defter 0.3.5

Self-hosted Zotero sync and file storage server, with metadata in SQLite and attachments in S3.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
//! The public profile at `/<orcid>`: the library owner's ORCID record, read by
//! commonmeta and laid out as on commonmeta.org's person page, and their My
//! Publications, as zotero.org publishes it. The page itself is rendered in
//! `ui`.

use std::sync::{Arc, Mutex};
use std::time::{Duration, Instant};

use commonmeta::Person;
use serde_json::Value;

use crate::app::AppState;
use crate::countries;
use crate::db;
use crate::error::AppError;
use crate::i18n::Lang;

/// Works per page of My Publications.
pub const PAGE_SIZE: usize = 25;

/// Values shown per facet, as on commonmeta.org.
pub const FACET_VALUES: usize = 10;

/// The length of a search term taken from one request.
pub const SEARCH_MAX: usize = 200;

/// Values of a facet taken from one request.
pub const FACET_PICKS_MAX: usize = 20;

/// Websites listed on the person card, as on commonmeta.org.
const URLS_MAX: usize = 5;

/// How long a fetched ORCID record is shown before it is fetched again.
const PERSON_TTL: Duration = Duration::from_secs(3600);

/// How long after a failed fetch the next one is tried, so that page views
/// during an ORCID outage do not each wait for it.
const PERSON_RETRY: Duration = Duration::from_secs(300);

/// How long a page view waits for ORCID.
const PERSON_TIMEOUT: Duration = Duration::from_secs(15);

/// The `meta` key recording that the owner hid the profile.
const HIDDEN_KEY: &str = "profile_hidden";

/// The bare iD (`0000-0003-1419-2405`) of an ORCID iD or URL, if valid.
pub fn normalize_orcid(input: &str) -> Option<String> {
    commonmeta::utils::validate_orcid(input.trim()).map(|id| id.replace(' ', "-"))
}

/// The last ORCID record fetched, and when to fetch it again.
#[derive(Default)]
pub struct PersonCache {
    slot: Mutex<PersonSlot>,
    /// Held while fetching, so that concurrent page views fetch only once.
    fetching: tokio::sync::Mutex<()>,
}

#[derive(Default)]
struct PersonSlot {
    person: Option<Arc<Person>>,
    next_fetch: Option<Instant>,
}

impl PersonCache {
    fn slot(&self) -> std::sync::MutexGuard<'_, PersonSlot> {
        self.slot.lock().unwrap_or_else(|e| e.into_inner())
    }

    pub fn set(&self, person: Person) -> Arc<Person> {
        let person = Arc::new(person);
        *self.slot() = PersonSlot {
            person: Some(person.clone()),
            next_fetch: Some(Instant::now() + PERSON_TTL),
        };
        person
    }

    /// Keep what there is, and fetch again after a while.
    fn fetch_failed(&self) {
        self.slot().next_fetch = Some(Instant::now() + PERSON_RETRY);
    }

    /// What to show until the next fetch is due: the record, if there is one;
    /// `None` when it is time to fetch.
    fn settled(&self) -> Option<Option<Arc<Person>>> {
        let slot = self.slot();
        let due = slot.next_fetch.is_none_or(|at| Instant::now() >= at);
        (!due).then(|| slot.person.clone())
    }
}

fn unavailable(orcid: &str) -> AppError {
    AppError::Upstream(format!("ORCID record {orcid} is not available"))
}

/// The ORCID record of `orcid`, from the cache while it is fresh. When ORCID
/// cannot be reached, a stale copy is better than no page.
pub async fn person(app: &AppState, orcid: &str) -> Result<Arc<Person>, AppError> {
    if let Some(person) = app.person.settled() {
        return person.ok_or_else(|| unavailable(orcid));
    }
    let _fetching = app.person.fetching.lock().await;
    // Another page view may have fetched it in the meantime.
    if let Some(person) = app.person.settled() {
        return person.ok_or_else(|| unavailable(orcid));
    }
    let id = orcid.to_string();
    let fetch = tokio::task::spawn_blocking(move || commonmeta::fetch_orcid(&id));
    let error = match tokio::time::timeout(PERSON_TIMEOUT, fetch).await {
        Ok(Ok(Ok(person))) => return Ok(app.person.set(person)),
        Ok(Ok(Err(error))) => error.to_string(),
        Ok(Err(error)) => format!("blocking task: {error}"),
        Err(_) => "timed out".to_string(),
    };
    tracing::warn!(orcid, %error, "fetching the ORCID record");
    app.person.fetch_failed();
    let person = app.person.slot().person.clone();
    person.ok_or_else(|| unavailable(orcid))
}

pub async fn hidden(app: &AppState) -> Result<bool, AppError> {
    let value = app.db.read(|c| db::get_meta(c, HIDDEN_KEY)).await?;
    Ok(value.as_deref() == Some("1"))
}

pub async fn set_hidden(app: &AppState, hidden: bool) -> Result<(), AppError> {
    app.db
        .write(move |c| db::set_meta(c, HIDDEN_KEY, if hidden { "1" } else { "0" }))
        .await
}

// ── what the page shows ──────────────────────────────────────────────────────

pub struct Link {
    pub name: String,
    pub url: String,
}

pub struct AffiliationView {
    pub name: String,
    /// The organization's ROR ID, as a URL.
    pub ror: Option<String>,
    pub role: String,
    pub dates: String,
}

/// The person card: what commonmeta.org shows for an ORCID iD.
pub struct PersonView {
    pub orcid_url: String,
    pub commonmeta_url: String,
    pub name: String,
    pub given_name: String,
    pub family_name: String,
    pub additional_names: String,
    /// The biography, as one paragraph.
    pub description: String,
    /// The start of the biography, for the page's meta description.
    pub summary: String,
    pub urls: Vec<Link>,
    pub country: String,
    pub affiliations: Vec<AffiliationView>,
    /// The record, for the copy button, as on commonmeta.org.
    pub json: String,
}

impl PersonView {
    pub fn new(orcid: &str, person: &Person, lang: Lang) -> Self {
        let name = if person.name.is_empty() {
            [person.given_name.as_str(), person.family_name.as_str()]
                .iter()
                .filter(|s| !s.is_empty())
                .copied()
                .collect::<Vec<_>>()
                .join(" ")
        } else {
            person.name.clone()
        };
        let description = person
            .description
            .split_whitespace()
            .collect::<Vec<_>>()
            .join(" ");
        let country = person.country.trim();
        PersonView {
            orcid_url: format!("https://orcid.org/{orcid}"),
            commonmeta_url: format!("https://commonmeta.org/{orcid}"),
            name: if name.is_empty() {
                orcid.to_string()
            } else {
                name
            },
            given_name: person.given_name.clone(),
            family_name: person.family_name.clone(),
            additional_names: person.additional_names.join(" · "),
            summary: summary(&description, 200),
            description,
            urls: person
                .urls
                .iter()
                .filter(|u| web_url(&u.url))
                .take(URLS_MAX)
                .map(|u| Link {
                    name: if u.name.is_empty() {
                        u.url.clone()
                    } else {
                        u.name.clone()
                    },
                    url: u.url.clone(),
                })
                .collect(),
            country: countries::name(&country.to_ascii_uppercase(), lang)
                .unwrap_or(country)
                .to_string(),
            affiliations: person
                .affiliations
                .iter()
                .filter(|a| !a.name.is_empty())
                .map(|a| AffiliationView {
                    name: a.name.clone(),
                    ror: a
                        .identifier
                        .starts_with("https://ror.org/")
                        .then(|| a.identifier.clone()),
                    role: a.role.clone(),
                    dates: lang.date_range(&a.start_date, &a.end_date),
                })
                .collect(),
            json: serde_json::to_string_pretty(person).unwrap_or_default(),
        }
    }
}

/// A work in the lists, as on commonmeta.org's work cards.
pub struct WorkView {
    pub title: String,
    /// The DOI as a URL, else the item's URL.
    pub link: Option<String>,
    pub doi_url: Option<String>,
    pub authors: String,
    /// When it was published, for people.
    pub date: String,
    pub container: String,
    pub kind: String,
    /// The name of the work's language.
    pub language: String,
    /// The abstract, without markup.
    pub description: String,
    /// The Rights field: what it says, and where it leads when it is a URL.
    pub license: String,
    pub license_url: Option<String>,
    /// As plain text, for the copy button. Not the item's JSON, as
    /// commonmeta.org has it: that would hold the owner's tags.
    pub citation: String,
}

fn web_url(url: &str) -> bool {
    url.starts_with("https://") || url.starts_with("http://")
}

fn text<'a>(data: &'a Value, field: &str) -> &'a str {
    data.get(field).and_then(Value::as_str).unwrap_or("").trim()
}

/// Where a work appeared: the first container field its item type has.
const CONTAINER_FIELDS: &[&str] = &[
    "publicationTitle",
    "blogTitle",
    "websiteTitle",
    "bookTitle",
    "proceedingsTitle",
    "meetingName",
    "repository",
    "institution",
    "university",
    "publisher",
];

/// Authors listed before "et al.".
const AUTHORS_MAX: usize = 5;

impl WorkView {
    pub fn new(data: &Value, lang: Lang) -> Self {
        let doi = text(data, "DOI");
        let doi_url = (!doi.is_empty()).then(|| format!("https://doi.org/{doi}"));
        let url = text(data, "url");
        let link = doi_url
            .clone()
            .or_else(|| web_url(url).then(|| url.to_string()));
        let creators: Vec<&Value> = data
            .get("creators")
            .and_then(Value::as_array)
            .map(|a| a.iter().collect())
            .unwrap_or_default();
        // Authors when there are any, else whoever is credited first.
        let main_type = if creators.iter().any(|c| text(c, "creatorType") == "author") {
            "author"
        } else {
            creators
                .first()
                .map(|c| text(c, "creatorType"))
                .unwrap_or("")
        };
        let names: Vec<String> = creators
            .iter()
            .filter(|c| text(c, "creatorType") == main_type)
            .map(|c| match text(c, "name") {
                "" => format!("{} {}", text(c, "firstName"), text(c, "lastName"))
                    .trim()
                    .to_string(),
                full => full.to_string(),
            })
            .filter(|n| !n.is_empty())
            .collect();
        let mut authors = names
            .iter()
            .take(AUTHORS_MAX)
            .cloned()
            .collect::<Vec<_>>()
            .join(", ");
        if names.len() > AUTHORS_MAX {
            authors.push_str(" et al.");
        }
        let title = match text(data, "title") {
            "" => "Untitled",
            title => title,
        }
        .to_string();
        let date = text(data, "date");
        let container = CONTAINER_FIELDS
            .iter()
            .map(|field| text(data, field))
            .find(|value| !value.is_empty())
            .unwrap_or("")
            .to_string();
        let rights = text(data, "rights");
        WorkView {
            citation: citation(&authors, date, &title, &container, link.as_deref()),
            title,
            link,
            doi_url,
            authors,
            date: lang.date(date),
            container,
            kind: lang.item_type(text(data, "itemType")),
            language: lang.language(text(data, "language")),
            description: plain_text(text(data, "abstractNote")),
            license: rights.trim_end_matches('.').to_string(),
            license_url: web_url(rights).then(|| rights.to_string()),
        }
    }
}

/// `Haak, Fenner (2012). Title. Container. https://doi.org/…`, leaving out what
/// a work does not have.
fn citation(authors: &str, date: &str, title: &str, container: &str, link: Option<&str>) -> String {
    let year = date
        .split(|c: char| !c.is_ascii_digit())
        .find(|part| part.len() == 4);
    let byline = match (authors, year) {
        ("", None) => String::new(),
        ("", Some(year)) => format!("({year})"),
        (authors, None) => authors.to_string(),
        (authors, Some(year)) => format!("{authors} ({year})"),
    };
    [byline.as_str(), title, container, link.unwrap_or("")]
        .iter()
        .filter(|part| !part.is_empty())
        .map(|part| part.trim_end_matches('.'))
        .collect::<Vec<_>>()
        .join(". ")
}

/// `text` without tags: abstracts can hold JATS or HTML markup. A lone `<`, as
/// in "p < 0.05", stays.
fn plain_text(text: &str) -> String {
    let mut out = String::with_capacity(text.len());
    let mut rest = text;
    while let Some(at) = rest.find('<') {
        let (head, tail) = rest.split_at(at);
        out.push_str(head);
        let opens_tag = tail[1..]
            .chars()
            .next()
            .is_some_and(|c| c.is_ascii_alphabetic() || c == '/');
        match tail.find('>').filter(|_| opens_tag) {
            Some(end) => rest = &tail[end + 1..],
            None => {
                out.push('<');
                rest = &tail[1..];
            }
        }
    }
    out.push_str(rest);
    out.trim().to_string()
}

/// The first `max` characters or so of `text`, cut at a word.
fn summary(text: &str, max: usize) -> String {
    if text.chars().count() <= max {
        return text.to_string();
    }
    let cut: String = text.chars().take(max).collect();
    let cut = cut.rsplit_once(' ').map_or(cut.as_str(), |(head, _)| head);
    format!("{}…", cut.trim_end_matches([',', ';', ':', '.']))
}

#[cfg(test)]
mod tests {
    use super::*;
    use serde_json::json;

    #[test]
    fn normalizes_orcid_ids() {
        assert_eq!(
            normalize_orcid("https://orcid.org/0000-0003-1419-2405").as_deref(),
            Some("0000-0003-1419-2405")
        );
        assert_eq!(
            normalize_orcid("0000-0003-1419-2405").as_deref(),
            Some("0000-0003-1419-2405")
        );
        // Wrong check digit.
        assert_eq!(normalize_orcid("0000-0003-1419-2404"), None);
        assert_eq!(normalize_orcid("1"), None);
    }

    #[test]
    fn a_failed_fetch_is_not_retried_at_once() {
        let cache = PersonCache::default();
        assert!(cache.settled().is_none(), "nothing fetched yet");
        cache.fetch_failed();
        assert!(matches!(cache.settled(), Some(None)));
        cache.set(Person::default());
        assert!(matches!(cache.settled(), Some(Some(_))));
        // A failure keeps the record it has.
        cache.fetch_failed();
        assert!(matches!(cache.settled(), Some(Some(_))));
    }

    #[test]
    fn describes_works_as_citations() {
        let w = WorkView::new(
            &json!({
                "itemType": "journalArticle",
                "title": "ORCID: a system to uniquely identify researchers",
                "date": "2012-10-01",
                "DOI": "10.1087/20120404",
                "url": "https://example.org/orcid",
                "publicationTitle": "Learned Publishing",
                "language": "en-US",
                "rights": "https://creativecommons.org/licenses/by/4.0/",
                "creators": [
                    {"firstName": "Laurel", "lastName": "Haak", "creatorType": "author"},
                    {"name": "ORCID", "creatorType": "author"},
                    {"firstName": "Eve", "lastName": "Editor", "creatorType": "editor"},
                ],
            }),
            Lang::En,
        );
        assert_eq!(w.link.as_deref(), Some("https://doi.org/10.1087/20120404"));
        assert_eq!(w.authors, "Laurel Haak, ORCID");
        assert_eq!(w.date, "October 1, 2012");
        assert_eq!(w.container, "Learned Publishing");
        assert_eq!(w.kind, "Journal article");
        assert_eq!(w.language, "English");
        assert!(w.license_url.is_some());
        assert_eq!(
            w.citation,
            "Laurel Haak, ORCID (2012). ORCID: a system to uniquely identify researchers. \
             Learned Publishing. https://doi.org/10.1087/20120404"
        );

        let many: Vec<Value> = (0..7)
            .map(|i| json!({"lastName": format!("A{i}"), "creatorType": "author"}))
            .collect();
        let w = WorkView::new(
            &json!({
                "itemType": "blogPost", "url": "javascript:alert(1)", "creators": many,
                "rights": "CC BY 4.0.", "tags": [{"tag": "secret"}],
            }),
            Lang::De,
        );
        assert_eq!(w.link, None);
        assert_eq!(w.title, "Untitled");
        assert_eq!(w.authors, "A0, A1, A2, A3, A4 et al.");
        assert_eq!(w.kind, "Blogbeitrag");
        assert_eq!(w.license, "CC BY 4.0");
        assert_eq!(w.license_url, None);
        assert!(!w.citation.contains("secret"));
    }

    #[test]
    fn reads_the_person_card() {
        let person: Person = serde_json::from_value(json!({
            "id": "https://orcid.org/0000-0003-1419-2405",
            "given_name": "Martin",
            "family_name": "Fenner",
            "additional_names": ["Martin Hellmut Fenner"],
            "description": "First paragraph.\nSecond paragraph.",
            "affiliations": [
                {"name": "Front Matter", "role": "Founder", "start_date": "2021-08-01"},
                {"identifier": "https://ror.org/04wxnsj81", "identifier_type": "ROR",
                 "name": "DataCite", "start_date": "2015-08", "end_date": "2021-07-31"},
            ],
            "urls": [
                {"name": "Homepage", "url": "https://front-matter.de/mfenner"},
                {"name": "Bad", "url": "javascript:alert(1)"},
            ],
            "country": "DE",
        }))
        .unwrap();
        let view = PersonView::new("0000-0003-1419-2405", &person, Lang::En);
        assert_eq!(view.name, "Martin Fenner");
        assert_eq!(view.description, "First paragraph. Second paragraph.");
        assert_eq!(view.urls.len(), 1);
        assert_eq!(view.country, "Germany");
        assert_eq!(view.affiliations[0].dates, "Started August 1, 2021");
        assert_eq!(view.affiliations[0].ror, None);
        assert_eq!(
            view.affiliations[1].ror.as_deref(),
            Some("https://ror.org/04wxnsj81")
        );
        assert!(view.json.contains("Fenner"));
        let view = PersonView::new("0000-0003-1419-2405", &person, Lang::De);
        assert_eq!(view.country, "Deutschland");
        assert_eq!(view.affiliations[0].dates, "Beginn 1. August 2021");
    }

    #[test]
    fn abstracts_lose_their_markup() {
        assert_eq!(
            plain_text("<jats:p>Results: p < 0.05 for <i>all</i></jats:p>"),
            "Results: p < 0.05 for all"
        );
        assert_eq!(plain_text("unclosed <b"), "unclosed <b");
    }

    #[test]
    fn summaries_end_at_a_word() {
        assert_eq!(summary("short", 200), "short");
        assert_eq!(summary("one two three four", 12), "one two…");
    }
}