Skip to content

Commit 22c3482

Browse files
judacasjudacas
authored
Merge branch 'main' into dependabot/pip/commitizen-4.6.0
2 parents 094f4ce + ff74664 commit 22c3482

35 files changed

+7743
-2985
lines changed

‎.github/dependabot.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55

66
version: 2
77
updates:
8-
- package-ecosystem: "pip" # See documentation for possible values
9-
directory: "/" # Location of package manifests
8+
- package-ecosystem: "pip"
9+
directory: "/"
1010
schedule:
1111
interval: "weekly"

‎.github/workflows/dependabot-auto-merge.yml‎

Lines changed: 33 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
name: Dependabot Auto-Merge
2+
3+
on:
4+
pull_request_target:
5+
types: [opened, synchronize]
6+
7+
permissions:
8+
contents: write
9+
pull-requests: write
10+
11+
jobs:
12+
auto-merge:
13+
if: ${{ github.actor == 'dependabot[bot]' }}
14+
runs-on: ubuntu-latest
15+
steps:
16+
- name: Fetch metadata
17+
id: metadata
18+
uses: dependabot/fetch-metadata@v1
19+
with:
20+
github-token: "${{ secrets.GITHUB_TOKEN }}"
21+
22+
- name: Approve PR
23+
run: gh pr review --approve "$PR_URL"
24+
env:
25+
PR_URL: ${{ github.event.pull_request.html_url }}
26+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
27+
28+
- name: Enable auto-merge
29+
if: ${{ steps.metadata.outputs.update-type != 'version-update:semver-major' }}
30+
run: gh pr merge --auto --squash "$PR_URL"
31+
env:
32+
PR_URL: ${{ github.event.pull_request.html_url }}
33+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.pre-commit-config.yaml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -26,6 +26,7 @@ repos:
2626
- id: debug-statements
2727
- id: check-merge-conflict
2828
- id: check-added-large-files
29+
args: ["--maxkb=102400"]
2930
repo: https://github.com/pre-commit/pre-commit-hooks
3031
rev: v5.0.0
3132
- hooks:

‎output/allTrials/identified/NCT00001073_identified.json‎

Lines changed: 9 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@
3030
"criterion": "gender",
3131
"requirements": [
3232
{
33-
"requirement_type": "expected_value",
33+
"requirement_type": "expected gender",
3434
"expected_value": "female"
3535
}
3636
]
@@ -88,7 +88,7 @@
8888
"line": "* Are at least 13 years old. (Need consent of parent or guardian if under 18.)",
8989
"criterions": [
9090
{
91-
"exact_snippets": "Are at least 13 years old.",
91+
"exact_snippets": "at least 13 years old",
9292
"criterion": "age",
9393
"requirements": [
9494
{
@@ -102,16 +102,12 @@
102102
]
103103
},
104104
{
105-
"exact_snippets": "Need consent of parent or guardian if under 18.",
106-
"criterion": "age",
105+
"exact_snippets": "Need consent of parent or guardian if under 18",
106+
"criterion": "parental consent",
107107
"requirements": [
108108
{
109-
"requirement_type": "parental consent",
110-
"expected_value": {
111-
"operator": "<",
112-
"value": 18,
113-
"unit": "years"
114-
}
109+
"requirement_type": "requirement",
110+
"expected_value": "required if under 18"
115111
}
116112
]
117113
}
@@ -187,13 +183,9 @@
187183
{
188184
"requirement_type": "time since procedure",
189185
"expected_value": {
190-
"comparisons": [
191-
{
192-
"operator": "<=",
193-
"value": 4,
194-
"unit": "months"
195-
}
196-
]
186+
"operator": "<=",
187+
"value": 4,
188+
"unit": "months"
197189
}
198190
}
199191
]

‎output/allTrials/identified/NCT00001120_identified.json‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -63,7 +63,7 @@
6363
"line": "* Have a CD4+ cell count of 200 cells/mm3 or below.",
6464
"criterions": [
6565
{
66-
"exact_snippets": "CD4+ cell count of 200 cells/mm3 or below",
66+
"exact_snippets": "CD4+ cell count ... 200 cells/mm3 or below",
6767
"criterion": "CD4+ cell count",
6868
"requirements": [
6969
{
@@ -86,7 +86,7 @@
8686
"criterion": "age",
8787
"requirements": [
8888
{
89-
"requirement_type": "minimum",
89+
"requirement_type": "minimum age",
9090
"expected_value": {
9191
"operator": ">=",
9292
"value": 18,

‎output/allTrials/identified/NCT00001148_identified.json‎

Lines changed: 39 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -58,23 +58,14 @@
5858
},
5959
{
6060
"exact_snippets": "WHO grade III and IV, WHO classification of glial tumors",
61-
"criterion": "tumor grade",
61+
"criterion": "WHO grade",
6262
"requirements": [
6363
{
6464
"requirement_type": "classification",
65-
"expected_value": {
66-
"operator": "=",
67-
"value": 3,
68-
"unit": "WHO grade"
69-
}
70-
},
71-
{
72-
"requirement_type": "classification",
73-
"expected_value": {
74-
"operator": "=",
75-
"value": 4,
76-
"unit": "WHO grade"
77-
}
65+
"expected_value": [
66+
"III",
67+
"IV"
68+
]
7869
}
7970
]
8071
}
@@ -268,7 +259,7 @@
268259
"requirements": [
269260
{
270261
"requirement_type": "level",
271-
"expected_value": "> 3 times the upper limit of normal"
262+
"expected_value": "greater than 3 times the upper limit of normal"
272263
}
273264
]
274265
}
@@ -292,7 +283,7 @@
292283
]
293284
},
294285
{
295-
"exact_snippets": "Coagulopathy ... activated partial thromboplastin time [APTT] > 1.5 times control)",
286+
"exact_snippets": "Coagulopathy ... activated partial thromboplastin time [APTT] > 1.5 times control",
296287
"criterion": "activated partial thromboplastin time (APTT)",
297288
"requirements": [
298289
{
@@ -349,7 +340,7 @@
349340
"line": "Acute infection.",
350341
"criterions": [
351342
{
352-
"exact_snippets": "Acute infection.",
343+
"exact_snippets": "Acute infection",
353344
"criterion": "acute infection",
354345
"requirements": [
355346
{
@@ -364,7 +355,7 @@
364355
"line": "Acute medical problems.",
365356
"criterions": [
366357
{
367-
"exact_snippets": "Acute medical problems.",
358+
"exact_snippets": "Acute medical problems",
368359
"criterion": "acute medical problems",
369360
"requirements": [
370361
{
@@ -413,7 +404,7 @@
413404
"line": "Allergy to CT contrast agents.",
414405
"criterions": [
415406
{
416-
"exact_snippets": "Allergy to CT contrast agents",
407+
"exact_snippets": "Allergy to CT contrast agents.",
417408
"criterion": "allergy",
418409
"requirements": [
419410
{
@@ -428,7 +419,7 @@
428419
"line": "Absence of tumor-specific gene mutation.",
429420
"criterions": [
430421
{
431-
"exact_snippets": "Absence of tumor-specific gene mutation",
422+
"exact_snippets": "Absence of tumor-specific gene mutation.",
432423
"criterion": "tumor-specific gene mutation",
433424
"requirements": [
434425
{
@@ -438,16 +429,28 @@
438429
]
439430
}
440431
]
432+
}
433+
],
434+
"failed_inclusion": [],
435+
"failed_exclusion": [],
436+
"failed_miscellaneous": [
437+
{
438+
"line": "INCLUSION CRITERIA:",
439+
"criterions": []
440+
},
441+
{
442+
"line": "EXCLUSION CRITERIA:",
443+
"criterions": []
441444
},
442445
{
443446
"line": "Pregnant women. Women of child-bearing potential will undergo a urine and/or serum pregnancy test. Women who are pregnant will not be allowed to participate in this study.",
444447
"criterions": [
445448
{
446-
"exact_snippets": "Pregnant women ... Women who are pregnant will not be allowed to participate",
449+
"exact_snippets": "Pregnant women. Women who are pregnant will not be allowed to participate",
447450
"criterion": "pregnancy",
448451
"requirements": [
449452
{
450-
"requirement_type": "status",
453+
"requirement_type": "presence",
451454
"expected_value": false
452455
}
453456
]
@@ -457,24 +460,25 @@
457460
"criterion": "child-bearing potential",
458461
"requirements": [
459462
{
460-
"requirement_type": "status",
463+
"requirement_type": "presence",
461464
"expected_value": true
462465
}
463466
]
467+
},
468+
{
469+
"exact_snippets": "urine and/or serum pregnancy test",
470+
"criterion": "pregnancy test",
471+
"requirements": [
472+
{
473+
"requirement_type": "type",
474+
"expected_value": [
475+
"urine",
476+
"serum"
477+
]
478+
}
479+
]
464480
}
465481
]
466482
}
467-
],
468-
"failed_inclusion": [],
469-
"failed_exclusion": [],
470-
"failed_miscellaneous": [
471-
{
472-
"line": "INCLUSION CRITERIA:",
473-
"criterions": []
474-
},
475-
{
476-
"line": "EXCLUSION CRITERIA:",
477-
"criterions": []
478-
}
479483
]
480484
}

0 commit comments

Comments
 (0)