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yh202109 committed Aug 27, 2024
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6 changes: 3 additions & 3 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
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2 changes: 1 addition & 1 deletion _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
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<?xml version="1.0" ?>
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<sources>
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4 changes: 2 additions & 2 deletions _sources/std_iso_pdf.ipynb.txt
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Expand Up @@ -147,8 +147,6 @@
},
"outputs": [],
"source": [
"from IPython.display import Image \n",
"\n",
"display.Image(img, width=300)"
]
},
Expand All @@ -173,6 +171,8 @@
},
"outputs": [],
"source": [
"from IPython.display import Image \n",
"\n",
"img_path = pfr.get_image(page_index=3, image_index=1, outfolder='.')\n",
"img = Image(filename=img_path, width=300)\n",
"display(img)"
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2 changes: 1 addition & 1 deletion _static/reports/coverage/coverage.xml
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<?xml version="1.0" ?>
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<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.1 -->
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<sources>
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2 changes: 1 addition & 1 deletion _static/reports/junit/junit.xml
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<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="35" time="8.844" timestamp="2024-08-27T22:29:49.869135+00:00" hostname="fv-az1205-210"><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_include" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_outfmt" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_load_list" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_show_ctoc_tree" time="0.201" /><testcase classname="tests.test_health_emt.TestEmt" name="test_expected_file_lists" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_files" time="0.005" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlgt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_llt" time="0.007" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc_primary_only" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_soc" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_list_files" time="0.025" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.767" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.808" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.906" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_invalid_input" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_missing_column" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_with_difference" time="0.004" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_without_difference" time="0.002" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_existing_column" time="0.009" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_column" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_group" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_same_group_and_column" time="0.001" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_boxplot" time="0.406" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_lineplot" time="0.347" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_update_parameters" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_dataframe" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_json" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_list" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_string" time="0.000" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_tree" time="0.014" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_tree2" time="0.009" /></testsuite></testsuites>
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6 changes: 3 additions & 3 deletions _static/reports/junit/report.html
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8 changes: 4 additions & 4 deletions example_cdtg.html
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Expand Up @@ -129,13 +129,13 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 5.6% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 33.3% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
warnings.warn(msg, UserWarning)
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 30.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 40.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
warnings.warn(msg, UserWarning)
</pre></div>
</div>
<img alt="_images/a656aaccdb3694d7775653a1cf6015dcaa93597b11d8781dc738810c96cfb77f.png" src="_images/a656aaccdb3694d7775653a1cf6015dcaa93597b11d8781dc738810c96cfb77f.png" />
<img alt="_images/1a7d12d317dcda45dc7920a7551b91ce1870fb6e7480d72777fda07bf81d8acf.png" src="_images/1a7d12d317dcda45dc7920a7551b91ce1870fb6e7480d72777fda07bf81d8acf.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -147,7 +147,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/fd836e8f450653c4f883d5155140d65cf378517c181e7aa3320e906e21ca3c34.png" src="_images/fd836e8f450653c4f883d5155140d65cf378517c181e7aa3320e906e21ca3c34.png" />
<img alt="_images/c6ecbd49d2027a956d0d6e0037dfbe2f68a698886b74287ae7ecd2c6a26bf938.png" src="_images/c6ecbd49d2027a956d0d6e0037dfbe2f68a698886b74287ae7ecd2c6a26bf938.png" />
</div>
</div>
</section>
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76 changes: 38 additions & 38 deletions example_clinical.html
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Expand Up @@ -127,8 +127,8 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit meal calorie
0 STD1 TRT1 SUBJ01 VISIT1 1 582
1 STD1 TRT1 SUBJ01 VISIT1 2 1987
0 STD1 TRT1 SUBJ01 VISIT1 1 1433
1 STD1 TRT1 SUBJ01 VISIT1 2 1595
</pre></div>
</div>
</div>
Expand All @@ -145,12 +145,12 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit N(0&lt;=X&lt;500) N(500&lt;=X&lt;1000) \
0 STD1 TRT1 SUBJ01 VISIT1 0 2
1 STD1 TRT1 SUBJ01 VISIT2 0 0
0 STD1 TRT1 SUBJ01 VISIT1 0 0
1 STD1 TRT1 SUBJ01 VISIT2 1 3

N(1000&lt;=V&lt;=2000) N(all)
0 1 3
1 3 3
0 2 2
1 1 5
</pre></div>
</div>
</div>
Expand All @@ -165,22 +165,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit N(0&lt;=X&lt;3) N(3&lt;=X&lt;5) N(5&lt;=V&lt;=7) N(all)
0 STD1 TRT1 VISIT1 6 9 5 20
1 STD1 TRT1 VISIT2 2 7 5 14
2 STD1 TRT1 VISIT3 4 6 2 12
3 STD1 TRT1 VISIT4 3 5 0 8
4 STD1 TRT2 VISIT1 5 11 4 20
5 STD1 TRT2 VISIT2 3 9 4 16
6 STD1 TRT2 VISIT3 4 7 1 12
7 STD1 TRT2 VISIT4 0 2 4 6
8 STD2 TRT1 VISIT1 5 14 1 20
9 STD2 TRT1 VISIT2 5 5 2 12
10 STD2 TRT1 VISIT3 1 2 4 7
11 STD2 TRT1 VISIT4 0 1 1 2
12 STD2 TRT2 VISIT1 0 16 4 20
13 STD2 TRT2 VISIT2 4 8 1 13
14 STD2 TRT2 VISIT3 4 4 1 9
15 STD2 TRT2 VISIT4 0 2 3 5
0 STD1 TRT1 VISIT1 7 9 4 20
1 STD1 TRT1 VISIT2 4 4 7 15
2 STD1 TRT1 VISIT3 2 6 2 10
3 STD1 TRT1 VISIT4 4 2 3 9
4 STD1 TRT2 VISIT1 4 11 5 20
5 STD1 TRT2 VISIT2 4 7 4 15
6 STD1 TRT2 VISIT3 2 7 1 10
7 STD1 TRT2 VISIT4 2 4 0 6
8 STD2 TRT1 VISIT1 6 9 5 20
9 STD2 TRT1 VISIT2 5 3 4 12
10 STD2 TRT1 VISIT3 2 5 2 9
11 STD2 TRT1 VISIT4 2 0 2 4
12 STD2 TRT2 VISIT1 8 9 3 20
13 STD2 TRT2 VISIT2 5 10 3 18
14 STD2 TRT2 VISIT3 2 4 2 8
15 STD2 TRT2 VISIT4 2 1 1 4
</pre></div>
</div>
</div>
Expand All @@ -194,22 +194,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit Sum(0&lt;=X&lt;3) Sum(3&lt;=X&lt;5) Sum(5&lt;=V&lt;=7) Sum(all)
0 STD1 TRT1 VISIT1 12 30 25 67
1 STD1 TRT1 VISIT2 4 24 25 53
2 STD1 TRT1 VISIT3 8 19 10 37
3 STD1 TRT1 VISIT4 6 16 0 22
4 STD1 TRT2 VISIT1 10 41 20 71
5 STD1 TRT2 VISIT2 6 31 20 57
6 STD1 TRT2 VISIT3 8 26 5 39
7 STD1 TRT2 VISIT4 0 8 20 28
8 STD2 TRT1 VISIT1 10 50 5 65
9 STD2 TRT1 VISIT2 10 20 10 40
10 STD2 TRT1 VISIT3 2 7 20 29
11 STD2 TRT1 VISIT4 0 3 5 8
12 STD2 TRT2 VISIT1 0 55 20 75
13 STD2 TRT2 VISIT2 8 30 5 43
14 STD2 TRT2 VISIT3 8 15 5 28
15 STD2 TRT2 VISIT4 0 7 15 22
0 STD1 TRT1 VISIT1 14 32 20 66
1 STD1 TRT1 VISIT2 8 13 35 56
2 STD1 TRT1 VISIT3 4 23 10 37
3 STD1 TRT1 VISIT4 8 8 15 31
4 STD1 TRT2 VISIT1 8 36 25 69
5 STD1 TRT2 VISIT2 8 22 20 50
6 STD1 TRT2 VISIT3 4 24 5 33
7 STD1 TRT2 VISIT4 4 15 0 19
8 STD2 TRT1 VISIT1 12 30 25 67
9 STD2 TRT1 VISIT2 10 10 20 40
10 STD2 TRT1 VISIT3 4 18 10 32
11 STD2 TRT1 VISIT4 4 0 10 14
12 STD2 TRT2 VISIT1 16 33 15 64
13 STD2 TRT2 VISIT2 10 35 15 60
14 STD2 TRT2 VISIT3 4 14 10 28
15 STD2 TRT2 VISIT4 4 4 5 13
</pre></div>
</div>
</div>
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3 changes: 0 additions & 3 deletions example_ectd.html
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Expand Up @@ -725,9 +725,6 @@ <h2>Module 5<a class="headerlink" href="#module-5" title="Link to this heading">
└── 5.4 Literature references
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
</div>
</section>
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