 49638 0 264206214 1.119659e+13
#> alm_twitterCount 0 3438 49638 0 304236 8.148536e+07
#> mean stddev
#> counter_total_all 5322.660341 14044.1498
#> alm_twitterCount 6.129095 40.0507
out$facet
#> $counter_total_all
#> $counter_total_all$volume
#> # A tibble: 17 x 9
#> volume min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 11 0 287793 5264 0 18895052 343471377354 3589. 7237.
#> 2 12 0 516798 5076 0 14049766 457686530584 2768. 9084.
#> 3 13 0 153970 4715 0 5936439 86585551129 1259. 4097.
#> 4 14 0 141744 3293 0 2631930 53269058704 799. 3942.
#> 5 15 0 50449 380 0 1602416 24738162692 4217. 6888.
#> 6 16 0 36261 154 0 829924 8698444092 5389. 5255.
#> 7 17 0 42811 108 0 228662 2794636940 2117. 4647.
#> 8 1 2127 331494 81 0 1989864 220314081736 24566. 46291.
#> 9 2 2141 155085 482 0 7419080 277345781732 15392. 18417.
#> 10 3 1621 138038 741 0 9765264 305018983590 13178. 15436.
#> 11 4 866 404016 1010 0 12543775 550954124849 12420. 19790.
#> 12 5 125 248082 1539 0 16437056 451150556196 10680. 13386.
#> 13 6 95 396324 2948 0 25087216 729164435884 8510. 13228.
#> 14 7 62 270034 4825 0 36102767 872710683283 7482. 11176.
#> 15 8 34 611601 6360 0 42214728 1329098761134 6638. 12843.
#> 16 9 57 1322780 6620 0 40933803 3662802686107 6183. 22697.
#> 17 10 428 887162 6042 0 27538472 1820785780330 4558. 16752.
#>
#> $counter_total_all$journal
#> # A tibble: 9 x 9
#> journal min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 1 0 391184 1272 0 22099069 1251395524029 17373. 26125.
#> 2 2 0 270034 335 0 6608325 400062632503 19726. 28417.
#> 3 3 1354 221758 1249 0 9088713 227814882055 7277. 11382.
#> 4 4 9348 18512 2 0 27860 430079248 13930 6480.
#> 5 5 0 887162 41465 0 187628028 6833430419632 4525. 12014.
#> 6 6 0 138374 906 0 7870667 145153611759 8687. 9211.
#> 7 7 0 153848 1101 0 10283498 199515141164 9340. 9698.
#> 8 8 0 323752 2290 0 12009181 244148093179 5244. 8897.
#> 9 9 0 1322780 1018 0 8590873 1894639252767 8439. 42328.
#>
#>
#> $alm_twitterCount
#> $alm_twitterCount$volume
#> # A tibble: 17 x 9
#> volume min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 11 0 2142 5264 0 52248 11395704 9.93 45.5
#> 2 12 0 1877 5076 0 38615 10903883 7.61 45.7
#> 3 13 0 578 4715 0 15920 2404482 3.38 22.3
#> 4 14 0 984 3293 0 14247 3956965 4.33 34.4
#> 5 15 0 453 380 0 5640 906810 14.8 46.6
#> 6 16 0 456 154 0 2830 414458 18.4 48.7
#> 7 17 0 44 108 0 170 4882 1.57 6.57
#> 8 1 0 47 81 0 208 6306 2.57 8.49
#> 9 2 0 125 482 0 1116 63658 2.32 11.3
#> 10 3 0 504 741 0 1407 271861 1.90 19.1
#> 11 4 0 313 1010 0 1655 155545 1.64 12.3
#> 12 5 0 165 1539 0 2694 142070 1.75 9.45
#> 13 6 0 968 2948 0 5709 1631337 1.94 23.4
#> 14 7 0 860 4825 0 21860 2578512 4.53 22.7
#> 15 8 0 2029 6360 0 40719 10854695 6.40 40.8
#> 16 9 0 1880 6620 0 55292 17030904 8.35 50.0
#> 17 10 0 3438 6042 0 43906 18763286 7.27 55.3
#>
#> $alm_twitterCount$journal
#> # A tibble: 9 x 9
#> journal min max count missing sum sumOfSquares mean stddev
#> <chr> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 1 0 2142 1272 0 39045 15091795 30.7 105.
#> 2 2 0 831 335 0 5826 1217690 17.4 57.8
#> 3 3 0 455 1249 0 7368 576290 5.90 20.7
#> 4 4 0 3 2 0 3 9 1.5 2.12
#> 5 5 0 3438 41465 0 211665 60964301 5.10 38.0
#> 6 6 0 250 906 0 8476 414748 9.36 19.3
#> 7 7 0 230 1101 0 9237 461117 8.39 18.7
#> 8 8 0 968 2290 0 11804 1555638 5.15 25.6
#> 9 9 0 578 1018 0 10812 1203770 10.6 32.7
More like this
solr_mlt is a function to return similar documents to the one
out <- conn$mlt(params = list(q = 'title:"ecology" AND body:"cell"', mlt.fl = 'title', mlt.mindf = 1, mlt.mintf = 1, fl = 'counter_total_all', rows = 5))
out$docs
#> # A tibble: 5 x 2
#> id counter_total_all
#> <chr> <int>
#> 1 10.1371/journal.pbio.1001805 23958
#> 2 10.1371/journal.pbio.0020440 26090
#> 3 10.1371/journal.pbio.1002559 11628
#> 4 10.1371/journal.pone.0087217 16196
#> 5 10.1371/journal.pbio.1002191 27371
out$mlt
#> $`10.1371/journal.pbio.1001805`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 4678 0 10.1371/journal.pone.0098876 4047
#> 2 4678 0 10.1371/journal.pone.0082578 3244
#> 3 4678 0 10.1371/journal.pone.0102159 2434
#> 4 4678 0 10.1371/journal.pone.0193049 1274
#> 5 4678 0 10.1371/journal.pcbi.1003408 11685
#>
#> $`10.1371/journal.pbio.0020440`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 1375 0 10.1371/journal.pone.0162651 3463
#> 2 1375 0 10.1371/journal.pone.0003259 3417
#> 3 1375 0 10.1371/journal.pntd.0003377 4613
#> 4 1375 0 10.1371/journal.pone.0068814 9701
#> 5 1375 0 10.1371/journal.pone.0101568 6017
#>
#> $`10.1371/journal.pbio.1002559`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 6288 0 10.1371/journal.pone.0155028 2881
#> 2 6288 0 10.1371/journal.pone.0023086 9361
#> 3 6288 0 10.1371/journal.pone.0041684 26571
#> 4 6288 0 10.1371/journal.pone.0155989 2519
#> 5 6288 0 10.1371/journal.pone.0129394 2111
#>
#> $`10.1371/journal.pone.0087217`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 5565 0 10.1371/journal.pone.0204743 103
#> 2 5565 0 10.1371/journal.pone.0175497 1088
#> 3 5565 0 10.1371/journal.pone.0159131 4937
#> 4 5565 0 10.1371/journal.pcbi.0020092 26453
#> 5 5565 0 10.1371/journal.pone.0133941 1336
#>
#> $`10.1371/journal.pbio.1002191`
#> # A tibble: 5 x 4
#> numFound start id counter_total_all
#> <int> <int> <chr> <int>
#> 1 14595 0 10.1371/journal.pbio.1002232 3055
#> 2 14595 0 10.1371/journal.pone.0191705 1040
#> 3 14595 0 10.1371/journal.pone.0070448 2497
#> 4 14595 0 10.1371/journal.pone.0131700 3353
#> 5 14595 0 10.1371/journal.pone.0121680 4980
Groups
solr_groups() is a function to return similar documents to the one
conn$group(params = list(q = 'ecology', group.field = 'journal', group.limit = 1, fl = c('id', 'alm_twitterCount')))
#> groupValue numFound start
#> 1 plos one 41465 0
#> 2 plos computational biology 1018 0
#> 3 plos biology 1272 0
#> 4 plos neglected tropical diseases 2290 0
#> 5 plos pathogens 906 0
#> 6 plos genetics 1101 0
#> 7 none 1249 0
#> 8 plos medicine 335 0
#> 9 plos clinical trials 2 0
#> id alm_twitterCount
#> 1 10.1371/journal.pone.0001248 0
#> 2 10.1371/journal.pcbi.1003594 21
#> 3 10.1371/journal.pbio.0060300 0
#> 4 10.1371/journal.pntd.0004689 13
#> 5 10.1371/journal.ppat.1005780 19
#> 6 10.1371/journal.pgen.1005860 135
#> 7 10.1371/journal.pone.0043894 0
#> 8 10.1371/journal.pmed.1000303 1
#> 9 10.1371/journal.pctr.0020010 0
Parsing
solr_parse() is a general purpose parser function with extension methods for parsing outputs from functions in solr. solr_parse() is used internally within functions to do parsing after retrieving data from the server. You can optionally get back raw json, xml, or csv with the raw=TRUE, and then parse afterwards with solr_parse().
For example:
(out <- conn$highlight(params = list(q = 'alcohol', hl.fl = 'abstract', rows = 2), raw = TRUE))
#> [1] "{\n \"response\":{\"numFound\":31528,\"start\":0,\"maxScore\":4.6573215,\"docs\":[\n {\n \"id\":\"10.1371/journal.pone.0201042\",\n \"journal\":\"PLOS ONE\",\n \"eissn\":\"1932-6203\",\n \"publication_date\":\"2018-07-26T00:00:00Z\",\n \"article_type\":\"Research Article\",\n \"author_display\":[\"Graeme Knibb\",\n \"Carl. A. Roberts\",\n \"Eric Robinson\",\n \"Abi Rose\",\n \"Paul Christiansen\"],\n \"abstract\":[\"\\nAcute alcohol administration can lead to a loss of control over drinking. Several models argue that this ‘alcohol priming effect’ is mediated by the effect of alcohol on inhibitory control. Alternatively, beliefs about how alcohol affects behavioural regulation may also underlie alcohol priming and alcohol-induced inhibitory impairments. Here two studies examine the extent to which the alcohol priming effect and inhibitory impairments are moderated by beliefs regarding the effects of alcohol on the ability to control behaviour. In study 1, following a priming drink (placebo or .5g/kg of alcohol), participants were provided with bogus feedback regarding their performance on a measure of inhibitory control (stop-signal task; SST) suggesting that they had high or average self-control. However, the bogus feedback manipulation was not successful. In study 2, before a SST, participants were exposed to a neutral or experimental message suggesting acute doses of alcohol reduce the urge to drink and consumed a priming drink and this manipulation was successful. In both studies craving was assessed throughout and a bogus taste test which measured ad libitum drinking was completed. Results suggest no effect of beliefs on craving or ad lib consumption within either study. However, within study 2, participants exposed to the experimental message displayed evidence of alcohol-induced impairments of inhibitory control, while those exposed to the neutral message did not. These findings do not suggest beliefs about the effects of alcohol moderate the alcohol priming effect but do suggest beliefs may, in part, underlie the effect of alcohol on inhibitory control.\\n\"],\n \"title_display\":\"The effect of beliefs about alcohol’s acute effects on alcohol priming and alcohol-induced impairments of inhibitory control\",\n \"score\":4.6573215},\n {\n \"id\":\"10.1371/journal.pone.0185457\",\n \"journal\":\"PLOS ONE\",\n \"eissn\":\"1932-6203\",\n \"publication_date\":\"2017-09-28T00:00:00Z\",\n \"article_type\":\"Research Article\",\n \"author_display\":[\"Jacqueline Willmore\",\n \"Terry-Lynne Marko\",\n \"Darcie Taing\",\n \"Hugues Sampasa-Kanyinga\"],\n \"abstract\":[\"Objectives: Alcohol-related morbidity and mortality are significant public health issues. The purpose of this study was to describe the prevalence and trends over time of alcohol consumption and alcohol-related morbidity and mortality; and public attitudes of alcohol use impacts on families and the community in Ottawa, Canada. Methods: Prevalence (2013–2014) and trends (2000–2001 to 2013–2014) of alcohol use were obtained from the Canadian Community Health Survey. Data on paramedic responses (2015), emergency department (ED) visits (2013–2015), hospitalizations (2013–2015) and deaths (2007–2011) were used to quantify the acute and chronic health effects of alcohol in Ottawa. Qualitative data were obtained from the “Have Your Say” alcohol survey, an online survey of public attitudes on alcohol conducted in 2016. Results: In 2013–2014, an estimated 595,300 (83%) Ottawa adults 19 years and older drank alcohol, 42% reported binge drinking in the past year. Heavy drinking increased from 15% in 2000–2001 to 20% in 2013–2014. In 2015, the Ottawa Paramedic Service responded to 2,060 calls directly attributable to alcohol. Between 2013 and 2015, there were an average of 6,100 ED visits and 1,270 hospitalizations per year due to alcohol. Annually, alcohol use results in at least 140 deaths in Ottawa. Men have higher rates of alcohol-attributable paramedic responses, ED visits, hospitalizations and deaths than women, and young adults have higher rates of alcohol-attributable paramedic responses. Qualitative data of public attitudes indicate that alcohol misuse has greater repercussions not only on those who drink, but also on the family and community. Conclusions: Results highlight the need for healthy public policy intended to encourage a culture of drinking in moderation in Ottawa to support lower risk alcohol use, particularly among men and young adults. \"],\n \"title_display\":\"The burden of alcohol-related morbidity and mortality in Ottawa, Canada\",\n \"score\":4.65702}]\n },\n \"highlighting\":{\n \"10.1371/journal.pone.0201042\":{\n \"abstract\":[\"\\nAcute <em>alcohol</em> administration can lead to a loss of control over drinking. Several models argue\"]},\n \"10.1371/journal.pone.0185457\":{\n \"abstract\":[\"Objectives: <em>Alcohol</em>-related morbidity and mortality are significant public health issues\"]}}}\n"
#> attr(,"class")
#> [1] "sr_high"
#> attr(,"wt")
#> [1] "json"
Then parse
solr_parse(out, 'df')
#> # A tibble: 2 x 2
#> names abstract
#> <chr> <chr>
#> 1 10.1371/journal.pone… "\nAcute <em>alcohol</em> administration can lead …
#> 2 10.1371/journal.pone… Objectives: <em>Alcohol</em>-related morbidity and…
Please report any issues or bugs.
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