Automated report

hubmapconsortium · Aug 22, 2022 · 0689a12 · 0689a12
1 parent 340d2b8
commit 0689a12
Show file tree

Hide file tree

Showing 150 changed files with 33,097 additions and 7,357 deletions.
diff --git a/graphs/ccf_Blood_graph.pdf b/graphs/ccf_Blood_graph.pdf
diff --git a/graphs/ccf_Blood_vasculature_graph.pdf b/graphs/ccf_Blood_vasculature_graph.pdf
diff --git a/graphs/ccf_Bone-Marrow_graph.pdf b/graphs/ccf_Bone-Marrow_graph.pdf
diff --git a/graphs/ccf_Brain_graph.pdf b/graphs/ccf_Brain_graph.pdf
diff --git a/graphs/ccf_Eye_graph.pdf b/graphs/ccf_Eye_graph.pdf
diff --git a/graphs/ccf_Fallopian_tube_graph.pdf b/graphs/ccf_Fallopian_tube_graph.pdf
diff --git a/graphs/ccf_Heart_graph.pdf b/graphs/ccf_Heart_graph.pdf
diff --git a/graphs/ccf_Kidney_graph.pdf b/graphs/ccf_Kidney_graph.pdf
diff --git a/graphs/ccf_Knee_graph.pdf b/graphs/ccf_Knee_graph.pdf
diff --git a/graphs/ccf_Large_intestine_graph.pdf b/graphs/ccf_Large_intestine_graph.pdf
diff --git a/graphs/ccf_Liver_graph.pdf b/graphs/ccf_Liver_graph.pdf
diff --git a/graphs/ccf_Lung_graph.pdf b/graphs/ccf_Lung_graph.pdf
diff --git a/graphs/ccf_Lymph_node_graph.pdf b/graphs/ccf_Lymph_node_graph.pdf
diff --git a/graphs/ccf_Lymph_vasculature_graph.pdf b/graphs/ccf_Lymph_vasculature_graph.pdf
diff --git a/graphs/ccf_Ovary_graph.pdf b/graphs/ccf_Ovary_graph.pdf
diff --git a/graphs/ccf_Pancreas_graph.pdf b/graphs/ccf_Pancreas_graph.pdf
diff --git a/graphs/ccf_Peripheral_nervous_system_graph.pdf b/graphs/ccf_Peripheral_nervous_system_graph.pdf
diff --git a/graphs/ccf_Placenta_graph.pdf b/graphs/ccf_Placenta_graph.pdf
diff --git a/graphs/ccf_Prostate_graph.pdf b/graphs/ccf_Prostate_graph.pdf
diff --git a/graphs/ccf_Skin_graph.pdf b/graphs/ccf_Skin_graph.pdf
diff --git a/graphs/ccf_Small_intestine_graph.pdf b/graphs/ccf_Small_intestine_graph.pdf
diff --git a/graphs/ccf_Spinal_Cord_graph.pdf b/graphs/ccf_Spinal_Cord_graph.pdf
diff --git a/graphs/ccf_Spleen_graph.pdf b/graphs/ccf_Spleen_graph.pdf
diff --git a/graphs/ccf_Thymus_graph.pdf b/graphs/ccf_Thymus_graph.pdf
diff --git a/graphs/ccf_Ureter_graph.pdf b/graphs/ccf_Ureter_graph.pdf
diff --git a/graphs/ccf_Urinary_bladder_graph.pdf b/graphs/ccf_Urinary_bladder_graph.pdf
diff --git a/graphs/ccf_Uterus_graph.pdf b/graphs/ccf_Uterus_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Blood_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Blood_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Blood_vasculature_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Blood_vasculature_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Brain_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Brain_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Eye_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Eye_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Fallopian_tube_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Fallopian_tube_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Heart_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Heart_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Kidney_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Kidney_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Knee_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Knee_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Large_intestine_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Large_intestine_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Liver_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Liver_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lung_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lung_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lymph_node_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lymph_node_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lymph_vasculature_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lymph_vasculature_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Ovary_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Ovary_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Pancreas_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Pancreas_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Peripheral_nervous_system_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Peripheral_nervous_system_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Prostate_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Prostate_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Skin_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Skin_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Small_intestine_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Small_intestine_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Spleen_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Spleen_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Thymus_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Thymus_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Ureter_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Ureter_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Urinary_bladder_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Urinary_bladder_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Uterus_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Uterus_graph.pdf
diff --git a/logs/error_class_Brain.log b/logs/error_class_Brain.log
diff --git a/logs/error_class_Heart.log b/logs/error_class_Heart.log
@@ -72,4 +72,4 @@ WARNING - No valid ID provided for 'FMA:83539', label: myocardium, user_label: M
 WARNING - No valid ID provided for 'FMA:83539', label: myocardium, user_label: Myocardium of interventricular septum
 WARNING - No valid ID provided for 'FMA:9535', label: myocardium, user_label: Myocardium of right ventricle
 WARNING - No valid ID provided for 'FMA:9535', label: myocardium, user_label: Myocardium of right ventricle
-WARNING - Unrecognised UBERON/CL entity 'CL:0002542'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:0002542'
diff --git a/logs/error_class_Kidney.log b/logs/error_class_Kidney.log
@@ -80,10 +80,10 @@ WARNING - No valid ID provided for '', label: descending thin limb of loop of He
 WARNING - No valid ID provided for '', label: descending thin limb of loop of Henle 2, user_label: 
 WARNING - No valid ID provided for '', label: descending thin limb of loop of Henle 2, user_label: 
 WARNING - No valid ID provided for '', label: descending thin limb of loop of Henle 3, user_label: 
-WARNING - Unrecognised UBERON/CL entity 'CL:4030016'
-WARNING - Unrecognised UBERON/CL entity 'CL:4030017'
-WARNING - Unrecognised UBERON/CL entity 'CL:4030018'
-WARNING - Unrecognised UBERON/CL entity 'CL:4030019'
-WARNING - Unrecognised UBERON/CL entity 'CL:4030020'
-WARNING - Unrecognised UBERON/CL entity 'CL:4030021'
-WARNING - Unrecognised UBERON/CL entity 'CL:4030022'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:4030016'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:4030017'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:4030018'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:4030019'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:4030020'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:4030021'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:4030022'
diff --git a/logs/error_class_Large_intestine.log b/logs/error_class_Large_intestine.log
@@ -117,4 +117,4 @@ WARNING - No valid ID provided for '', label: subepithelial membrane, user_label
 WARNING - No valid ID provided for '', label: subepithelial membrane, user_label: 
 WARNING - No valid ID provided for '', label: subepithelial membrane, user_label: 
 WARNING - No valid ID provided for '', label: subepithelial membrane, user_label: 
-WARNING - Unrecognised UBERON/CL entity 'CL:0008364'
+WARNING - Unrecognised UBERON/CL/PCL entity 'CL:0008364'
diff --git a/logs/report_images_Blood_vasculature.tsv b/logs/report_images_Blood_vasculature.tsv
@@ -10,8 +10,8 @@ UBERON:0001138	http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png
 UBERON:0001139	https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif
 UBERON:0001140	http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png
 UBERON:0001142	http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png
-UBERON:0001182	http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png
 UBERON:0001182	http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif
+UBERON:0001182	http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png
 UBERON:0001183	http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png
 UBERON:0001184	http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png
 UBERON:0001185	http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png

diff --git a/logs/report_images_Brain.tsv b/logs/report_images_Brain.tsv
@@ -31,8 +31,8 @@ UBERON:0002150	http://upload.wikimedia.org/wikipedia/commons/9/97/Gray704.png
 UBERON:0002151	http://upload.wikimedia.org/wikipedia/commons/d/dc/Lower_pons_horizontal_KB.svg
 UBERON:0002152	http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray705.png
 UBERON:0002163	http://upload.wikimedia.org/wikipedia/commons/f/fc/Gray677.png
-UBERON:0002264	http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg
 UBERON:0002264	http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg
+UBERON:0002264	http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg
 UBERON:0002265	http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png
 UBERON:0002285	http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png
 UBERON:0002289	http://upload.wikimedia.org/wikipedia/commons/d/da/Cn3nucleus.png

diff --git a/logs/report_images_Heart.tsv b/logs/report_images_Heart.tsv
@@ -12,10 +12,10 @@ UBERON:0002134	http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the
 UBERON:0002135	http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg
 UBERON:0002137	http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg
 UBERON:0002146	http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg
-UBERON:0002351	http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg
 UBERON:0002351	http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg
-UBERON:0002352	http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png
+UBERON:0002351	http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg
 UBERON:0002352	http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png
+UBERON:0002352	http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png
 UBERON:0002353	http://upload.wikimedia.org/wikipedia/commons/b/b6/ECG_Principle_fast.gif
 UBERON:0002353	http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png
 UBERON:0005438	http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray491.png

diff --git a/logs/report_images_Lung.tsv b/logs/report_images_Lung.tsv
@@ -1,7 +1,7 @@
 term	image_url
 UBERON:0001004	http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg
-UBERON:0001558	http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg
 UBERON:0001558	http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg
+UBERON:0001558	http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg
 UBERON:0002012	https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png
 UBERON:0002016	https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png
 UBERON:0002040	http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png
@@ -11,7 +11,7 @@ UBERON:0002184	http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung
 UBERON:0002187	https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png
 UBERON:0002188	https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png
 UBERON:0002299	https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg
-UBERON:0003126	http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg
 UBERON:0003126	http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg
+UBERON:0003126	http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg
 UBERON:0003604	http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png
 UBERON:0006679	http://upload.wikimedia.org/wikipedia/commons/f/f2/Diagrama_de_los_pulmones-c.svg
diff --git a/logs/report_images_Ovary.tsv b/logs/report_images_Ovary.tsv
@@ -4,8 +4,8 @@ UBERON:0000086	http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png
 UBERON:0000156	http://upload.wikimedia.org/wikipedia/commons/5/50/Mature_Graffian_follicle.jpg
 UBERON:0000992	http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png
 UBERON:0000992	https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png
-UBERON:0001305	https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG
 UBERON:0001305	http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg
+UBERON:0001305	https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG
 UBERON:0001306	http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray1164.png
 UBERON:0001342	http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray1111.png
 UBERON:0002512	http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg
diff --git a/logs/report_images_Peripheral_nervous_system.tsv b/logs/report_images_Peripheral_nervous_system.tsv
@@ -5,8 +5,8 @@ UBERON:0000377	http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png
 UBERON:0001148	http://upload.wikimedia.org/wikipedia/commons/a/a7/Nerves_of_the_left_upper_extremity.gif
 UBERON:0001322	http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray1244.png
 UBERON:0001492	http://upload.wikimedia.org/wikipedia/commons/e/e2/Gray818.png
-UBERON:0001493	https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg
 UBERON:0001493	http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg
+UBERON:0001493	https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg
 UBERON:0001494	https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg
 UBERON:0001494	http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg
 UBERON:0001579	http://upload.wikimedia.org/wikipedia/commons/b/be/Gray771.png
@@ -20,8 +20,8 @@ UBERON:0001649	http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png
 UBERON:0001650	http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png
 UBERON:0001759	http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png
 UBERON:0001780	https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg
-UBERON:0001785	http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg
 UBERON:0001785	http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg
+UBERON:0001785	http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg
 UBERON:0001814	http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png
 UBERON:0001814	http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg
 UBERON:0001884	http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png

diff --git a/logs/report_images_Skin.tsv b/logs/report_images_Skin.tsv
@@ -1,7 +1,7 @@
 term	image_url
 UBERON:0001821	http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png
-UBERON:0002027	https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png
 UBERON:0002027	http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png
+UBERON:0002027	https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png
 UBERON:0002067	http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg
 UBERON:0002072	http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg
 UBERON:0002073	https://upload.wikimedia.org/wikipedia/commons/4/4d/Hair_follicle-en.svg

diff --git a/logs/report_images_Spleen.tsv b/logs/report_images_Spleen.tsv
@@ -6,5 +6,5 @@ UBERON:0001251	http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png
 UBERON:0001473	http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg
 UBERON:0001959	http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png
 UBERON:0002106	https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg
-UBERON:0003713	http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png
 UBERON:0003713	http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png
+UBERON:0003713	http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png
diff --git a/logs/report_images_Uterus.tsv b/logs/report_images_Uterus.tsv
@@ -1,6 +1,6 @@
 term	image_url
-UBERON:0000995	https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png
 UBERON:0000995	http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png
+UBERON:0000995	https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png
 UBERON:0001295	https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg
 UBERON:0002451	http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png
 UBERON:0002493	http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png