🎊 release major version

.gitignore

@@ -1,18 +1,15 @@
-# Build and Release Folders
-bin-debug/
-bin-release/
-[Oo]bj/
-[Bb]in/
+# Mac
+.DS_Store
 
-# Other files and folders
-.settings/
+# JetBrains
+.idea/
 
-# Executables
-*.swf
-*.air
-*.ipa
-*.apk
+# Visual Studio Code
+.vscode/
+
+# Python
+__pycache__/
+
+# Tests
+testing/
 
-# Project files, i.e. `.project`, `.actionScriptProperties` and `.flexProperties`
-# should NOT be excluded as they contain compiler settings and other important
-# information for Eclipse / Flash Builder.

Dockerfile

@@ -0,0 +1,21 @@
+FROM ubuntu
+
+RUN apt-get update \
+    && apt-get install -y git python3-pip python3.6 \
+    && apt-get install -y openslide-tools vim
+
+COPY ./*.py /opt/
+COPY requirements.txt /opt/
+
+COPY ./images.sh /usr/bin/images
+RUN chmod 0755 /usr/bin/images
+COPY ./annotations.sh /usr/bin/annotations
+RUN chmod 0755 /usr/bin/annotations
+
+RUN cd /opt \
+    && pip3 install -r /opt/requirements.txt
+
+COPY run.sh /tmp/run.sh
+RUN chmod 755 /tmp/run.sh
+
+CMD ["sh", "/tmp/run.sh"]

README.md

@@ -1,2 +1,32 @@
 # quip_reports
-Report generator
+For SEER VTR Pilot
+
+## Usage
+
+**Output directory:** `/data/reports`
+
+1. **Print images**
+
+Prints a list of images for a given collection, with Collection, Study ID, Subject ID, Image ID, Date.  
+
+For all collections, pass "all" instead of "collection name".
+<!-- python3.6 images.py username password "collection name" -->
+
+```
+docker exec quip-reports images username password "collection name"
+```
+
+2. **Print annotations**
+
+Prints list of images and their associated annotations, for a given collection.  Output columns: Collection, Study ID, Subject ID, Image ID, Segmentation Exec ID, Heatmap Exec ID, Featuremap ID.
+
+<!-- For all collections, pass "all" instead of "collection name". -->
+<!-- python3.6 annotations.py username password "collection name" -->
+
+```
+docker exec quip-reports annotations username password "collection name"
+```
+
+<!-- 
+docker build -t quip_reports . && docker run --network="quip_distro_default" --name quip-reports -it -d quip_reports /bin/bash
+-->

annotations.py

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+import csv
+import datetime
+import re
+import sys
+import time
+
+from mongoapi import *
+from pathdbapi import *
+
+
+def usage():
+    print('Usage: ' + sys.argv[0] + ' [username] [password] [collection name | "all"]')
+    exit(1)
+
+
+if len(sys.argv) == 4:
+    username = sys.argv[1]
+    password = sys.argv[2]
+    collection = sys.argv[3]
+else:
+    usage()
+
+if 'all' in collection.lower():
+    usage()
+
+host = "http://quip-pathdb"
+api = MyApi(host, username, password)
+
+hasNext = True
+count = 0
+collection_id = 0
+collection_name = ''
+out_dir = '/data/reports/'
+everything = False
+stamp = datetime.datetime.fromtimestamp(time.time()).strftime('%Y%m%d_%H%M%S')
+
+# if 'all' in collection.lower():
+# everything = True
+# images_url = '/listofimages?_format=json'
+# lookup_table = api.get_collection_lookup_table()
+# name = 'all'
+# else:
+everything = False
+collection_id, collection_name = api.get_collection_info(collection)
+if len(collection_name) == 0:
+    print("Could not find collection:", collection)
+    exit(1)
+images_url = '/listofimages/' + str(collection_id) + '?_format=json'
+name = re.sub('\W+', '', collection_name).lower()
+
+with open(out_dir + 'annotations_' + name + '_' + stamp + '.csv', mode='w') as csv_file:
+    csv_writer = csv.writer(csv_file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+    csv_writer.writerow(
+        ['Collection', 'Study ID', 'Subject ID', 'Image ID', 'Segmentation ExecID', 'Heatmap ExecID', 'Featuremap ID'])
+    first_nid = 0
+    while hasNext:
+        count += 1
+
+        url = images_url
+        if count > 1:
+            url += '&page=' + str(count)
+
+        response = api.get_data(url)
+        if len(response) > 0:
+            if count == 1:
+                first_nid = response[0]['nid'][0]['value']
+            if count > 1:
+                nid = response[0]['nid'][0]['value']
+                if nid == first_nid:
+                    break
+            for r in response:
+                nid = r['nid'][0]['value']
+                imageid = r['imageid'][0]['value']
+                studyid = r['studyid'][0]['value']
+                subjectid = r['clinicaltrialsubjectid'][0]['value']
+
+                my_set = segmentations(nid, imageid, studyid, subjectid)
+                if len(my_set) > 0:
+                    for i in my_set:
+                        csv_writer.writerow([collection_name, studyid, subjectid, imageid, i])
+                else:
+                    csv_writer.writerow([collection_name, studyid, subjectid, imageid, 'None'])
+
+                my_set = heatmaps(nid, imageid, studyid, subjectid)
+                if len(my_set) > 0:
+                    for i in my_set:
+                        csv_writer.writerow([collection_name, studyid, subjectid, imageid, ' ', i])
+                else:
+                    csv_writer.writerow([collection_name, studyid, subjectid, imageid, ' ', 'None'])
+
+                my_set = api.get_featuremaps(nid)
+                if len(my_set) > 0:
+                    for i in my_set:
+                        csv_writer.writerow([collection_name, studyid, subjectid, imageid, ' ', ' ', i])
+                else:
+                    csv_writer.writerow([collection_name, studyid, subjectid, imageid, ' ', ' ', 'None'])
+        else:
+            hasNext = False
+
+exit(0)

annotations.sh

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+#!/usr/bin/env bash
+# A convenience script to call annotations.py
+# -------------------------------------------------------
+if [ "$#" -ne 3 ]; then
+  echo "Usage: $0 username password collection"
+  exit 1
+fi
+
+SECONDS=0
+pythonFile="/opt/annotations.py"
+python3.6 "$pythonFile" "$@"
+exit_code="$?"
+ELAPSED="$(($SECONDS / 3600))hrs $(($SECONDS / 60 % 60))min $(($SECONDS % 60))sec"
+
+if [ "$exit_code" -eq 0 ]; then
+  echo "Done. $ELAPSED"
+else
+  NORMAL="\\033[0;39m"
+  RED="\\033[1;31m"
+  printf "${RED}Something went wrong.${NORMAL}\n"
+fi

docker-compose.yml

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+version: '3.5'
+
+services:
+  reports:
+    build:
+      context: .
+    image: quip_reports
+    container_name: quip-reports
+    volumes:
+      - /data/reports:/data/reports
+    networks:
+      - quip_distro_default
+
+networks:
+  quip_distro_default:
+   name: quip_distro_default

images.py

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+import csv
+import datetime
+import re
+import sys
+import time
+
+from pathdbapi import *
+
+
+def usage():
+    print('Usage: ' + sys.argv[0] + ' [username] [password] [collection name | "all"]')
+    exit(1)
+
+
+if len(sys.argv) == 4:
+    username = sys.argv[1]
+    password = sys.argv[2]
+    collection = sys.argv[3]
+else:
+    usage()
+
+host = "http://quip-pathdb"
+api = MyApi(host, username, password)
+
+hasNext = True
+count = 0
+collection_id = 0
+collection_name = ''
+out_dir = '/data/reports/'
+everything = False
+stamp = datetime.datetime.fromtimestamp(time.time()).strftime('%Y%m%d_%H%M%S')
+
+if 'all' in collection.lower():
+    everything = True
+    images_url = '/listofimages?_format=json'
+    lookup_table = api.get_collection_lookup_table()
+    name = 'all'
+else:
+    everything = False
+    collection_id, collection_name = api.get_collection_info(collection)
+    if len(collection_name) == 0:
+        print("Could not find collection:", collection)
+        exit(1)
+    images_url = '/listofimages/' + str(collection_id) + '?_format=json'
+    name = re.sub('\W+', '', collection_name).lower()
+
+with open(out_dir + 'images_' + name + '_' + stamp + '.csv', mode='w') as csv_file:
+    csv_writer = csv.writer(csv_file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+    csv_writer.writerow(['Collection', 'Study ID', 'Subject ID', 'Image ID', 'Date'])
+    first_nid = 0
+    while hasNext:
+        count += 1
+
+        url = images_url
+        if count > 1:
+            url += '&page=' + str(count)
+
+        response = api.get_data(url)
+        if len(response) > 0:
+            if count == 1:
+                first_nid = response[0]['nid'][0]['value']
+            if count > 1:
+                nid = response[0]['nid'][0]['value']
+                if nid == first_nid:
+                    break
+            for r in response:
+                datetime_str = r['created'][0]['value'].replace("T", " ")
+                datetime_str = datetime_str.replace("+00:00", "")
+
+                if everything:
+                    collection_id = r['field_collection'][0]['target_id']
+                    collection_name = lookup_table[collection_id]
+
+                csv_writer.writerow([collection_name, r['studyid'][0]['value'], r['clinicaltrialsubjectid'][0]['value'],
+                                     r['imageid'][0]['value'], datetime_str])
+        else:
+            hasNext = False
+
+exit(0)

images.sh

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+#!/usr/bin/env bash
+# A convenience script to call images.py
+# -------------------------------------------------------
+if [ "$#" -ne 3 ]; then
+  echo "Usage: $0 username password collection"
+  exit 1
+fi
+
+SECONDS=0
+pythonFile="/opt/images.py"
+python3.6 "$pythonFile" "$@"
+exit_code="$?"
+ELAPSED="$(($SECONDS / 3600))hrs $(($SECONDS / 60 % 60))min $(($SECONDS % 60))sec"
+
+if [ "$exit_code" -eq 0 ]; then
+  echo "Done. $ELAPSED"
+else
+  NORMAL="\\033[0;39m"
+  RED="\\033[1;31m"
+  printf "${RED}Something went wrong.${NORMAL}\n"
+fi

mongoapi.py

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+import pymongo
+
+host = 'ca-mongo'
+my_client = pymongo.MongoClient("mongodb://" + host + ":27017/")
+my_db = my_client["camic"]
+heat_col = my_db['heatmap']
+mark_col = my_db['mark']
+
+
+def get_data(query, collection):
+    my_set = set()
+    for x in collection.find(query, {
+        "provenance.analysis.execution_id": 1,
+        "_id": 0
+    }):
+        my_set.add(x['provenance']['analysis']['execution_id'])
+    return my_set
+
+
+def segmentations(nid, imageid, studyid, subjectid):
+    return get_data({
+        "provenance.image.slide": str(nid),
+        "provenance.image.imageid": imageid,
+        "provenance.image.study": studyid,
+        "provenance.image.subject": subjectid
+    }, mark_col)
+
+
+def heatmaps(nid, imageid, studyid, subjectid):
+    return get_data({
+        "provenance.image.slide": str(nid),
+        "provenance.image.subject_id": subjectid,
+        "provenance.image.case_id": imageid,
+        "provenance.analysis.study_id": studyid
+    }, heat_col)