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| author | zsloan | 2020-10-19 13:43:32 -0500 |
|---|---|---|
| committer | GitHub | 2020-10-19 13:43:32 -0500 |
| commit | 8eaae7296e2d66726975ddba0de8aecae256e63b (patch) | |
| tree | 5505b932195a454c1ada10677f0e76faba6b588f | |
| parent | 5fdb3b83566516782542d04b92a5be97f41c2330 (diff) | |
| parent | 3f242af74af814d9344e1e80c5f94914c6d9b621 (diff) | |
| download | genenetwork2-8eaae7296e2d66726975ddba0de8aecae256e63b.tar.gz | |
Merge branch 'testing' into scroller_testing
48 files changed, 1693 insertions, 561 deletions
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 789d6a57..7d7e34a5 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -26,7 +26,8 @@ If applicable, add screenshots to help explain your problem. **Environment setup (please complete the following information):** - OS: [e.g. Linux] -- Racket Version [e.g. v7.6] +- Guix Version (optional) +- [Anything else you think is relevant] **Additional context** diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 00000000..2fd9a886 --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,48 @@ +name: tests + +# Run actions when pushing to the testing branch or when you create a +# PR against it +on: + push: + branches: [ testing ] + pull_request: + branches: [ testing ] + +jobs: + unittest: + runs-on: ubuntu-latest + container: bonfacekilz/python2-genenetwork2:latest + + steps: + # First start with mariadb set then checkout. The checkout gives + # the mysqld enough time to start + - name: Set up mariadb + run: | + mysql_install_db --user=mysql --datadir=/usr/local/mysql + # Wait for the mysqld_safe process to start + mysqld_safe --user=mysql --datadir=/usr/local/mysql & + + # Use v1 of checkout since v2 fails + - name: Checkout Project + uses: actions/checkout@v1 + + # Redis is required by some of the tests 6379 + - name: Start Redis + run: | + /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server + + # Redis is required by some of the tests 6379 + - name: Bootstrap tables + run: | + mysql -u root -e "SHOW DATABASES;" + mysql -u root -e "CREATE DATABASE db_webqtl_s;" + mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';" + mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;" + + - name: Run the unit tests + run: | + env GN2_PROFILE=/gn2-profile \ + TMPDIR=/tmp SERVER_PORT=5004 \ + WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ + etc/default_settings.py -c -m unittest discover -v diff --git a/README.md b/README.md index 46264252..cd35defb 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ [](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2) [](http://joss.theoj.org/papers/10.21105/joss.00025) +[](https://github.com/genenetwork/genenetwork2/actions) # GeneNetwork @@ -42,9 +43,17 @@ Also mariadb and redis need to be running, see ## Testing To have tests pass, the redis and mariadb instance should be running, because of -asserts sprinkled in the code base(these will be removed in due time). +asserts sprinkled in the code base. + +Right now, the only tests running in CI are unittests. Please make +sure the existing unittests are green when submitting a PR. + +See +[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/doc/docker-container.org) +for more details. #### Mechanical Rob + We are building 'Mechanical Rob' automated testing using Python [requests](https://github.com/genenetwork/genenetwork2/tree/testing/test/requests) which can be run with: diff --git a/api_readme.md b/api_readme.md new file mode 100644 index 00000000..96e8b246 --- /dev/null +++ b/api_readme.md @@ -0,0 +1,155 @@ +# API Query Documentation # +--- +# Fetching Dataset/Trait info/data # +--- +## Fetch Species List ## + +To get a list of species with data available in GN (and their associated names and ids): +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species +[ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ] +``` + +Or to get a single species info: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json +``` + +*For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* + +## Fetch Groups/RISets ## + +This query can optionally filter by species: + +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species) +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse groups/RISets) +[ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] +``` + +## Fetch Genotypes for Group/RISet ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD +``` +Returns a CSV file with metadata in the first few rows, sample/strain names as columns, and markers as rows. Currently only works for genotypes we have stored in .geno files; I'll add the option to download BIMBAM files soon. + +## Fetch Datasets ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd +[ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ] +``` +(I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) + +## Fetch Sample Data for Dataset ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +``` + +Returns a CSV file with sample/strain names as the columns and trait IDs as rows + +## Fetch Individual Dataset Info ## +### For mRNA Assay/"ProbeSet" ### + +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` +{ "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 } +``` +(This also has the option to specify group/riset) + +### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ### +For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001 +{ "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } +``` + +## Fetch Sample Data for Single Trait ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at +[ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] +``` + +## Fetch Trait Info (Name, Description, Location, etc) ## +### For mRNA Expression/"ProbeSet" ### +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at +{ "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" } +``` + +### For "Phenotypes" ### +For phenotypes this just gets the max LRS, its location, and additive effect (as calculated by qtlreaper) + +Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001 +{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } +``` + +--- + +# Analyses # +--- +## Mapping ## +Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper + +Each method's query takes the following parameters respectively (more will be added): +### GEMMA ### +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false) +* maf - minor allele frequency (default = 0.01) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +``` + +### R/qtl ### +(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf) +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function. +* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function +* num_perm - number of permutations; 0 by default +* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate +* interval_mapping - Whether to use interval mapping; "false" by default +* pair_scan - *NYI* + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +``` + +Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) + +## Calculate Correlation ## +Currently only Sample and Tissue correlations are implemented + +This query currently takes the following parameters (though more will be added): +* trait_id (*required*) - ID for trait used for correlation +* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets) +* target_db (*required*) - Target DB name to be correlated against +* type - sample (default) | tissue +* method - pearson (default) | spearman +* return - Number of results to return (default = 500) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 +[ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ] +``` diff --git a/doc/docker-container.org b/doc/docker-container.org new file mode 100644 index 00000000..ec91824a --- /dev/null +++ b/doc/docker-container.org @@ -0,0 +1,89 @@ +#+TITLE: Genenetwork2 Dockerized + +* Table of Contents :TOC: +- [[#introduction][Introduction]] +- [[#creating-the-docker-images][Creating the Docker Images]] +- [[#pushing-to-dockerhub][Pushing to DockerHub]] + +* Introduction + +The CI(Continuous Integration) system for Genenetwork2 uses [[https://github.com/features/actions][Github +Actions]]. As such, it's important to have a way to run tests using +facilities provided by GUIX in a reproducible way. This project +leverages GUIX to generate a docker container from which the unittests +are ran from. + +Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This +document will not get into that. It's assumed that you have a working +docker setup. + +The rest of this document outlines how the docker container used in +the CI builds was created. + +* Creating the Docker Images + +The general idea is that GUIX is used to generate a set of binaries, +which will be added to a base mariaDB image. + +First create the gn2 tar archive by running: + +#+begin_src sh +# For the Python 2 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack --no-grafts\ + -S /gn2-profile=/ \ + screen genenetwork2 + +# For the Python 3 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack --no-grafts\ + -S /gn2-profile=/ \ + screen python3-genenetwork2 + #+end_src + +The output will look something similar to: + +: /gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz + +Now create a folder from which will host the following dockerfile. You +can name this file Dockerfile. Note that mariadb is the base image +since it already has mariadb installed for us. + +#+begin_src conf :mkdirp yes :tangle ~/docker/Dockerfile +FROM mariadb:latest + +COPY ./gn2.tar.gz /tmp/gn2.tar.gz +RUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \ + mkdir -p /usr/local/mysql /genotype_files/genotype/json +#+end_src + +Build the image(Note the fullstop at the end): + +: sudo docker build -t python2-genenetwork2:latest -f Dockerfile . + +To load the image interactively you've just created: + +: docker run -ti "python2-genenetwork2:latest" bash + +Assuming you have a docker instance running, you could always run +commands in it e.g: + +: docker run "python2-genenetwork2:latest" python --version + +* Pushing to DockerHub + +We use DockerHub to store the docker images from which we use on our +CI environment using Github Actions. + +To push to dockerhub, first get the image name by running =docker +images=. Push to dockerhub using a command similar to: + +: docker push bonfacekilz/python2-genenetwork2:latest + +Right now, we have 2 images on DockerHub: + +- https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2: + Contains the python2 version of gn2. Don't use this. Please use the + python3 image! +- https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2: + Contains the python3 version of gn2. diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py index d070dab9..d4c3b1ad 100644 --- a/test/requests/main_web_functionality.py +++ b/test/requests/main_web_functionality.py @@ -20,7 +20,7 @@ def check_search_page(host): , search_terms_or="" , search_terms_and="MEAN=(15 16) LRS=(23 46)") result = requests.get(host+"/search", params=data) - found = result.text.find("records are shown below") + found = result.text.find("records were found") assert(found >= 0) assert(result.status_code == 200) print("OK") diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index afffe780..2f1549ae 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -150,10 +150,12 @@ Publish or ProbeSet. E.g. "geno": "Geno", } + group_name = name if t in ['pheno', 'other_pheno']: - name = name.replace("Publish", "") + group_name = name.replace("Publish", "") - if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())): + results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone() + if results: self.datasets[name] = dataset_name_mapping[t] self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) return True @@ -1173,40 +1175,6 @@ class TempDataSet(DataSet): self.fullname = 'Temporary Storage' self.shortname = 'Temp' - @staticmethod - def handle_pca(desc): - if 'PCA' in desc: - # Todo: Modernize below lines - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - return desc - - def get_desc(self): - query = 'SELECT description FROM Temp WHERE Name=%s' % self.name - logger.sql(query) - g.db.execute(query) - desc = g.db.fetchone()[0] - desc = self.handle_pca(desc) - return desc - - def retrieve_sample_data(self, trait): - query = """ - SELECT - Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - FROM - TempData, Temp, Strain - WHERE - TempData.StrainId = Strain.Id AND - TempData.Id = Temp.DataId AND - Temp.name = '%s' - Order BY - Strain.Name - """ % escape(trait.name) - - logger.sql(query) - results = g.db.execute(query).fetchall() - def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7666348e..7ebbc4bb 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,4 +1,10 @@ from __future__ import absolute_import, division, print_function +from utility.logger import getLogger +from flask import Flask, g, request, url_for, redirect, make_response, render_template +from pprint import pformat as pf +from MySQLdb import escape_string as escape +import simplejson as json +from wqflask import app import os import string @@ -16,22 +22,19 @@ from utility import webqtlUtil from utility import hmac from utility.authentication_tools import check_resource_availability from utility.tools import GN2_BASE_URL, GN_VERSION -from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info -Redis = get_redis_conn() +from utility.redis_tools import get_redis_conn +from utility.redis_tools import get_resource_id +from utility.redis_tools import get_resource_info -from wqflask import app +Redis = get_redis_conn() -import simplejson as json -from MySQLdb import escape_string as escape -from pprint import pformat as pf -from flask import Flask, g, request, url_for, redirect, make_response, render_template +logger = getLogger(__name__) -from utility.logger import getLogger -logger = getLogger(__name__ ) def create_trait(**kw): - assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; + assert bool(kw.get('dataset')) != bool( + kw.get('dataset_name')), "Needs dataset ob. or name" permitted = True if kw.get('name'): @@ -43,18 +46,21 @@ def create_trait(**kw): if kw.get('dataset_name') != "Temp": if dataset.type == 'Publish': - permissions = check_resource_availability(dataset, kw.get('name')) + permissions = check_resource_availability( + dataset, kw.get('name')) else: permissions = check_resource_availability(dataset) if "view" in permissions['data']: the_trait = GeneralTrait(**kw) if the_trait.dataset.type != "Temp": - the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info')) + the_trait = retrieve_trait_info( + the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info')) return the_trait else: return None + class GeneralTrait(object): """ Trait class defines a trait in webqtl, can be either Microarray, @@ -64,12 +70,15 @@ class GeneralTrait(object): def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): # xor assertion - assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; - self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. + assert bool(kw.get('dataset')) != bool( + kw.get('dataset_name')), "Needs dataset ob. or name" + # Trait ID, ProbeSet ID, Published ID, etc. + self.name = kw.get('name') if kw.get('dataset_name'): if kw.get('dataset_name') == "Temp": temp_group = self.name.split("_")[2] - self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + self.dataset = create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name=temp_group) else: self.dataset = create_dataset(kw.get('dataset_name')) else: @@ -77,7 +86,8 @@ class GeneralTrait(object): self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') self.haveinfo = kw.get('haveinfo', False) - self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet + # Blat sequence, available for ProbeSet + self.sequence = kw.get('sequence') self.data = kw.get('data', {}) self.view = True @@ -125,11 +135,11 @@ class GeneralTrait(object): vals.append(sample_data.value) the_vars.append(sample_data.variance) sample_aliases.append(sample_data.name2) - return samples, vals, the_vars, sample_aliases + return samples, vals, the_vars, sample_aliases @property def description_fmt(self): - '''Return a text formated description''' + """Return a text formated description""" if self.dataset.type == 'ProbeSet': if self.description: formatted = self.description @@ -149,7 +159,7 @@ class GeneralTrait(object): @property def alias_fmt(self): - '''Return a text formatted alias''' + """Return a text formatted alias""" alias = 'Not available' if getattr(self, "alias", None): @@ -160,16 +170,20 @@ class GeneralTrait(object): @property def wikidata_alias_fmt(self): - '''Return a text formatted alias''' + """Return a text formatted alias""" alias = 'Not available' if self.symbol: - human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) - mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) - other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) + human_response = requests.get( + GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get( + GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get( + GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) if human_response and mouse_response and other_response: - alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) + alias_list = json.loads(human_response.content) + json.loads( + mouse_response.content) + json.loads(other_response.content) filtered_aliases = [] seen = set() @@ -183,31 +197,31 @@ class GeneralTrait(object): return alias - @property def location_fmt(self): - '''Return a text formatted location + """Return a text formatted location While we're at it we set self.location in case we need it later (do we?) - ''' + """ if self.chr and self.mb: - self.location = 'Chr %s @ %s Mb' % (self.chr,self.mb) + self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) elif self.chr: self.location = 'Chr %s @ Unknown position' % (self.chr) else: self.location = 'Not available' fmt = self.location - ##XZ: deal with direction + # XZ: deal with direction if self.strand_probe == '+': fmt += (' on the plus strand ') elif self.strand_probe == '-': fmt += (' on the minus strand ') return fmt - + + def retrieve_sample_data(trait, dataset, samplelist=None): if samplelist == None: samplelist = [] @@ -225,16 +239,19 @@ def retrieve_sample_data(trait, dataset, samplelist=None): all_samples_ordered = dataset.group.all_samples_ordered() for i, item in enumerate(results): try: - trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item)) + trait.data[all_samples_ordered[i]] = webqtlCaseData( + all_samples_ordered[i], float(item)) except: pass else: for item in results: name, value, variance, num_cases, name2 = item if not samplelist or (samplelist and name in samplelist): - trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) + # name, value, variance, num_cases) + trait.data[name] = webqtlCaseData(*item) return trait + @app.route("/trait/get_sample_data") def get_sample_data(): params = request.args @@ -250,7 +267,8 @@ def get_sample_data(): trait_dict['group'] = trait_ob.dataset.group.name trait_dict['tissue'] = trait_ob.dataset.tissue trait_dict['species'] = trait_ob.dataset.group.species - trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset) + trait_dict['url'] = url_for( + 'show_trait_page', trait_id=trait, dataset=dataset) trait_dict['description'] = trait_ob.description_display if trait_ob.dataset.type == "ProbeSet": trait_dict['symbol'] = trait_ob.symbol @@ -260,22 +278,24 @@ def get_sample_data(): trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text - return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) + return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems()}]) else: return None - + + def jsonable(trait): """Return a dict suitable for using as json Actual turning into json doesn't happen here though""" - dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name) - + dataset = create_dataset(dataset_name=trait.dataset.name, + dataset_type=trait.dataset.type, group_name=trait.dataset.group.name) + if dataset.type == "ProbeSet": return dict(name=trait.name, symbol=trait.symbol, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, description=trait.description_display, mean=trait.mean, location=trait.location_repr, @@ -287,7 +307,7 @@ def jsonable(trait): if trait.pubmed_id: return dict(name=trait.name, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, @@ -300,7 +320,7 @@ def jsonable(trait): else: return dict(name=trait.name, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, @@ -312,19 +332,20 @@ def jsonable(trait): elif dataset.type == "Geno": return dict(name=trait.name, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, location=trait.location_repr ) else: return dict() + def jsonable_table_row(trait, dataset_name, index): """Return a list suitable for json and intended to be displayed in a table Actual turning into json doesn't happen here though""" dataset = create_dataset(dataset_name) - + if dataset.type == "ProbeSet": if trait.mean == "": mean = "N/A" @@ -336,11 +357,13 @@ def jsonable_table_row(trait, dataset_name, index): additive = "%.3f" % round(float(trait.additive), 2) return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, - '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + '<a href="/show_trait?trait_id=' + + str(trait.name)+'&dataset='+dataset.name + + '">'+str(trait.name)+'</a>', trait.symbol, trait.description_display, trait.location_repr, - mean, + mean, trait.LRS_score_repr, trait.LRS_location_repr, additive] @@ -352,7 +375,9 @@ def jsonable_table_row(trait, dataset_name, index): if trait.pubmed_id: return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, - '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + '<a href="/show_trait?trait_id=' + + str(trait.name)+'&dataset='+dataset.name + + '">'+str(trait.name)+'</a>', trait.description_display, trait.authors, '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>', @@ -362,7 +387,9 @@ def jsonable_table_row(trait, dataset_name, index): else: return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, - '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + '<a href="/show_trait?trait_id=' + + str(trait.name)+'&dataset='+dataset.name + + '">'+str(trait.name)+'</a>', trait.description_display, trait.authors, trait.pubmed_text, @@ -372,7 +399,9 @@ def jsonable_table_row(trait, dataset_name, index): elif dataset.type == "Geno": return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, - '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + '<a href="/show_trait?trait_id=' + + str(trait.name)+'&dataset='+dataset.name + + '">'+str(trait.name)+'</a>', trait.location_repr] else: return dict() @@ -383,14 +412,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): resource_id = get_resource_id(dataset, trait.name) if dataset.type == 'Publish': - the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) + the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format( + resource_id, g.user_session.user_id) else: - the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) + the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format( + resource_id, g.user_session.user_id, trait.name) try: response = requests.get(the_url).content trait_info = json.loads(response) - except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait + except: # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait if dataset.type == 'Publish': query = """ SELECT @@ -419,8 +450,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): logger.sql(query) trait_info = g.db.execute(query).fetchone() - #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name - #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. + # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name + # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. elif dataset.type == 'ProbeSet': display_fields_string = ', ProbeSet.'.join(dataset.display_fields) display_fields_string = 'ProbeSet.' + display_fields_string @@ -433,14 +464,15 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): ProbeSetFreeze.Name = '%s' AND ProbeSet.Name = '%s' """ % (escape(display_fields_string), - escape(dataset.name), - escape(str(trait.name))) + escape(dataset.name), + escape(str(trait.name))) logger.sql(query) trait_info = g.db.execute(query).fetchone() - #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name + # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. elif dataset.type == 'Geno': - display_fields_string = string.join(dataset.display_fields,',Geno.') + display_fields_string = string.join( + dataset.display_fields, ',Geno.') display_fields_string = 'Geno.' + display_fields_string query = """ SELECT %s @@ -451,21 +483,21 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): GenoFreeze.Name = '%s' AND Geno.Name = '%s' """ % (escape(display_fields_string), - escape(dataset.name), - escape(trait.name)) + escape(dataset.name), + escape(trait.name)) logger.sql(query) trait_info = g.db.execute(query).fetchone() - else: #Temp type + else: # Temp type query = """SELECT %s FROM %s WHERE Name = %s""" logger.sql(query) trait_info = g.db.execute(query, - (string.join(dataset.display_fields,','), - dataset.type, trait.name)).fetchone() + (string.join(dataset.display_fields, ','), + dataset.type, trait.name)).fetchone() if trait_info: trait.haveinfo = True for i, field in enumerate(dataset.display_fields): - holder = trait_info[i] + holder = trait_info[i] setattr(trait, field, holder) if dataset.type == 'Publish': @@ -478,9 +510,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): description = trait.post_publication_description - #If the dataset is confidential and the user has access to confidential - #phenotype traits, then display the pre-publication description instead - #of the post-publication description + # If the dataset is confidential and the user has access to confidential + # phenotype traits, then display the pre-publication description instead + # of the post-publication description if trait.confidential: trait.abbreviation = trait.pre_publication_abbreviation trait.description_display = trait.pre_publication_description @@ -491,9 +523,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: trait.description_display = "" - trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.abbreviation = unicode(str(trait.abbreviation).strip( + codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.description_display = unicode(str(trait.description_display).strip( + codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.authors = unicode(str(trait.authors).strip( + codecs.BOM_UTF8), 'utf-8', errors="replace") if not trait.year.isdigit(): trait.pubmed_text = "N/A" @@ -504,16 +539,19 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id if dataset.type == 'ProbeSet' and dataset.group: - description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') + description_string = unicode( + str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') + target_string = unicode( + str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') - if len(description_string) > 1 and description_string != 'None': + if str(description_string or "") != "" and description_string != 'None': description_display = description_string else: description_display = trait.symbol - if (len(description_display) > 1 and description_display != 'N/A' and - len(target_string) > 1 and target_string != 'None'): + if (str(description_display or "") != "" and + description_display != 'N/A' and + str(target_string or "") != "" and target_string != 'None'): description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template @@ -521,15 +559,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.location_repr = 'N/A' if trait.chr and trait.mb: - trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) + trait.location_repr = 'Chr%s: %.6f' % ( + trait.chr, float(trait.mb)) elif dataset.type == "Geno": trait.location_repr = 'N/A' if trait.chr and trait.mb: - trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) + trait.location_repr = 'Chr%s: %.6f' % ( + trait.chr, float(trait.mb)) if get_qtl_info: - #LRS and its location + # LRS and its location trait.LRS_score_repr = "N/A" trait.LRS_location_repr = "N/A" trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = "" @@ -599,12 +639,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" else: trait.locus = trait.lrs = trait.additive = "" - - if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "": - trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) - if trait.lrs != "": + if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "": + trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( + trait.locus_chr, float(trait.locus_mb)) + if str(trait.lrs or "") != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: - raise KeyError, `trait.name`+' information is not found in the database.' - - return trait \ No newline at end of file + raise KeyError, `trait.name`+ ' information is not found in the database.' + + return trait diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py index 94780a5d..dd7f5051 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -66,7 +66,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_key_mrna(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) @@ -84,7 +84,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_key_pheno(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) @@ -93,7 +93,6 @@ class TestDataSetTypes(unittest.TestCase): redis_mock.set.assert_called_once_with( "dataset_structure", '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" db_mock.db.execute.assert_called_with( ("SELECT InfoFiles.GN_AccesionId " + "FROM InfoFiles, PublishFreeze, InbredSet " + @@ -105,7 +104,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_other_pheno(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) @@ -114,7 +113,6 @@ class TestDataSetTypes(unittest.TestCase): redis_mock.set.assert_called_once_with( "dataset_structure", '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" db_mock.db.execute.assert_called_with( ("SELECT PublishFreeze.Name " + "FROM PublishFreeze, InbredSet " + @@ -125,7 +123,7 @@ class TestDataSetTypes(unittest.TestCase): @mock.patch('base.data_set.g') def test_set_dataset_geno(self, db_mock): with app.app_context(): - db_mock.db.execute.return_value = [1, 2, 3] + db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3] redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset data_set = DatasetType(redis_mock) diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py new file mode 100644 index 00000000..1a3820f2 --- /dev/null +++ b/wqflask/tests/base/test_trait.py @@ -0,0 +1,235 @@ +# -*- coding: utf-8 -*- +"""Tests wqflask/base/trait.py""" +import unittest +import mock + +from base.trait import GeneralTrait +from base.trait import retrieve_trait_info + + +class TestResponse: + """Mock Test Response after a request""" + @property + def content(self): + """Mock the content from Requests.get(params).content""" + return "[1, 2, 3, 4]" + + +class TestNilResponse: + """Mock Test Response after a request""" + @property + def content(self): + """Mock the content from Requests.get(params).content""" + return "{}" + + +class MockTrait(GeneralTrait): + @property + def wikidata_alias_fmt(self): + return "Mock alias" + + +class TestRetrieveTraitInfo(unittest.TestCase): + """Tests for 'retrieve_trait_info'""" + def test_retrieve_trait_info_with_empty_dataset(self): + """Test that an exception is raised when dataset is empty""" + with self.assertRaises(AssertionError): + retrieve_trait_info(trait=mock.MagicMock(), + dataset={}) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + def test_retrieve_trait_info_with_empty_trait_info(self, + g_mock, + requests_mock): + """Empty trait info""" + requests_mock.return_value = TestNilResponse() + with self.assertRaises(KeyError): + retrieve_trait_info(trait=mock.MagicMock(), + dataset=mock.MagicMock()) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + def test_retrieve_trait_info_with_non_empty_trait_info(self, + g_mock, + requests_mock): + """Test that attributes are set""" + mock_dataset = mock.MagicMock() + requests_mock.return_value = TestResponse() + type(mock_dataset).display_fields = mock.PropertyMock( + return_value=["a", "b", "c", "d"]) + test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset), + dataset=mock_dataset) + self.assertEqual(test_trait.a, 1) + self.assertEqual(test_trait.b, 2) + self.assertEqual(test_trait.c, 3) + self.assertEqual(test_trait.d, 4) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + def test_retrieve_trait_info_utf8_parsing(self, + g_mock, + requests_mock): + """Test that utf-8 strings are parsed correctly""" + utf_8_string = "test_string" + mock_dataset = mock.MagicMock() + requests_mock.return_value = TestResponse() + type(mock_dataset).display_fields = mock.PropertyMock( + return_value=["a", "b", "c", "d"]) + type(mock_dataset).type = 'Publish' + + mock_trait = MockTrait( + dataset=mock_dataset, + pre_publication_description=utf_8_string + ) + trait_attrs = { + "group_code": "test_code", + "pre_publication_description": "test_pre_pub", + "pre_publication_abbreviation": "ファイルを画面毎に見て行くには、次のコマンドを使います。", + "post_publication_description": None, + "pubmed_id": None, + 'year': "2020", + "authors": "Jane Doe かいと", + } + for key, val in list(trait_attrs.items()): + setattr(mock_trait, key, val) + test_trait = retrieve_trait_info(trait=mock_trait, + dataset=mock_dataset) + self.assertEqual(test_trait.abbreviation, + "ファイルを画面毎に見て行くには、次のコマンドを使います。".decode('utf-8')) + self.assertEqual(test_trait.authors, + "Jane Doe かいと".decode('utf-8')) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + @mock.patch('base.trait.get_resource_id') + def test_retrieve_trait_info_with_non_empty_lrs(self, + resource_id_mock, + g_mock, + requests_mock): + """Test """ + resource_id_mock.return_value = 1 + g_mock.db.execute.return_value.fetchone = mock.Mock() + g_mock.db.execute.return_value.fetchone.side_effect = [ + [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone() + [1, 2.37, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone() + [2.7333, 2.1204] # trait_info = g.db.execute(query).fetchone() + ] + requests_mock.return_value = None + + mock_dataset = mock.MagicMock() + type(mock_dataset).display_fields = mock.PropertyMock( + return_value=["a", "b", "c", "d"]) + type(mock_dataset).type = "ProbeSet" + type(mock_dataset).name = "RandomName" + + mock_trait = MockTrait( + dataset=mock_dataset, + pre_publication_description="test_string" + ) + trait_attrs = { + "description": "some description", + "probe_target_description": "some description", + "cellid": False, + "chr": 2.733, + "mb": 2.1204 + } + + for key, val in list(trait_attrs.items()): + setattr(mock_trait, key, val) + test_trait = retrieve_trait_info(trait=mock_trait, + dataset=mock_dataset, + get_qtl_info=True) + self.assertEqual(test_trait.LRS_score_repr, + "2.4") + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + @mock.patch('base.trait.get_resource_id') + def test_retrieve_trait_info_with_empty_lrs_field(self, + resource_id_mock, + g_mock, + requests_mock): + """Test retrieve trait info with empty lrs field""" + resource_id_mock.return_value = 1 + g_mock.db.execute.return_value.fetchone = mock.Mock() + g_mock.db.execute.return_value.fetchone.side_effect = [ + [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone() + [1, None, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone() + [2, 3] # trait_info = g.db.execute(query).fetchone() + ] + requests_mock.return_value = None + + mock_dataset = mock.MagicMock() + type(mock_dataset).display_fields = mock.PropertyMock( + return_value=["a", "b", "c", "d"]) + type(mock_dataset).type = "ProbeSet" + type(mock_dataset).name = "RandomName" + + mock_trait = MockTrait( + dataset=mock_dataset, + pre_publication_description="test_string" + ) + trait_attrs = { + "description": "some description", + "probe_target_description": "some description", + "cellid": False, + "chr": 2.733, + "mb": 2.1204 + } + + for key, val in list(trait_attrs.items()): + setattr(mock_trait, key, val) + test_trait = retrieve_trait_info(trait=mock_trait, + dataset=mock_dataset, + get_qtl_info=True) + self.assertEqual(test_trait.LRS_score_repr, + "N/A") + self.assertEqual(test_trait.LRS_location_repr, + "Chr2: 3.000000") + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g') + @mock.patch('base.trait.get_resource_id') + def test_retrieve_trait_info_with_empty_chr_field(self, + resource_id_mock, + g_mock, + requests_mock): + """Test retrieve trait info with empty chr field""" + resource_id_mock.return_value = 1 + g_mock.db.execute.return_value.fetchone = mock.Mock() + g_mock.db.execute.return_value.fetchone.side_effect = [ + [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone() + [1, 2, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone() + [None, 3] # trait_info = g.db.execute(query).fetchone() + ] + + requests_mock.return_value = None + + mock_dataset = mock.MagicMock() + type(mock_dataset).display_fields = mock.PropertyMock( + return_value=["a", "b", "c", "d"]) + type(mock_dataset).type = "ProbeSet" + type(mock_dataset).name = "RandomName" + + mock_trait = MockTrait( + dataset=mock_dataset, + pre_publication_description="test_string" + ) + trait_attrs = { + "description": "some description", + "probe_target_description": "some description", + "cellid": False, + "chr": 2.733, + "mb": 2.1204 + } + + for key, val in list(trait_attrs.items()): + setattr(mock_trait, key, val) + test_trait = retrieve_trait_info(trait=mock_trait, + dataset=mock_dataset, + get_qtl_info=True) + self.assertEqual(test_trait.LRS_score_repr, + "N/A") + self.assertEqual(test_trait.LRS_location_repr, + "N/A") diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py new file mode 100644 index 00000000..99c74245 --- /dev/null +++ b/wqflask/tests/utility/test_authentication_tools.py @@ -0,0 +1,193 @@ +"""Tests for authentication tools""" +import unittest +import mock + +from utility.authentication_tools import check_resource_availability +from utility.authentication_tools import add_new_resource + + +class TestResponse: + """Mock Test Response after a request""" + @property + def content(self): + """Mock the content from Requests.get(params).content""" + return '["foo"]' + + +class TestUser: + """Mock user""" + @property + def user_id(self): + """Mockes user id. Used in Flask.g.user_session.user_id""" + return "Jane" + + +class TestUserSession: + """Mock user session""" + @property + def user_session(self): + """Mock user session. Mocks Flask.g.user_session object""" + return TestUser() + + +def mock_add_resource(resource_ob, update=False): + return resource_ob + + +class TestCheckResourceAvailability(unittest.TestCase): + """Test methods related to checking the resource availability""" + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_default_mask( + self, + resource_id_mock, + g_mock, + redis_mock, + add_new_resource_mock): + """Test the resource availability with default mask""" + resource_id_mock.return_value = 1 + g_mock.return_value = mock.Mock() + redis_mock.smembers.return_value = [] + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + add_new_resource_mock.return_value = {"default_mask": 2} + self.assertEqual(check_resource_availability(test_dataset), 2) + + @mock.patch('utility.authentication_tools.requests.get') + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_non_default_mask( + self, + resource_id_mock, + g_mock, + redis_mock, + add_new_resource_mock, + requests_mock): + """Test the resource availability with default mask""" + resource_id_mock.return_value = 1 + g_mock.return_value = mock.Mock() + redis_mock.smembers.return_value = [] + add_new_resource_mock.return_value = {"default_mask": 2} + requests_mock.return_value = TestResponse() + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + self.assertEqual(check_resource_availability(test_dataset), + ['foo']) + + @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES', + "SUPERUSER") + @mock.patch('utility.authentication_tools.requests.get') + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g', TestUserSession()) + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_of_super_user( + self, + resource_id_mock, + redis_mock, + add_new_resource_mock, + requests_mock): + """Test the resource availability if the user is the super user""" + resource_id_mock.return_value = 1 + redis_mock.smembers.return_value = ["Jane"] + add_new_resource_mock.return_value = {"default_mask": 2} + requests_mock.return_value = TestResponse() + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + self.assertEqual(check_resource_availability(test_dataset), + "SUPERUSER") + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + def test_check_resource_availability_string_dataset(self): + """Test the resource availability if the dataset is a string""" + self.assertEqual(check_resource_availability("Test"), + "John Doe") + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + def test_check_resource_availability_temp(self): + """Test the resource availability if the dataset is a string""" + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Temp") + self.assertEqual(check_resource_availability(test_dataset), + "John Doe") + + +class TestAddNewResource(unittest.TestCase): + """Test cases for add_new_resource method""" + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_publish_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is 'publish'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Publish") + type(test_dataset).id = mock.PropertyMock(return_value=10) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Test_None", + "data": { + "dataset": 10, + "trait": None + }, + "type": "dataset-publish" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_geno_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is 'geno'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).name = mock.PropertyMock(return_value="Geno") + type(test_dataset).type = mock.PropertyMock(return_value="Geno") + type(test_dataset).id = mock.PropertyMock(return_value=20) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Geno", + "data": { + "dataset": 20, + }, + "type": "dataset-geno" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_other_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is not 'geno' or 'publish'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).name = mock.PropertyMock(return_value="Geno") + type(test_dataset).type = mock.PropertyMock(return_value="other") + type(test_dataset).id = mock.PropertyMock(return_value=20) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Geno", + "data": { + "dataset": 20, + }, + "type": "dataset-probeset" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py new file mode 100644 index 00000000..16b50771 --- /dev/null +++ b/wqflask/tests/utility/test_hmac.py @@ -0,0 +1,39 @@ +# -*- coding: utf-8 -*- +"""Test hmac utility functions""" + +import unittest +import mock + +from utility.hmac import data_hmac +from utility.hmac import url_for_hmac +from utility.hmac import hmac_creation + + +class TestHmacUtil(unittest.TestCase): + """Test Utility method for hmac creation""" + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + def test_hmac_creation(self): + """Test hmac creation with a utf-8 string""" + self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + def test_data_hmac(self): + """Test data_hmac fn with a utf-8 string""" + self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_plain_url(self, mock_url): + """Test url_for_hmac without params""" + mock_url.return_value = "https://mock_url.com/ファイ/" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_param_in_url(self, mock_url): + """Test url_for_hmac with params""" + mock_url.return_value = "https://mock_url.com/?ファイ=1" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79") diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py new file mode 100644 index 00000000..6b8d7931 --- /dev/null +++ b/wqflask/tests/wqflask/test_collect.py @@ -0,0 +1,57 @@ +"""Test cases for some methods in collect.py""" + +import unittest +import mock + +from flask import Flask +from wqflask.collect import process_traits + +app = Flask(__name__) + + +class MockSession: + """Helper class for mocking wqflask.collect.g.user_session.logged_in""" + def __init__(self, is_logged_in=False): + self.is_logged_in = is_logged_in + + @property + def logged_in(self): + return self.is_logged_in + + +class MockFlaskG: + """Helper class for mocking wqflask.collect.g.user_session""" + def __init__(self, is_logged_in=False): + self.is_logged_in = is_logged_in + + @property + def user_session(self): + if self.is_logged_in: + return MockSession(is_logged_in=True) + return MockSession() + + +class TestCollect(unittest.TestCase): + + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("wqflask.collect.g", MockFlaskG()) + def test_process_traits_when_user_is_logged_out(self): + """ + Test that the correct traits are returned when the user is logged + out + """ + self.assertEqual(process_traits( + b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,' + b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,' + b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,' + b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'), + set(['1429252_at:HC_M2_0606_P', + '1451401_a_at:HC_M2_0606_P', + '1452447_at:HC_M2_0606_P', + '1452452_at:HC_M2_0606_P'])) diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 3553b92b..239b08e3 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -1,4 +1,6 @@ from __future__ import absolute_import, print_function, division +import logging +from flask import Flask, g, redirect, url_for import json import requests @@ -9,33 +11,31 @@ from utility import hmac from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource Redis = get_redis_conn() -from flask import Flask, g, redirect, url_for -import logging -logger = logging.getLogger(__name__ ) +logger = logging.getLogger(__name__) + def check_resource_availability(dataset, trait_id=None): - #At least for now assume temporary entered traits are accessible - if type(dataset) == str: - return webqtlConfig.DEFAULT_PRIVILEGES - if dataset.type == "Temp": + # At least for now assume temporary entered traits are accessible + if type(dataset) == str or dataset.type == "Temp": return webqtlConfig.DEFAULT_PRIVILEGES resource_id = get_resource_id(dataset, trait_id) - if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno + if resource_id: # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno resource_info = get_resource_info(resource_id) - if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges + if not resource_info: # ZS: If resource isn't already in redis, add it with default privileges resource_info = add_new_resource(dataset, trait_id) - #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy + # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy if g.user_session.user_id in Redis.smembers("super_users"): - return webqtlConfig.SUPER_PRIVILEGES + return webqtlConfig.SUPER_PRIVILEGES response = None - the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) + the_url = "http://localhost:8080/available?resource={}&user={}".format( + resource_id, g.user_session.user_id) try: response = json.loads(requests.get(the_url).content) except: @@ -43,18 +43,19 @@ def check_resource_availability(dataset, trait_id=None): return response + def add_new_resource(dataset, trait_id=None): resource_ob = { - 'owner_id' : "none", # webqtlConfig.DEFAULT_OWNER_ID, + 'owner_id': "none", # webqtlConfig.DEFAULT_OWNER_ID, 'default_mask': webqtlConfig.DEFAULT_PRIVILEGES, - 'group_masks' : {} + 'group_masks': {} } if dataset.type == "Publish": resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id) resource_ob['data'] = { 'dataset': dataset.id, - 'trait' : trait_id + 'trait': trait_id } resource_ob['type'] = 'dataset-publish' elif dataset.type == "Geno": @@ -74,15 +75,19 @@ def add_new_resource(dataset, trait_id=None): return resource_info + def get_group_code(dataset): - results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone() + results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format( + dataset.group.name)).fetchone() if results[0]: return results[0] else: return "" + def check_admin(resource_id=None): - the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id) + the_url = "http://localhost:8080/available?resource={}&user={}".format( + resource_id, g.user_session.user_id) try: response = json.loads(requests.get(the_url).content)['admin'] except: @@ -96,6 +101,7 @@ def check_admin(resource_id=None): else: return "not-admin" + def check_owner(dataset=None, trait_id=None, resource_id=None): if resource_id: resource_info = get_resource_info(resource_id) @@ -110,6 +116,7 @@ def check_owner(dataset=None, trait_id=None, resource_id=None): return False + def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): if not resource_id: if dataset.type == "Temp": diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py index b08be97e..fd75803e 100644 --- a/wqflask/utility/hmac.py +++ b/wqflask/utility/hmac.py @@ -7,11 +7,11 @@ from flask import url_for from wqflask import app + def hmac_creation(stringy): """Helper function to create the actual hmac""" secret = app.config['SECRET_HMAC_CODE'] - hmaced = hmac.new(secret, stringy, hashlib.sha1) hm = hmaced.hexdigest() # ZS: Leaving the below comment here to ask Pjotr about @@ -20,10 +20,12 @@ def hmac_creation(stringy): hm = hm[:20] return hm + def data_hmac(stringy): - """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with""" + """Takes arbitrary data string and appends :hmac so we know data hasn't been tampered with""" return stringy + ":" + hmac_creation(stringy) + def url_for_hmac(endpoint, **values): """Like url_for but adds an hmac at the end to insure the url hasn't been tampered with""" @@ -36,5 +38,6 @@ def url_for_hmac(endpoint, **values): combiner = "?" return url + combiner + "hm=" + hm + app.jinja_env.globals.update(url_for_hmac=url_for_hmac, - data_hmac=data_hmac) \ No newline at end of file + data_hmac=data_hmac) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 81ba04ea..ef02268e 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -4,23 +4,21 @@ import uuid import simplejson as json import datetime -import redis # used for collections - -import logging - -from flask import (render_template, flash) - -from utility import hmac +import redis # used for collections +from utility.hmac import hmac_creation from utility.logger import getLogger logger = getLogger(__name__) + def get_redis_conn(): Redis = redis.StrictRedis(port=6379) return Redis + Redis = get_redis_conn() + def is_redis_available(): try: Redis.ping() @@ -28,6 +26,7 @@ def is_redis_available(): return False return True + def get_user_id(column_name, column_value): user_list = Redis.hgetall("users") key_list = [] @@ -38,6 +37,7 @@ def get_user_id(column_name, column_value): return None + def get_user_by_unique_column(column_name, column_value): item_details = None @@ -52,9 +52,11 @@ def get_user_by_unique_column(column_name, column_value): return item_details + def get_users_like_unique_column(column_name, column_value): - """ - Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """Like previous function, but this only checks if the input is a + subset of a field and can return multiple results + """ matched_users = [] @@ -74,7 +76,6 @@ def get_users_like_unique_column(column_name, column_value): return matched_users -# def search_users_by_unique_column(column_name, column_value): def set_user_attribute(user_id, column_name, column_value): user_info = json.loads(Redis.hget("users", user_id)) @@ -82,6 +83,7 @@ def set_user_attribute(user_id, column_name, column_value): Redis.hset("users", user_id, json.dumps(user_info)) + def get_user_collections(user_id): collections = None collections = Redis.hget("collections", user_id) @@ -91,22 +93,27 @@ def get_user_collections(user_id): else: return [] + def save_user(user, user_id): Redis.hset("users", user_id, json.dumps(user)) + def save_collections(user_id, collections_ob): Redis.hset("collections", user_id, collections_ob) + def save_verification_code(user_email, code): Redis.hset("verification_codes", code, user_email) + def check_verification_code(code): email_address = None user_details = None email_address = Redis.hget("verification_codes", code) if email_address: - user_details = get_user_by_unique_column('email_address', email_address) + user_details = get_user_by_unique_column( + 'email_address', email_address) if user_details: return user_details else: @@ -114,10 +121,12 @@ def check_verification_code(code): else: return None + def get_user_groups(user_id): - #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups - admin_group_ids = [] #ZS: Group IDs where user is an admin - user_group_ids = [] #ZS: Group IDs where user is a regular user + # ZS: Get the groups where a user is an admin or a member and + # return lists corresponding to those two sets of groups + admin_group_ids = [] # ZS: Group IDs where user is an admin + user_group_ids = [] # ZS: Group IDs where user is a regular user groups_list = Redis.hgetall("groups") for key in groups_list: try: @@ -142,6 +151,7 @@ def get_user_groups(user_id): return admin_groups, user_groups + def get_group_info(group_id): group_json = Redis.hget("groups", group_id) group_info = None @@ -150,6 +160,7 @@ def get_group_info(group_id): return group_info + def get_group_by_unique_column(column_name, column_value): """ Get group by column; not sure if there's a faster way to do this """ @@ -158,7 +169,8 @@ def get_group_by_unique_column(column_name, column_value): all_group_list = Redis.hgetall("groups") for key in all_group_list: group_info = json.loads(all_group_list[key]) - if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + # ZS: Since these fields are lists, search in the list + if column_name == "admins" or column_name == "members": if column_value in group_info[column_name]: matched_groups.append(group_info) else: @@ -167,9 +179,11 @@ def get_group_by_unique_column(column_name, column_value): return matched_groups + def get_groups_like_unique_column(column_name, column_value): - """ - Like previous function, but this only checks if the input is a subset of a field and can return multiple results + """Like previous function, but this only checks if the input is a + subset of a field and can return multiple results + """ matched_groups = [] @@ -178,7 +192,8 @@ def get_groups_like_unique_column(column_name, column_value): if column_name != "group_id": for key in group_list: group_info = json.loads(group_list[key]) - if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list + # ZS: Since these fields are lists, search in the list + if column_name == "admins" or column_name == "members": if column_value in group_info[column_name]: matched_groups.append(group_info) else: @@ -190,13 +205,15 @@ def get_groups_like_unique_column(column_name, column_value): return matched_groups -def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"): + +def create_group(admin_user_ids, member_user_ids=[], + group_name="Default Group Name"): group_id = str(uuid.uuid4()) new_group = { - "id" : group_id, + "id": group_id, "admins": admin_user_ids, - "members" : member_user_ids, - "name" : group_name, + "members": member_user_ids, + "name": group_name, "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') } @@ -205,8 +222,9 @@ def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Gro return new_group + def delete_group(user_id, group_id): - #ZS: If user is an admin of a group, remove it from the groups hash + # ZS: If user is an admin of a group, remove it from the groups hash group_info = get_group_info(group_id) if user_id in group_info["admins"]: Redis.hdel("groups", group_id) @@ -214,9 +232,15 @@ def delete_group(user_id, group_id): else: None -def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set + +# ZS "admins" is just to indicate whether the users should be added to +# the groups admins or regular users set +def add_users_to_group(user_id, group_id, user_emails=[], admins=False): group_info = get_group_info(group_id) - if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are + # ZS: Just to make sure that the user is an admin for the group, + # even though they shouldn't be able to reach this point unless + # they are + if user_id in group_info["admins"]: if admins: group_users = set(group_info["admins"]) else: @@ -231,25 +255,36 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS else: group_info["members"] = list(group_users) - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) return group_info else: return None -def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins + +# ZS: User type is because I assume admins can remove other admins +def remove_users_from_group(user_id, + users_to_remove_ids, + group_id, + user_type="members"): group_info = get_group_info(group_id) if user_id in group_info["admins"]: users_to_remove_set = set(users_to_remove_ids) - if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less + # ZS: Make sure an admin can't remove themselves from a group, + # since I imagine we don't want groups to be able to become + # admin-less + if user_type == "admins" and user_id in users_to_remove_set: users_to_remove_set.remove(user_id) group_users = set(group_info[user_type]) group_users -= users_to_remove_set group_info[user_type] = list(group_users) - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') Redis.hset("groups", group_id, json.dumps(group_info)) + def change_group_name(user_id, group_id, new_name): group_info = get_group_info(group_id) if user_id in group_info["admins"]: @@ -259,22 +294,28 @@ def change_group_name(user_id, group_id, new_name): else: return None + def get_resources(): resource_list = Redis.hgetall("resources") return resource_list + def get_resource_id(dataset, trait_id=None): resource_id = False if dataset.type == "Publish": if trait_id: - resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id)) + resource_id = hmac_creation("{}:{}:{}".format( + 'dataset-publish', dataset.id, trait_id)) elif dataset.type == "ProbeSet": - resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id)) + resource_id = hmac_creation( + "{}:{}".format('dataset-probeset', dataset.id)) elif dataset.type == "Geno": - resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id)) + resource_id = hmac_creation( + "{}:{}".format('dataset-geno', dataset.id)) return resource_id + def get_resource_info(resource_id): resource_info = Redis.hget("resources", resource_id) if resource_info: @@ -282,17 +323,23 @@ def get_resource_info(resource_id): else: return None + def add_resource(resource_info, update=True): if 'trait' in resource_info['data']: - resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait']))) + resource_id = hmac_creation('{}:{}:{}'.format( + str(resource_info['type']), str( + resource_info['data']['dataset']), + str(resource_info['data']['trait']))) else: - resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']))) + resource_id = hmac_creation('{}:{}'.format( + str(resource_info['type']), str(resource_info['data']['dataset']))) if update or not Redis.hexists("resources", resource_id): Redis.hset("resources", resource_id, json.dumps(resource_info)) return resource_info + def add_access_mask(resource_id, group_id, access_mask): the_resource = get_resource_info(resource_id) the_resource['group_masks'][group_id] = access_mask @@ -301,9 +348,10 @@ def add_access_mask(resource_id, group_id, access_mask): return the_resource + def change_resource_owner(resource_id, new_owner_id): - the_resource= get_resource_info(resource_id) + the_resource = get_resource_info(resource_id) the_resource['owner_id'] = new_owner_id Redis.delete("resource") - Redis.hset("resources", resource_id, json.dumps(the_resource)) \ No newline at end of file + Redis.hset("resources", resource_id, json.dumps(the_resource)) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index d729aef5..7ed9c7b8 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -12,13 +12,24 @@ logging.basicConfig(level=logging.INFO) app = Flask(__name__) -app.config.from_envvar('GN2_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files +# See http://flask.pocoo.org/docs/config/#configuring-from-files # Note no longer use the badly named WQFLASK_OVERRIDES (nyi) - +app.config.from_envvar('GN2_SETTINGS') app.jinja_env.globals.update( - undefined = jinja2.StrictUndefined, - numify = formatting.numify -) + undefined=jinja2.StrictUndefined, + numify=formatting.numify) from wqflask.api import router +from wqflask import group_manager +from wqflask import resource_manager +from wqflask import search_results +from wqflask import export_traits +from wqflask import gsearch +from wqflask import update_search_results +from wqflask import docs +from wqflask import news +from wqflask import db_info +from wqflask import user_login +from wqflask import user_session + import wqflask.views diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 42a09fed..4c558bfe 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -1,41 +1,30 @@ from __future__ import print_function, division, absolute_import - -import os -import hashlib import datetime -import time - -import uuid -import hashlib -import base64 - -import urlparse - import simplejson as json -from flask import (Flask, g, render_template, url_for, request, make_response, - redirect, flash, jsonify) +from flask import g +from flask import render_template +from flask import url_for +from flask import request +from flask import redirect +from flask import flash from wqflask import app - -from pprint import pformat as pf - -from wqflask.database import db_session - -from wqflask import model - -from utility import Bunch, Struct, hmac +from utility import hmac from utility.formatting import numify from utility.redis_tools import get_redis_conn -Redis = get_redis_conn() -from base.trait import create_trait, retrieve_trait_info, jsonable +from base.trait import create_trait +from base.trait import retrieve_trait_info +from base.trait import jsonable from base.data_set import create_dataset -import logging from utility.logger import getLogger + logger = getLogger(__name__) +Redis = get_redis_conn() + def process_traits(unprocessed_traits): if isinstance(unprocessed_traits, basestring): diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 819836b1..0f3d455c 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -17,8 +17,15 @@ class CorrScatterPlot(object): """Page that displays a correlation scatterplot with a line fitted to it""" def __init__(self, params): - self.dataset_1 = data_set.create_dataset(params['dataset_1']) - self.dataset_2 = data_set.create_dataset(params['dataset_2']) + if "Temp" in params['dataset_1']: + self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1]) + else: + self.dataset_1 = data_set.create_dataset(params['dataset_1']) + if "Temp" in params['dataset_2']: + self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1]) + else: + self.dataset_2 = data_set.create_dataset(params['dataset_2']) + #self.dataset_3 = data_set.create_dataset(params['dataset_3']) self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1) self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 0ac94139..3beee84f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -147,7 +147,7 @@ class CorrelationMatrix(object): if num_overlap < self.lowest_overlap: self.lowest_overlap = num_overlap - if num_overlap == 0: + if num_overlap < 2: corr_result_row.append([target_trait, 0, num_overlap]) pca_corr_result_row.append(0) else: diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py new file mode 100644 index 00000000..f04e38bf --- /dev/null +++ b/wqflask/wqflask/db_info.py @@ -0,0 +1,127 @@ +import httplib, urllib2 +import re + +from flask import Flask, g + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +class InfoPage(object): + def __init__(self, start_vars): + self.info = None + self.gn_accession_id = None + if 'gn_accession_id' in start_vars: + self.gn_accession_id = start_vars['gn_accession_id'] + self.info_page_name = start_vars['info_page_name'] + + self.get_info() + self.get_datasets_list() + + def get_info(self, create=False): + query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " + + "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " + + "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " + + "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " + + "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " + + "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " + + "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " + + "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " + + "FROM InfoFiles " + + "LEFT JOIN Species USING (SpeciesId) " + + "LEFT JOIN Tissue USING (TissueId) " + + "LEFT JOIN InbredSet USING (InbredSetId) " + + "LEFT JOIN GeneChip USING (GeneChipId) " + + "LEFT JOIN AvgMethod USING (AvgMethodId) " + + "LEFT JOIN Datasets USING (DatasetId) " + + "LEFT JOIN Investigators USING (InvestigatorId) " + + "LEFT JOIN Organizations USING (OrganizationId) " + + "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ") + + if self.gn_accession_id: + final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id) + results = g.db.execute(final_query).fetchone() + if self.info_page_name and not results: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + elif self.info_page_name: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + results = g.db.execute(final_query).fetchone() + else: + raise 'No correct parameter found' + + if results: + self.info = process_query_results(results) + + if (not results or len(results) < 1) and self.info_page_name and create: + insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name) + return self.get_info() + + if not self.gn_accession_id and self.info: + self.gn_accession_id = self.info['accession_id'] + if not self.info_page_name and self.info: + self.info_page_name = self.info['info_page_name'] + + def get_datasets_list(self): + self.filelist = [] + try: + response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) + data = response.read() + + matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL) + for i, match in enumerate(matches): + if i == 0: + continue + cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL) + full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip() + filename = full_filename.split("/")[-1] + filesize = re.search(r">(.+?)<", cells[2]).group(1).strip() + filedate = "N/A" #ZS: Since we can't get it for now + + self.filelist.append([filename, filedate, filesize]) + except Exception, e: + pass + +def process_query_results(results): + info_ob = { + 'info_page_name': results[0], + 'accession_id': results[1], + 'menu_name': results[2], + 'taxonomy_id': results[3], + 'tissue_name': results[4], + 'group_name': results[5], + 'gene_chip_name': results[6], + 'geo_platform': results[7], + 'avg_method_name': results[8], + 'dataset_name': results[9], + 'geo_series': results[10], + 'publication_title': results[11], + 'dataset_status_name': results[12], + 'dataset_summary': results[13], + 'about_cases': results[14], + 'about_tissue': results[15], + 'about_data_processing': results[16], + 'acknowledgement': results[17], + 'experiment_design': results[18], + 'contributors': results[19], + 'citation': results[20], + 'notes': results[21], + 'investigator_firstname': results[22], + 'investigator_lastname': results[23], + 'investigator_address': results[24], + 'investigator_city': results[25], + 'investigator_state': results[26], + 'investigator_zipcode': results[27], + 'investigator_country': results[28], + 'investigator_phone': results[29], + 'investigator_email': results[30], + 'investigator_url': results[31], + 'organization_name': results[32], + 'investigator_id': results[33], + 'dataset_id': results[34], + 'dataset_status_is': results[35], + 'about_platform': results[36], + 'info_file_title': results[37], + 'specifics': results[38] + } + + return info_ob + \ No newline at end of file diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 78407e22..9fad1cf1 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -11,7 +11,7 @@ class Docs(object): def __init__(self, entry, start_vars={}): sql = """ - SELECT Docs.title, Docs.content + SELECT Docs.title, CAST(Docs.content AS BINARY) FROM Docs WHERE Docs.entry LIKE %s """ @@ -22,7 +22,7 @@ class Docs(object): self.content = "" else: self.title = result[0] - self.content = result[1].encode("latin1") + self.content = result[1] self.editable = "false" # ZS: Removing option to edit to see if text still gets vandalized diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 9bde343c..8a44b3fd 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -401,9 +401,7 @@ class RunMapping(object): rs = marker['name'], pos = this_ps ) - #if 'p_value' in marker: - # logger.debug("P EXISTS:", marker['p_value']) - #else: + if 'lrs_value' in marker and marker['lrs_value'] > 0: browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61) elif 'lod_score' in marker and marker['lod_score'] > 0: @@ -417,6 +415,12 @@ class RunMapping(object): if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": highest_chr = marker['chr'] if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): + if 'Mb' in marker.keys(): + marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['Mb']) + elif 'cM' in marker.keys(): + marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM']) + else: + marker['display_pos'] = "N/A" self.qtl_results.append(marker) with Bench("Exporting Results"): diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 39a07310..14ff2183 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -25,16 +25,16 @@ def manage_resource(): group_masks_with_names = get_group_names(group_masks) default_mask = resource_info['default_mask']['data'] owner_id = resource_info['owner_id'] - owner_info = get_user_by_unique_column("user_id", owner_id) - - if 'name' in owner_info: - owner_display_name = owner_info['full_name'] - elif 'user_name' in owner_info: - owner_display_name = owner_info['user_name'] - elif 'email_address' in owner_info: - owner_display_name = owner_info['email_address'] - else: - owner_display_name = None + + owner_display_name = None + if owner_id != "none": + owner_info = get_user_by_unique_column("user_id", owner_id) + if 'name' in owner_info: + owner_display_name = owner_info['full_name'] + elif 'user_name' in owner_info: + owner_display_name = owner_info['user_name'] + elif 'email_address' in owner_info: + owner_display_name = owner_info['email_address'] return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status) diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css index f1a26a83..e0a5ceea 100644 --- a/wqflask/wqflask/static/new/css/marker_regression.css +++ b/wqflask/wqflask/static/new/css/marker_regression.css @@ -62,6 +62,10 @@ table.dataTable tbody td { padding: 4px 20px 2px 10px; } +table.dataTable tbody tr.selected { + background-color: #ffee99; +} + table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { border-top: 1px solid #ccc; border-right: 1px solid #ccc; diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 853819ea..7a7f5455 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -54,4 +54,8 @@ table.dataTable.cell-border tbody tr td:first-child { .trait_value_input { text-align: right; + +.glyphicon { + position: relative; + top: 2px; } \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js index 4e87d67a..86660126 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -93,7 +93,7 @@ $(function() { }); - add = function() { + add_to_collection = function() { var traits; traits = $("#trait_table input:checked").map(function() { return $(this).val(); @@ -250,7 +250,7 @@ $(function() { $("#select_all").click(select_all); $("#deselect_all").click(deselect_all); $("#invert").click(invert); - $("#add").click(add); + $("#add").click(add_to_collection); $("#submit_bnw").click(submit_bnw); $("#export_traits").click(export_traits); $('.trait_checkbox, .btn').click(change_buttons); @@ -259,14 +259,22 @@ $(function() { let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"] let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"] + let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A + + function extract_inner_text(the_string){ + var span = document.createElement('span'); + span.innerHTML = the_string; + return span.textContent || span.innerText; + } + function sort_NAs(a, b, sort_function){ - if (a === "N/A" && b === "N/A") { + if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) { return 0; } - if (a === "N/A"){ + if (na_equivalent_vals.includes(a)){ return 1 } - if (b === "N/A") { + if (na_equivalent_vals.includes(b)) { return -1; } return sort_function(a, b) @@ -274,11 +282,25 @@ $(function() { $.extend( $.fn.dataTableExt.oSort, { "natural-minus-na-asc": function (a, b) { - return sort_NAs(a, b, naturalAsc) + return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalAsc) }, "natural-minus-na-desc": function (a, b) { - return sort_NAs(a, b, naturalDesc) + return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalDesc) } }); + $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $('input', td).prop('checked') ? '1' : '0'; + } ); + }; + + $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $(td).text(); + } ); + } + }); \ No newline at end of file diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 50562200..b44538cf 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -4,7 +4,9 @@ <head> <meta charset="utf-8"> - <title>{% block title %}{% endblock %}</title> + + <title>{% block title %}{% endblock %} GeneNetwork 2</title> + <meta name="description" content=""> <meta name="author" content=""> <link rel="icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png"> @@ -19,6 +21,14 @@ {% block css %} {% endblock %} + <style> + table.dataTable thead .sorting_asc { + background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }}); + } + table.dataTable thead .sorting_desc { + background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }}); + } + </style> </head> <body style="width: 100%"> diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html index 825dfb84..62b6abb5 100644 --- a/wqflask/wqflask/templates/collections/add.html +++ b/wqflask/wqflask/templates/collections/add.html @@ -5,7 +5,7 @@ or add to an existing collection.</p> </div> <div class="modal-body" style="margin-left: 20px;"> - <form action="/collections/new" data-validate="parsley" id="add_form"> + <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form"> {% if traits is defined %} <input type="hidden" name="traits" value="{{ traits }}" /> {% else %} diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index dce814dd..d1a97310 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -8,7 +8,7 @@ {% block content %} <!-- Start of body --> - <div class="container" style="min-width: 2050px;"> + <div class="container"> <h1> <span id="collection_name">{{ uc.name }}</span> <input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}"> @@ -16,8 +16,6 @@ </h1> <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3> - <!--<hr style="height: 1px; background-color: #A9A9A9;">--> - <div> <form id="collection_form" action="/delete" method="post"> <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> @@ -77,7 +75,7 @@ <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> <input type="hidden" name="file_name" id="file_name" value="collection_table"> - <button class="btn btn-default" id="export_traits">Download CSV</button> + <button class="btn btn-default" id="export_traits">Download</button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> @@ -87,7 +85,7 @@ <div style="margin-top: 10px; margin-bottom: 5px;"> <b>Show/Hide Columns:</b> </div> - <div> + <div style="min-width: 1500px;"> <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;"> <thead> <tr> @@ -99,9 +97,9 @@ <th data-export="Description">Description</th> <th data-export="Location">Location</th> <th data-export="Mean">Mean</th> - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup>?</sup></a></th> - <th data-export="Max LRS Location">Max LRS Location</th> - <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th> + <th data-export="Max LRS">High P <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th> + <th data-export="Peak Location">Peak Location</th> + <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th> </tr> </thead> @@ -144,7 +142,7 @@ <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD> {% endif %} <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD> - {% if this_trait.additive|float > 0 %} + {% if this_trait.additive|float != 0 %} <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD> {% else %} <TD data-export="{{ this_trait.additive }}" align="right">N/A</TD> @@ -166,13 +164,13 @@ {% block js %} <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> - <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script> + <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script language="javascript" type="text/javascript"> @@ -187,22 +185,22 @@ console.time("Creating table"); $('#trait_table').dataTable( { "columns": [ - { "type": "natural", "width": 10 }, + { + "orderDataType": "dom-checkbox", + "orderSequence": [ "desc", "asc"], + "width": 10 + }, { "type": "natural", "width": 50 }, { "type": "natural" }, - { "type": "natural", "width": 120 }, + { 'type': "natural-minus-na", "width": 120 }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural", "width": 130 }, - { "type": "natural", "width": 35 }, - { "type": "natural", "width": 35 }, - { "type": "natural", "width": 130 }, - { "type": "natural" } + { "type": "natural", "width": 125 }, + { "type": "natural", "width": 60 }, + { "type": "natural", "width": 60 }, + { "type": "natural", "width": 125 }, + { "type": "natural", "width": 85 } ], - "columnDefs": [ { - "targets": 0, - "orderable": false - } ], "order": [[1, "asc" ]], buttons: [ { diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 9b96de1c..d556f31a 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -51,7 +51,7 @@ {% if result[0].name == trait.name and result[0].dataset == trait.dataset %} <td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td> {% else %} - <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> {% endif %} {% endfor %} </tr> diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index e597bea9..fb218e29 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -144,7 +144,7 @@ <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD> <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td> <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %} @@ -164,22 +164,26 @@ <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Publish" %} {% if trait.abbreviation %} - <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD> + <td title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</td> {% else %} - <TD data-export="N/A">N/A</TD> + <td data-export="N/A">N/A</td> {% endif %} <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td> {% if trait.authors %} <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td> {% else %} - <TD data-export="N/A">N/A</TD> + <td data-export="N/A">N/A</td> {% endif %} <td data-export="{{ trait.pubmed_text }}"> + {% if trait.pubmed_text != "N/A" %} <a href="{{ trait.pubmed_link }}"> {{ trait.pubmed_text }} </a> + {% else %} + {{ trait.pubmed_text }} + {% endif %} </td> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> <td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td> @@ -187,7 +191,7 @@ <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Geno" %} <td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> {% endif %} @@ -365,9 +369,9 @@ { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, { "type": "scientific" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" } + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" } ], "createdRow": function ( row, data, index ) { $('td', row).eq(4).attr('title', $('td', row).eq(4).text()); @@ -419,13 +423,13 @@ { "type": "natural" }, { "type": "natural", "width": "20%" }, { "type": "natural", "width": "12%" }, - { "orderDataType": "dom-innertext" }, + { "type": "natural-minus-na" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, { "type": "natural" }, { "type": "scientific" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" } + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" } ], "order": [[9, "asc" ]], "sDom": "Btir", @@ -461,7 +465,7 @@ { "type": "natural" }, { "type": "natural" }, { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, - { "type": "natural" }, + { "type": "natural-minus-na" }, { "type": "scientific" } ], "order": [[6, "asc" ]], diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 478d6f5f..d2c78d65 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -59,20 +59,6 @@ </script> <script type="text/javascript" charset="utf-8"> - $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $('input', td).prop('checked') ? '1' : '0'; - } ); - }; - - $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $(td).text(); - } ); - } - $(document).ready( function () { $('#trait_table tr').click(function(event) { @@ -252,7 +238,7 @@ 'sDom': "pitirp", 'autoWidth': true, 'iDisplayLength': 500, - 'deferRender': true, + 'deferRender': false, 'paging': true, 'orderClasses': true, 'processing': true, diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index eb998d15..c44231f3 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -59,20 +59,6 @@ </script> <script type="text/javascript" charset="utf-8"> - $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $('input', td).prop('checked') ? '1' : '0'; - } ); - }; - - $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $(td).text(); - } ); - } - $(document).ready( function () { $('#trait_table tr').click(function(event) { @@ -172,6 +158,7 @@ 'title': "Record", 'type': "natural", 'data': null, + 'orderDataType': "dom-inner-text", 'render': function(data, type, row, meta) { return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>' } @@ -252,7 +239,7 @@ 'order': [[1, "asc" ]], 'sDom': "pitirp", 'autoWidth': false, - 'deferRender': true, + 'deferRender': false, 'iDisplayLength': 500, 'paging': true, 'orderClasses': true, diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 06b71f53..6b3bec9a 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -17,13 +17,13 @@ </header> --> - <div class="container-fluid" style="min-width: 1200px;"> + <div class="container-fluid" style="min-width: 1210px;"> {{ flash_me() }} <div class="row" style="width: 100%;"> - <div class="col-xs-5" style="min-width: 530px; max-width: 550px;"> + <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;"> <section id="search"> <div> <h1>Select and search</h1> @@ -84,7 +84,7 @@ <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> <div class="col-xs-10 controls" style="padding-left: 20px;"> <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea> + <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea> </div> </div> </div> @@ -105,7 +105,7 @@ <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> <div class="col-xs-10 controls" style="padding-left: 20px;"> <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea> + <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea> </div> </div> </div> @@ -184,7 +184,7 @@ </section> </div> - <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;"> + <div class="col-xs-4" style="width: 600px !important;"> <section id="affiliates"> <div class="page-header"> <h1>Affiliates</h1> diff --git a/wqflask/wqflask/templates/info_page.html b/wqflask/wqflask/templates/info_page.html new file mode 100644 index 00000000..d8b7d74c --- /dev/null +++ b/wqflask/wqflask/templates/info_page.html @@ -0,0 +1,92 @@ +{% extends "base.html" %} +{% block title %}Policies{% endblock %} +{% block content %} + +<h1 id="parent-fieldname-title">Data Set Group: {{ info.dataset_name }} +<!--<a href="/infoshare/manager/member-studies-edit.html?DatasetId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--> +<span style="color:red;">{{ info.info_page_name }}</span> +</h1> +<table border="0" width="100%"> +<tr> +<td valign="top" width="50%"> +<table name="info_table" cellSpacing=0 cellPadding=5 width=100% border=0> + <tr><td><b>Data Set:</b> {{ info.info_file_title }} <!--<a href="/infoshare/manager/member-infofile-edit.html?GN_AccesionId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--></td></tr> + <tr><td><b>GN Accession:</b> GN{{ gn_accession_id }}</td></tr> + <tr><td><b>GEO Series:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_series }}" target="_blank">{{ info.geo_series }}</a></td></tr> + <tr><td><b>Title:</b> {{ info.publication_title }}</td></tr> + <tr><td><b>Organism:</b> <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id={{ info.taxonomy_id }}" target="_blank">{{ info.menu_name }}</a></td></tr> + <tr><td><b>Group:</b> {{ info.group_name }}</td></tr> + <tr><td><b>Tissue:</b> {{ info.tissue_name }}</td></tr> + <tr><td><b>Dataset Status:</b> {{ info.dataset_status_name }}</td></tr> + <tr><td><b>Platforms:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_platform }}" target="_blank">{{ info.gene_chip_name }}</a></td></tr> + <tr><td><b>Normalization:</b> {{ info.avg_method_name }}</td></tr> +</table> +</td> +<td valign="top" width="50%"> +<table border="0" width="100%"> + <tr> + <td><b>Contact Information</b></td> + </tr> + <tr> + <td> + {{ info.investigator_first_name }} {{ info.inveestigator_last_name }}<br> + {{ info.organization_name }} <br> + {{ info.investigator_address }}<br> + {{ info.investigator_city }}, {{ info.investigator_state }} {{ info.investigator_zipcode }} {{ info.investigator_country }}<br> + Tel. {{ info.investigator_phone }}<br> + {{ info.investigator_email }}<br> + <a href="{{ info.investigator_url }}" target="_blank">Website</a> + </td> + </tr> + +<tr> + <td><b>Download datasets and supplementary data files</b></td> +</tr> +<tr> + <td> + <ul style="line-height: 160%"> + {% for file in filelist %} + <li><a href="http://datafiles.genenetwork.org/download/GN{{ gn_accession_id }}/{{ file[0] }}">{{ file[0] }} ({{ file[2] }})</a></li> + {% endfor %} + </ul> + </td> +</tr> + +<tr><td> +</td></tr> + +</table> +</td> +</tr> +</table> +<HR> +<p> +<table name="info_table" width="100%" border="0" cellpadding="5" cellspacing="0"> +<tr><td><span style="font-size:115%%;font-weight:bold;">Specifics of this Data Set:</span></td></tr> + <tr><td> {{ info.specifics|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%%;font-weight:bold;">Summary:</span></td></tr> + <tr><td> {{ info.dataset_summary|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">About the cases used to generate this set of data:</span></td></tr> + <tr><td> {{ info.about_cases|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">About the tissue used to generate this set of data:</span></td></tr> + <tr><td> {{ info.about_tissue|safe }}<br><br></td></tr> + <tr><td><span style="font-size:115%; font-weight:bold;">About the array platform:</span></td></tr> + <tr><td> {{ info.about_platform|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">About data values and data processing:</span></td></tr> + <tr><td> {{ info.about_data_processing|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Notes:</span></td></tr> + <tr><td> {{ info.notes|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Experiment Type:</span></td></tr> + <tr><td> {{ info.experiment_design|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Contributor:</span></td></tr> + <tr><td> {{ info.contributors|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Citation:</span></td></tr> + <tr><td> {{ info.citation|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Data source acknowledgment:</span></td></tr> + <tr><td> {{ info.acknowledgement|safe }}<br><br></td></tr> +<tr><td><span style="font-size:115%; font-weight:bold;">Study Id:</span></td></tr> + <tr><td> {{ info.dataset_id }}<br><br></td></tr> +</table> +</p> + +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 8edda548..41d760c0 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -228,71 +228,61 @@ <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <br /> <br /> - <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;"> - <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer"> - <thead> - <tr> - <th></th> - <th>Row</th> - <th>Marker</th> - <th>{{ LRS_LOD }}</th> - <th>Chr</th> - {% if plotScale != "physic" %} - <th>cM</th> - {% else %} - <th align="right">Mb</th> - {% endif %} - {% if 'additive' in trimmed_markers[0] %} - <th>Add Eff</th> - {% endif %} - {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %} - <th>Dom Eff</th> - {% endif %} - </tr> - </thead> - <tbody> - {% for marker in trimmed_markers %} - <tr> - <td align="center" style="padding: 1px 0px 1px 0px;"> - <input type="checkbox" name="selectCheck" - class="checkbox trait_checkbox" - value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}"> - </td> - <td align="right">{{ loop.index }}</td> - <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td> - {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %} - {% if 'lod_score' in marker %} - <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td> - {% else %} - <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td> - {% endif %} - {% else %} - {% if 'lod_score' in marker %} - <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td> - {% else %} - <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td> - {% endif %} - {% endif %} - <td align="right">{{marker.chr}}</td> - {% if plotScale != "physic" %} - {% if 'cM' in marker %} - <td align="right">{{ '%0.3f' | format(marker.cM|float) }}</td> - {% else %} - <td align="right">{{ '%0.3f' | format(marker.Mb|float) }}</td> - {% endif %} - {% else %} - <td align="right">{{ '%0.6f' | format(marker.Mb|float) }}</td> - {% endif %} - {% if 'additive' in marker %} - <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td> - {% endif %} - {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %} - <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td> - {% endif %} - </tr> - {% endfor %} - </tbody> - </table> + <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;"> + <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer"> + <thead> + <tr> + <th></th> + <th>Row</th> + <th>Marker</th> + {% if LRS_LOD == "-log(p)" %} + <th>–log(p)</th> + {% else %} + <th>{{ LRS_LOD }}</th> + {% endif %} + <th>Position ({% if plotScale == "physic" %}Mb{% else %}cM{% endif %})</th> + {% if 'additive' in trimmed_markers[0] %} + <th>Add Eff</th> + {% endif %} + {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %} + <th>Dom Eff</th> + {% endif %} + </tr> + </thead> + <tbody> + {% for marker in trimmed_markers %} + <tr> + <td align="center" style="padding: 1px 0px 1px 0px;"> + <input type="checkbox" name="selectCheck" + class="checkbox trait_checkbox" + value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}"> + </td> + <td align="right">{{ loop.index }}</td> + <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td> + {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %} + {% if 'lod_score' in marker %} + <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td> + {% else %} + <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td> + {% endif %} + {% else %} + {% if 'lod_score' in marker %} + <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td> + {% else %} + <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td> + {% endif %} + {% endif %} + <td align="right">{{ marker.display_pos }}</td> + {% if 'additive' in marker %} + <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td> + {% endif %} + {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %} + <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td> + {% endif %} + </tr> + {% endfor %} + </tbody> + </table> </div> </div> {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %} @@ -362,8 +352,7 @@ "columns": [ { "type": "natural", "width": "5%" }, { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "25%" }, - { "type": "natural" }, + { "type": "natural", "width": "20%" }, { "type": "natural" }, { "type": "natural" }{% if 'additive' in qtlresults[0] %}, { "type": "natural" }{% endif %}{% if 'dominance' in qtlresults[0] and dataset.group.genetic_type != "riset" %}, @@ -395,16 +384,16 @@ $('td', row).eq(9).attr("align", "right"); }, "columns": [ - { "bSortable": false}, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, + { "orderDataType": "dom-checkbox" }, + { "type": "natural"}, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" , "orderDataType": "dom-inner-text" }, { "type": "natural" }, { "type": "natural" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" , "orderDataType": "dom-inner-text" }, { "type": "natural" } ], "columnDefs": [ { diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 53373b41..2318bfb8 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -127,7 +127,7 @@ <input type="hidden" name="export_data" id="export_data" value=""> <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button> <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> - <button class="btn btn-default" id="export_traits">Download CSV</button> + <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> @@ -140,7 +140,6 @@ <b>Show/Hide Columns:</b> </div> {% endif %} - <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">--> <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}> <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};"> <tbody> @@ -174,21 +173,6 @@ </script> <script type="text/javascript" charset="utf-8"> - - $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $('input', td).prop('checked') ? '1' : '0'; - } ); - }; - - $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $(td).text(); - } ); - } - $(document).ready( function () { $('#trait_table tr').click(function(event) { @@ -289,10 +273,9 @@ }, { 'title': "Record", - 'type': "natural", + 'type': "natural-minus-na", 'data': null, 'width': "60px", - 'orderDataType': "dom-inner-text", 'render': function(data, type, row, meta) { return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>' } @@ -306,7 +289,6 @@ { 'title': "Description", 'type': "natural", - 'width': "500px", 'data': null, 'render': function(data, type, row, meta) { try { @@ -319,7 +301,7 @@ { 'title': "Location", 'type': "natural-minus-na", - 'width': "120px", + 'width': "125px", 'data': "location" }, { @@ -330,23 +312,23 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "High P<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "lrs_score", - 'width': "80px", + 'width': "60px", 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS Location", + 'title': "Peak Location", 'type': "natural-minus-na", - 'width': "150px", + 'width': "125px", 'data': "lrs_location" }, { - 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "additive", - 'width': "120px", + 'width': "85px", 'orderSequence': [ "desc", "asc"] }{% elif dataset.type == 'Publish' %}, { @@ -382,17 +364,11 @@ author_string = data.authors } return author_string - // try { - // return decodeURIComponent(escape(author_string)) - // } catch(err){ - // return author_string - // } } }, { 'title': "Year", 'type': "natural-minus-na", - 'orderDataType': "dom-inner-text", 'data': null, 'width': "80px", 'render': function(data, type, row, meta) { @@ -405,20 +381,20 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "lrs_score", 'width': "80px", 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS Location", + 'title': "Peak Location", 'type': "natural-minus-na", - 'width': "150px", + 'width': "120px", 'data': "lrs_location" }, { - 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>", + 'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'width': "120px", 'data': "additive", @@ -427,7 +403,7 @@ { 'title': "Location", 'type': "natural-minus-na", - 'width': "140px", + 'width': "120px", 'data': "location" }{% endif %} ], diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 2d65f008..5ed7a90b 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -37,7 +37,7 @@ <input type="hidden" name="covariates" value=""> <input type="hidden" name="transform" value=""> - <div class="container" style="min-width: 1450px;"> + <div class="container" style="min-width: 700px;"> <div class="panel-group" id="accordion"> <div class="panel panel-default"> <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true"> diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 1378b91b..9420c9c6 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,5 +1,5 @@ <div> - <div class="col-xs-7"> + <div class="col-xs-6" style="min-width: 800px;"> <div style="padding: 20px" class="form-horizontal"> <div class="form-group"> @@ -39,7 +39,7 @@ <div class="form-group"> <label for="corr_return_results" class="col-xs-2 control-label">Return</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <select name="corr_return_results" class="form-control"> {% for return_result in corr_tools.return_results_menu %} <option value="{{ return_result }}" @@ -55,7 +55,7 @@ <div class="form-group"> <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <select name="corr_samples_group" class="form-control"> {% for group, pretty_group in sample_group_types.items() %} <option value="{{ group }}">{{ pretty_group }}</option> @@ -66,7 +66,7 @@ <div id="corr_sample_method" class="form-group"> <label for="corr_sample_method" class="col-xs-2 control-label">Type</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <select name="corr_sample_method" class="form-control"> <option value="pearson">Pearson</option> <option value="spearman">Spearman Rank</option> @@ -77,7 +77,7 @@ {% if dataset.type != "Publish" %} <div class="form-group"> <label class="col-xs-2 control-label">Min Expr</label> - <div class="col-xs-3 controls"> + <div class="col-xs-4 controls"> <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;"> </div> </div> @@ -114,7 +114,7 @@ </div> </div> </div> - <div class="col-xs-5"> + <div> <span id="sample_r_desc" class="correlation_desc fs12"> The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a> is computed diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 8b3e4907..4aced50c 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -215,43 +215,27 @@ <div style="margin-bottom:15px;" class="btn-toolbar"> <div class="btn-group"> - <a href="#redirect"> - <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button> - </a> + <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button> {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %} {% if this_trait.symbol != None %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene={{ this_trait.symbol }}&alias=1&species={{ dataset.group.species }}"> - <button type="button" class="btn btn-default" title="Find similar expression data">Find</button> - </a> + <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene={{ this_trait.symbol }}&alias=1&species={{ dataset.group.species }}', '_blank')">Find</button> {% endif %} {% if UCSC_BLAT_URL != "" %} - <a target="_blank" href="{{ UCSC_BLAT_URL }}"> - <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button> - </a> + <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button> {% endif %} {% if this_trait.symbol != None %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}"> - <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button> - </a> + <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">GeneWiki</button> {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %} - <a href="/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on"> - <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button> - </a> + <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button> {% endif %} {% endif %} {% if show_probes == "True" %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON"> - <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button> - </a> + <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button> {% endif %} {% endif %} - <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}"> - <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button> - </a> + <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button> {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %} - <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}"> - <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button> - </a> + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit</button> {% endif %} </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index 05a2be73..a8ed91b1 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -5,7 +5,7 @@ <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ..."> </div> <div style="padding-left: 10px; display: inline;"> - <input type="button" class="btn btn-default export" value="Export"> + <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button> <select class="select optional span2 export_format"> <option value="excel">Excel</option> <option value="csv">CSV</option> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 27040045..94388b2f 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -397,8 +397,8 @@ </div> </div> </div> - <div class="col-xs-7"> - <dl style="width: 500px;"> + <div> + <dl> {% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %} <dt style="padding-top: 20px;">GEMMA</dt> diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 974081d3..7bdb3ef9 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -76,11 +76,13 @@ <i class="icon-signal"></i> Sort By Value </button> </div> + <!-- <div class="btn-group"> - <button type="button" class="btn btn-default" id="color_by_trait"> + <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;"> <i class="icon-tint"></i> Color by Trait </button> </div> + --> <div id="bar_chart_container"> <div id="bar_chart"></div> </div> diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html index 3e6ef01c..f9d12ba5 100644 --- a/wqflask/wqflask/templates/tutorials.html +++ b/wqflask/wqflask/templates/tutorials.html @@ -15,3 +15,4 @@ and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</ </TR></TABLE> {% endblock %} + diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 9331f369..077a799b 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -453,7 +453,9 @@ def register_user(params): user_details['confirmed'] = 1 user_details['registration_info'] = basic_info() - save_user(user_details, user_details['user_id']) + + if len(errors) == 0: + save_user(user_details, user_details['user_id']) return errors diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index fc9949a8..94ec7137 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -29,14 +29,7 @@ import array import sqlalchemy from wqflask import app from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file -from wqflask import group_manager -from wqflask import resource_manager -from wqflask import search_results -from wqflask import export_traits -from wqflask import gsearch -from wqflask import update_search_results -from wqflask import docs -from wqflask import news + from wqflask.submit_bnw import get_bnw_input from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression from wqflask.show_trait import show_trait @@ -53,6 +46,12 @@ from wqflask.correlation import corr_scatter_plot from wqflask.wgcna import wgcna_analysis from wqflask.ctl import ctl_analysis from wqflask.snp_browser import snp_browser +from wqflask.search_results import SearchResultPage +from wqflask.export_traits import export_search_results_csv +from wqflask.gsearch import GSearch +from wqflask.update_search_results import GSearch as UpdateGSearch +from wqflask.docs import Docs, update_text +from wqflask.db_info import InfoPage from utility import temp_data from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH @@ -66,9 +65,6 @@ from utility.benchmark import Bench from pprint import pformat as pf -from wqflask import user_login -from wqflask import user_session - from wqflask import collect from wqflask.database import db_session @@ -215,7 +211,7 @@ def search_page(): logger.info("Skipping Redis cache (USE_REDIS=False)") logger.info("request.args is", request.args) - the_search = search_results.SearchResultPage(request.args) + the_search = SearchResultPage(request.args) result = the_search.__dict__ valid_search = result['search_term_exists'] @@ -233,7 +229,7 @@ def search_page(): @app.route("/gsearch", methods=('GET',)) def gsearchact(): logger.info(request.url) - result = gsearch.GSearch(request.args).__dict__ + result = GSearch(request.args).__dict__ type = request.args['type'] if type == "gene": return render_template("gsearch_gene.html", **result) @@ -244,7 +240,7 @@ def gsearchact(): def gsearch_updating(): logger.info("REQUEST ARGS:", request.values) logger.info(request.url) - result = update_search_results.GSearch(request.args).__dict__ + result = UpdateGSearch(request.args).__dict__ return result['results'] # type = request.args['type'] # if type == "gene": @@ -257,7 +253,7 @@ def docedit(): logger.info(request.url) try: if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com": - doc = docs.Docs(request.args['entry'], request.args) + doc = Docs(request.args['entry'], request.args) return render_template("docedit.html", **doc.__dict__) else: return "You shouldn't be here!" @@ -273,7 +269,7 @@ def generated_file(filename): @app.route("/help") def help(): logger.info(request.url) - doc = docs.Docs("help", request.args) + doc = Docs("help", request.args) return render_template("docs.html", **doc.__dict__) @app.route("/wgcna_setup", methods=('POST',)) @@ -308,54 +304,54 @@ def ctl_results(): @app.route("/news") def news(): - doc = docs.Docs("news", request.args) + doc = Docs("news", request.args) return render_template("docs.html", **doc.__dict__) @app.route("/references") def references(): - doc = docs.Docs("references", request.args) + doc = Docs("references", request.args) return render_template("docs.html", **doc.__dict__) #return render_template("reference.html") @app.route("/intro") def intro(): - doc = docs.Docs("intro", request.args) + doc = Docs("intro", request.args) return render_template("docs.html", **doc.__dict__) @app.route("/policies") def policies(): - doc = docs.Docs("policies", request.args) + doc = Docs("policies", request.args) #return render_template("policies.html") return render_template("docs.html", **doc.__dict__) @app.route("/links") def links(): - #doc = docs.Docs("links", request.args) + #doc = Docs("links", request.args) #return render_template("docs.html", **doc.__dict__) return render_template("links.html") @app.route("/tutorials") def tutorials(): - #doc = docs.Docs("links", request.args) + #doc = Docs("links", request.args) #return render_template("docs.html", **doc.__dict__) return render_template("tutorials.html") @app.route("/credits") def credits(): - #doc = docs.Docs("links", request.args) + #doc = Docs("links", request.args) #return render_template("docs.html", **doc.__dict__) return render_template("credits.html") @app.route("/environments") def environments(): - doc = docs.Docs("environments", request.args) + doc = Docs("environments", request.args) return render_template("docs.html", **doc.__dict__) #return render_template("environments.html", **doc.__dict__) @app.route("/update_text", methods=('POST',)) def update_page(): - docs.update_text(request.form) - doc = docs.Docs(request.form['entry_type'], request.form) + update_text(request.form) + doc = Docs(request.form['entry_type'], request.form) return render_template("docs.html", **doc.__dict__) @app.route("/submit_trait") @@ -370,7 +366,7 @@ def create_temp_trait(): #template_vars = submit_trait.SubmitTrait(request.form) - doc = docs.Docs("links") + doc = Docs("links") return render_template("links.html", **doc.__dict__) #return render_template("show_trait.html", **template_vars.__dict__) @@ -425,7 +421,7 @@ def export_traits_csv(): logger.info("In export_traits_csv") logger.info("request.form:", request.form) logger.info(request.url) - file_list = export_traits.export_search_results_csv(request.form) + file_list = export_search_results_csv(request.form) if len(file_list) > 1: now = datetime.datetime.now() @@ -908,12 +904,24 @@ def snp_browser_page(): return render_template("snp_browser.html", **template_vars.__dict__) +@app.route("/db_info", methods=('GET',)) +def db_info_page(): + template_vars = InfoPage(request.args) + + return render_template("info_page.html", **template_vars.__dict__) + @app.route("/tutorial/WebQTLTour", methods=('GET',)) def tutorial_page(): #ZS: Currently just links to GN1 logger.info(request.url) return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/") +@app.route("/tutorial/security", methods=('GET',)) +def security_tutorial_page(): + #ZS: Currently just links to GN1 + logger.info(request.url) + return render_template("admin/security_help.html") + @app.route("/submit_bnw", methods=('POST',)) def submit_bnw(): logger.info(request.url) diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 880a1cb2..70077703 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -1,5 +1,8 @@ -# WGCNA analysis for GN2 -# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com> +""" +WGCNA analysis for GN2 + +Author / Maintainer: Danny Arends <Danny.Arends@gmail.com> +""" import sys from numpy import * import scipy as sp # SciPy @@ -17,106 +20,138 @@ from utility import helper_functions from rpy2.robjects.packages import importr utils = importr("utils") -## Get pointers to some common R functions -r_library = ro.r["library"] # Map the library function -r_options = ro.r["options"] # Map the options function -r_read_csv = ro.r["read.csv"] # Map the read.csv function -r_dim = ro.r["dim"] # Map the dim function -r_c = ro.r["c"] # Map the c function -r_cat = ro.r["cat"] # Map the cat function -r_paste = ro.r["paste"] # Map the paste function -r_unlist = ro.r["unlist"] # Map the unlist function -r_unique = ro.r["unique"] # Map the unique function -r_length = ro.r["length"] # Map the length function -r_unlist = ro.r["unlist"] # Map the unlist function -r_list = ro.r.list # Map the list function -r_matrix = ro.r.matrix # Map the matrix function -r_seq = ro.r["seq"] # Map the seq function -r_table = ro.r["table"] # Map the table function -r_names = ro.r["names"] # Map the names function -r_sink = ro.r["sink"] # Map the sink function -r_is_NA = ro.r["is.na"] # Map the is.na function -r_file = ro.r["file"] # Map the file function -r_png = ro.r["png"] # Map the png function for plotting -r_dev_off = ro.r["dev.off"] # Map the dev.off function +# Get pointers to some common R functions +r_library = ro.r["library"] # Map the library function +r_options = ro.r["options"] # Map the options function +r_read_csv = ro.r["read.csv"] # Map the read.csv function +r_dim = ro.r["dim"] # Map the dim function +r_c = ro.r["c"] # Map the c function +r_cat = ro.r["cat"] # Map the cat function +r_paste = ro.r["paste"] # Map the paste function +r_unlist = ro.r["unlist"] # Map the unlist function +r_unique = ro.r["unique"] # Map the unique function +r_length = ro.r["length"] # Map the length function +r_unlist = ro.r["unlist"] # Map the unlist function +r_list = ro.r.list # Map the list function +r_matrix = ro.r.matrix # Map the matrix function +r_seq = ro.r["seq"] # Map the seq function +r_table = ro.r["table"] # Map the table function +r_names = ro.r["names"] # Map the names function +r_sink = ro.r["sink"] # Map the sink function +r_is_NA = ro.r["is.na"] # Map the is.na function +r_file = ro.r["file"] # Map the file function +r_png = ro.r["png"] # Map the png function for plotting +r_dev_off = ro.r["dev.off"] # Map the dev.off function + class WGCNA(object): def __init__(self): + # To log output from stdout/stderr to a file add `r_sink(log)` print("Initialization of WGCNA") - #log = r_file("/tmp/genenetwork_wcgna.log", open = "wt") - #r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file - #r_sink(log, type = "message") - r_library("WGCNA") # Load WGCNA - Should only be done once, since it is quite expensive - r_options(stringsAsFactors = False) + + # Load WGCNA - Should only be done once, since it is quite expensive + r_library("WGCNA") + r_options(stringsAsFactors=False) print("Initialization of WGCNA done, package loaded in R session") - self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"] # Map the enableWGCNAThreads function - self.r_pickSoftThreshold = ro.r["pickSoftThreshold"] # Map the pickSoftThreshold function - self.r_blockwiseModules = ro.r["blockwiseModules"] # Map the blockwiseModules function - self.r_labels2colors = ro.r["labels2colors"] # Map the labels2colors function - self.r_plotDendroAndColors = ro.r["plotDendroAndColors"] # Map the plotDendroAndColors function + # Map the enableWGCNAThreads function + self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"] + # Map the pickSoftThreshold function + self.r_pickSoftThreshold = ro.r["pickSoftThreshold"] + # Map the blockwiseModules function + self.r_blockwiseModules = ro.r["blockwiseModules"] + # Map the labels2colors function + self.r_labels2colors = ro.r["labels2colors"] + # Map the plotDendroAndColors function + self.r_plotDendroAndColors = ro.r["plotDendroAndColors"] print("Obtained pointers to WGCNA functions") def run_analysis(self, requestform): print("Starting WGCNA analysis on dataset") - self.r_enableWGCNAThreads() # Enable multi threading - self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] - print("Retrieved phenotype data from database", requestform['trait_list']) + # Enable multi threading + self.r_enableWGCNAThreads() + self.trait_db_list = [trait.strip() + for trait in requestform['trait_list'].split(',')] + print("Retrieved phenotype data from database", + requestform['trait_list']) helper_functions.get_trait_db_obs(self, self.trait_db_list) - self.input = {} # self.input contains the phenotype values we need to send to R - strains = [] # All the strains we have data for (contains duplicates) - traits = [] # All the traits we have data for (should not contain duplicates) + # self.input contains the phenotype values we need to send to R + self.input = {} + # All the strains we have data for (contains duplicates) + strains = [] + # All the traits we have data for (should not contain duplicates) + traits = [] for trait in self.trait_list: traits.append(trait[0].name) self.input[trait[0].name] = {} for strain in trait[0].data: strains.append(strain) - self.input[trait[0].name][strain] = trait[0].data[strain].value + self.input[trait[0].name][strain] = trait[0].data[strain].value # Transfer the load data from python to R - uStrainsR = r_unique(ro.Vector(strains)) # Unique strains in R vector + # Unique strains in R vector + uStrainsR = r_unique(ro.Vector(strains)) uTraitsR = r_unique(ro.Vector(traits)) # Unique traits in R vector r_cat("The number of unique strains:", r_length(uStrainsR), "\n") r_cat("The number of unique traits:", r_length(uTraitsR), "\n") - # rM is the datamatrix holding all the data in R /rows = strains columns = traits - rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(uTraitsR), dimnames = r_list(uStrainsR, uTraitsR)) + # rM is the datamatrix holding all the data in + # R /rows = strains columns = traits + rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length( + uTraitsR), dimnames=r_list(uStrainsR, uTraitsR)) for t in uTraitsR: - trait = t[0] # R uses vectors every single element is a vector + # R uses vectors every single element is a vector + trait = t[0] for s in uStrainsR: - strain = s[0] # R uses vectors every single element is a vector - #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0]) - rM.rx[strain, trait] = self.input[trait].get(strain) # Update the matrix location + # R uses vectors every single element is a vector + strain = s[0] + rM.rx[strain, trait] = self.input[trait].get( + strain) # Update the matrix location sys.stdout.flush() self.results = {} - self.results['nphe'] = r_length(uTraitsR)[0] # Number of phenotypes/traits - self.results['nstr'] = r_length(uStrainsR)[0] # Number of strains + # Number of phenotypes/traits + self.results['nphe'] = r_length(uTraitsR)[0] + self.results['nstr'] = r_length( + uStrainsR)[0] # Number of strains self.results['phenotypes'] = uTraitsR # Traits used - self.results['strains'] = uStrainsR # Strains used in the analysis - self.results['requestform'] = requestform # Store the user specified parameters for the output page + # Strains used in the analysis + self.results['strains'] = uStrainsR + # Store the user specified parameters for the output page + self.results['requestform'] = requestform - # Calculate soft threshold if the user specified the SoftThreshold variable + # Calculate soft threshold if the user specified the + # SoftThreshold variable if requestform.get('SoftThresholds') is not None: - powers = [int(threshold.strip()) for threshold in requestform['SoftThresholds'].rstrip().split(",")] - rpow = r_unlist(r_c(powers)) - print "SoftThresholds: {} == {}".format(powers, rpow) - self.sft = self.r_pickSoftThreshold(rM, powerVector = rpow, verbose = 5) - - print "PowerEstimate: {}".format(self.sft[0]) - self.results['PowerEstimate'] = self.sft[0] - if self.sft[0][0] is ri.NA_Integer: - print "No power is suitable for the analysis, just use 1" - self.results['Power'] = 1 # No power could be estimated - else: - self.results['Power'] = self.sft[0][0] # Use the estimated power + powers = [int(threshold.strip()) + for threshold in requestform['SoftThresholds'].rstrip().split(",")] + rpow = r_unlist(r_c(powers)) + print("SoftThresholds: {} == {}".format(powers, rpow)) + self.sft = self.r_pickSoftThreshold( + rM, powerVector=rpow, verbose=5) + + print("PowerEstimate: {}".format(self.sft[0])) + self.results['PowerEstimate'] = self.sft[0] + if self.sft[0][0] is ri.NA_Integer: + print "No power is suitable for the analysis, just use 1" + # No power could be estimated + self.results['Power'] = 1 + else: + # Use the estimated power + self.results['Power'] = self.sft[0][0] else: - # The user clicked a button, so no soft threshold selection - self.results['Power'] = requestform.get('Power') # Use the power value the user gives + # The user clicked a button, so no soft threshold selection + # Use the power value the user gives + self.results['Power'] = requestform.get('Power') # Create the block wise modules using WGCNA - network = self.r_blockwiseModules(rM, power = self.results['Power'], TOMType = requestform['TOMtype'], minModuleSize = requestform['MinModuleSize'], verbose = 3) + network = self.r_blockwiseModules( + rM, + power=self.results['Power'], + TOMType=requestform['TOMtype'], + minModuleSize=requestform['MinModuleSize'], + verbose=3) # Save the network for the GUI self.results['network'] = network @@ -130,7 +165,9 @@ class WGCNA(object): self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl'] r_png(self.results['imgloc'], width=1000, height=600, type='cairo-png') mergedColors = self.r_labels2colors(network[1]) - self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05) + self.r_plotDendroAndColors(network[5][0], mergedColors, + "Module colors", dendroLabels=False, + hang=0.03, addGuide=True, guideHang=0.05) r_dev_off() sys.stdout.flush() @@ -146,11 +183,9 @@ class WGCNA(object): print("Processing WGCNA output") template_vars = {} template_vars["input"] = self.input - template_vars["powers"] = self.sft[1:] # Results from the soft threshold analysis + # Results from the soft threshold analysis + template_vars["powers"] = self.sft[1:] template_vars["results"] = self.results self.render_image(results) sys.stdout.flush() - #r_sink(type = "message") # This restores R output to the stdout/stderr - #r_sink() # We should end the Rpy session more or less return(dict(template_vars)) - |